AXYS PHARMECUETICALS INC
S-3, 2000-03-10
PHARMACEUTICAL PREPARATIONS
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<PAGE>   1

     AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON MARCH 10, 2000

                                               REGISTRATION NO. 333-
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                            ------------------------

                                    FORM S-3
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
                            ------------------------

                           AXYS PHARMACEUTICALS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

<TABLE>
<S>                                              <C>
                    DELAWARE                                        22-2969941
          (STATE OR OTHER JURISDICTION                 (I.R.S. EMPLOYER IDENTIFICATION NO.)
       OF INCORPORATION OR ORGANIZATION)
</TABLE>

                            ------------------------

                                180 KIMBALL WAY
                         SOUTH SAN FRANCISCO, CA 94080
                                 (650) 829-1000
  (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
                   REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)
                            ------------------------

                            WILLIAM J. NEWELL, ESQ.
              SENIOR VICE PRESIDENT, GENERAL COUNSEL AND SECRETARY
                           AXYS PHARMACEUTICALS, INC.
                                180 KIMBALL WAY
                         SOUTH SAN FRANCISCO, CA 94080
                                 (650) 829-1000
 (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
                             OF AGENT FOR SERVICE)
                            ------------------------

                                   COPIES TO:
                             LAURA A. BEREZIN, ESQ.
                               COOLEY GODWARD LLP
                             FIVE PALO ALTO SQUARE
                              3000 EL CAMINO REAL
                            PALO ALTO, CA 94306-2155
                                 (650) 843-5000
                            ------------------------

        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
From time to time after the effective date of the Prospectus after the effective
                      date of this Registration Statement.
                            ------------------------

    If the only securities being registered on this Form are being offered
pursuant to dividend or interest reinvestment plans, please check the following
box. [ ]

    If any of the securities being registered on this Form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box. [X]

    If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering. [ ]

    If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [ ]

    If delivery of the Prospectus is expected to be made pursuant to Rule 434,
please check the following box. [ ]

                        CALCULATION OF REGISTRATION FEE

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<S>                        <C>                     <C>                     <C>                     <C>
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   TITLE OF EACH CLASS                                PROPOSED MAXIMUM        PROPOSED MAXIMUM
   OF SECURITIES TO BE          AMOUNT TO BE         OFFERING PRICE PER      AGGREGATE OFFERING          AMOUNT OF
       REGISTERED                REGISTERED              SHARE (1)                 PRICE              REGISTRATION FEE
- -------------------------------------------------------------------------------------------------------------------------
Common Stock ($0.001 par
  value).................     3,497,778 shares           $15.65625             $54,762,086.81            $14,457.19
- -------------------------------------------------------------------------------------------------------------------------
- -------------------------------------------------------------------------------------------------------------------------
</TABLE>

(1) Estimated solely for the purpose of computing the registration fee pursuant
    to Rule 457(c) of the Securities Act and based on the average of the high
    and low sales prices of the Common Stock of Axys Pharmaceuticals, Inc.
    reported on the Nasdaq National Market on March 7, 2000.
                            ------------------------

    THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL
FILE A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF
THE SECURITIES ACT OF 1933 OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SUCH SECTION 8(a),
MAY DETERMINE.
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
<PAGE>   2

        The information in this prospectus is not complete and may be changed.
        We may not sell these securities until the registration statement filed
        with the Securities and Exchange Commission is effective. This
        prospectus is not an offer to sell these securities and it is not
        soliciting an offer to buy these securities in any state where the offer
        or sale is not permitted.

                  SUBJECT TO COMPLETION, DATED MARCH   , 2000

                                3,497,778 shares

                           AXYS PHARMACEUTICALS, INC.

                                  Common Stock

     The selling stockholders listed on pages 12 and 13 are offering up to
3,497,778 shares of Axys Pharmaceuticals, Inc. Common Stock. We sold the shares
to the selling stockholders on March 3, 2000 in a private transaction.

     Our common stock is traded on the Nasdaq National Market under the symbol
"AXPH". On March 7, 2000, the last reported sale price for the Common Stock on
the Nasdaq National Market was $16.00 per share.

     We will not be paying any underwriting discounts or commissions in this
offering.

                           -------------------------

         INVESTING IN OUR COMMON STOCK INVOLVES A HIGH DEGREE OF RISK.
                    SEE "RISK FACTORS" BEGINNING ON PAGE 2.

                           -------------------------

NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED THESE SECURITIES OR DETERMINED IF THIS
PROSPECTUS IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.

                 The date of this prospectus is March   , 2000
<PAGE>   3

                               TABLE OF CONTENTS

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<CAPTION>
                                                              PAGE
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<S>                                                           <C>
About Axys..................................................    1
Risk Factors................................................    2
Cautionary Note Regarding Forward-Looking Statements........   11
Where You Can Find More Information About Axys and This
  Offering..................................................   11
Use of Proceeds.............................................   12
Selling Stockholders........................................   12
Plan of Distribution........................................   13
Legal Matters...............................................   15
Experts.....................................................   15
</TABLE>

                            ------------------------

     We have not authorized any dealer, salesperson or other person to give any
information or represent anything not contained in this prospectus. You should
not rely on any unauthorized information. This prospectus does not offer to sell
or buy any shares in any jurisdiction in which it is unlawful. The information
in this prospectus is current as of the date on the cover.

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                                   ABOUT AXYS

     Axys is a leader in the integration of life science technologies with a
focus on small molecule drug discovery. We seek to build shareholder value
through

     - the discovery and development of our own drugs for the treatment of
       cancer;

     - a broad and diversified pipeline of drug discovery and development
       programs for chronic diseases partnered with world-class pharmaceutical
       companies; and

     - the spin-out of affiliated businesses in combinatorial chemistry,
       pharmacogenomics and agricultural biotechnology that utilize the
       company's technologies. Our affiliated businesses are intended to provide
       capital for Axys' drug discovery and development programs. Our subsidiary
       AXYS ADVANCED TECHNOLOGIES, INC. conducts our combinatorial chemistry
       business. Our subsidiary PPGX, INC.manages our pharmacogenomics business.
       Our affiliate AKKADIX CORPORATION runs the agricultural biotechnology
       business.

     In recent years, the advent of new drug discovery technologies, including
functional genomics, bioinformatics, computational sciences, structure-based
drug design, combinatorial chemistry, high throughput screening and
pharmacogenomics, has offered great potential for streamlining the lengthy and
expensive process of drug discovery. Axys has assembled a premier platform for
drug discovery by combining and integrating these new technologies with the
traditional pharmaceutical sciences, including medicinal chemistry and
pharmacology. We are using these integrated technologies to identify more
quickly and efficiently both novel molecular targets associated with disease and
small molecule compounds, which are important for oral delivery, that can be
used as drugs against these targets.

     We are a Delaware corporation. Our executive offices are located at 180
Kimball Way, South San Francisco, CA 94080 and our telephone number is (650)
829-1000. Our World Wide Web address is http://www.axyspharm.com. Information
contained on our World Wide Web site should not be considered to be part of this
prospectus. In this prospectus, "Axys", "we", "us", and "our" refer to Axys
Pharmaceuticals, Inc. unless the context requires otherwise.

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                                  RISK FACTORS

     AN INVESTMENT IN OUR COMMON STOCK OFFERED PURSUANT TO THIS PROSPECTUS
INVOLVES A HIGH DEGREE OF RISK. OUR COMMON STOCK SHOULD NOT BE PURCHASED IF YOU
CANNOT AFFORD THE LOSS OF YOUR ENTIRE INVESTMENT. PURCHASERS SHOULD CAREFULLY
CONSIDER THE FOLLOWING RISK FACTORS IN CONJUNCTION WITH THE OTHER INFORMATION
INCLUDED AND INCORPORATED BY REFERENCE IN THIS PROSPECTUS BEFORE PURCHASING OR
OTHERWISE ACQUIRING OUR COMMON STOCK.

IF WE FAIL TO DISCOVER OR DEVELOP OR ARE DELAYED IN THE DEVELOPMENT OF
PHARMACEUTICALS, OUR BUSINESS AND RESULTS OF OPERATIONS WILL BE ADVERSELY
AFFECTED.

     All of our potential pharmaceutical products are in various stages of
research and development and will require significant additional research and
development efforts before we can sell them. These efforts include extensive
preclinical and clinical testing and lengthy regulatory review and approval by
the FDA. The development of our new pharmaceutical products is highly uncertain
and subject to a number of significant risks. We do not expect any of our
pharmaceuticals to be commercially available for a number of years.
Pharmaceuticals that appear to be promising at early stages of development may
not reach the market for a number of reasons, including the following:

     - We or our collaborators may not successfully complete any research and
       development efforts;

     - Any pharmaceuticals we develop may be found to be ineffective or to cause
       harmful side effects during preclinical testing or clinical trials;

     - We may fail to obtain required regulatory approvals for any products we
       develop;

     - We may be unable to manufacture enough of any potential products at an
       acceptable cost and with appropriate quality;

     - Our products may not be competitive with other existing or future
       products; and

     - Proprietary rights of third parties may prevent us from commercializing
       our products.

IF WE FAIL TO OBTAIN ADDITIONAL FINANCING TO FUND OUR OPERATIONS, WE WILL BE
UNABLE TO COMPLETE OUR PRODUCT DEVELOPMENT EFFORTS.

     The development of our potential drugs will require substantially more
money than we currently have. That means we will have to obtain commitments for
substantial funds in order to conduct the costly and time-consuming research and
preclinical and clinical testing activities necessary to develop our drugs. We
cannot be certain that any financing will be available when needed. If we fail
to secure additional financing, as we need it, we will have to delay or
terminate our drug development programs.

     We plan to be able to meet some of our needs for money through the sale of
our interests in our affiliated businesses and we are actively pursuing several
alternatives. However, those businesses are still in relatively early stages of
development. We cannot be certain that these businesses will prove to be
financially successful or that we will be able to sell our interest in these
businesses for a substantial amount of money or at all.

     Even if we are successful in obtaining financing from sale of our interests
in these affiliated businesses, we believe we will still need to pursue other
financing opportunities to fund our research and development. Our future
financing needs will depend on many factors, including the following:

     - scientific progress in the research and development of drug development
       programs;

     - the size and complexity of these programs;

     - the timing, range and results of preclinical studies and clinical trials;

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     - our ability to establish new and maintain existing collaborations;

     - our ability to achieve any milestones under such collaborations; and

     - the time and costs involved in getting regulatory approvals or in filing,
       enforcing or prosecuting patents.

     In February, 2000, we entered into definitive purchase agreements for the
sale of an aggregate 3.5 million newly issued shares of Axys Pharmaceuticals,
Inc. common stock to selected institutional and other accredited investors for
$31.5 million in gross proceeds. We intend to use net proceeds from this private
placement for working capital and other general corporate purposes.

     We expect that existing cash and investments, revenues from existing
collaborations, and the net proceeds from our recently completed private
placement, together with debt financing which we believe is available to us,
will enable us to maintain current and planned operations for 18-24 months. We
continue to actively pursue a variety of financing alternatives.

     The drug development process is expensive and we are at an early stage of
development. Therefore, we expect that we will need to continue to raise money
for a number of years until we achieve substantial product or royalty revenues,
if ever. We expect that we will seek additional funding through new
collaborations, the extension of existing collaborations, through sale of our
interests in our affiliated businesses, or through public or private equity or
debt financings. We cannot be certain that additional funding will be available
or that the terms will be acceptable. Existing stockholders will experience
dilution of their investment if we raise additional funds by issuing equity. If
adequate funds are not available, we may delay, reduce or eliminate any of our
research or development programs. Furthermore, we may obtain funds through
arrangements with collaborative partners or others that require us to give up
rights to technologies or products that we would otherwise seek to develop or
commercialize ourselves.

IF WE CONTINUE TO INCUR OPERATING LOSSES FOR LONGER THAN EXPECTED, WE MAY BE
UNABLE TO CONTINUE OPERATIONS AND OUR STOCK PRICE MAY DECLINE.

     We may never achieve and sustain profitability. We have experienced
significant operating losses since the company started. We have not generated
any pharmaceutical product sales revenue. For the year ended December 31, 1999,
we generated a net loss of approximately $48 million, and as of December 31,
1999, we had an accumulated deficit of approximately $277 million. We expect
that we will continue to incur significant operating losses over at least the
next several years as our research and development efforts and preclinical and
clinical testing activities continue. Our future profitability depends on our
ability to complete product development and obtain regulatory approval for our
drug candidates. If we fail to become profitable or are unable to sustain
profitability on a quarterly or annual basis, we may be unable to continue
operations and our stock price may decline.

IF WE FAIL TO MAINTAIN OUR EXISTING COLLABORATIVE RELATIONSHIPS AND ENTER INTO
NEW COLLABORATIVE RELATIONSHIPS, DEVELOPMENT OF OUR PRODUCTS COULD BE DELAYED OR
WE MAY NEED TO OBTAIN OTHER SOURCES OF REVENUE.

     Our strategy for the development, clinical testing, manufacturing and
commercialization of most of our pharmaceuticals has included entering into
collaborations with corporate partners. We rely to a large extent on the
activities of our collaborators with respect to the development and
commercialization of our pharmaceuticals. All of our collaboration agreements
may be canceled under certain circumstances. In addition, the amount and timing
of resources to be devoted to research, development, eventual clinical trials
and commercialization activities by our collaborators are not within our
control. We cannot guarantee that our partners will perform their obligations as
expected. If any of our collaborators terminate or elect to cancel their
agreements or otherwise fail to

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conduct their collaborative activities in a timely manner, the development or
commercialization of pharmaceuticals may be delayed. For example, virtually all
of our genomics collaborations have been cancelled or terminated over time. If
in some cases we assume responsibilities for continuing unpartnered programs
after cancellation of a collaboration, we may be required to devote additional
resources to product development and commercialization or we may cancel certain
development programs.

     A large portion of our revenues to date have resulted from these
collaborations. The research funding phase of most of our collaborations will
come to an end in the next few years unless continued or extended by agreement
with our collaborators. If our collaborations are not extended or we do not
enter into additional collaborative relationships, we will have to seek other
sources of revenue, including additional financing and/or sell interests in our
affiliated businesses. We cannot be certain that we will receive any additional
revenue from these arrangements beyond the minimum contractual commitments of
our partners.

     We have active pharmaceutical product research and development
collaborations with several different partners, including Bayer, Merck and
Aventis (formerly Rhone-Poulenc Rorer), and Signal Pharmaceuticals.

IF WE FAIL TO SATISFY FDA SAFETY AND EFFICACY REQUIREMENTS IN OUR CLINICAL
TRIALS FOR ANY PHARMACEUTICAL, WE WILL BE UNABLE TO COMPLETE THE DEVELOPMENT AND
COMMERCIALIZATION OF THAT PHARMACEUTICAL PRODUCT.

     Either we or our collaborators must show through preclinical studies and
clinical trials that each of our pharmaceuticals is safe and effective in humans
for each indication before obtaining regulatory clearance from the FDA for the
commercial sale of that pharmaceutical. If we fail to adequately show the safety
and effectiveness of a pharmaceutical, regulatory approval could be delayed or
denied. The results from preclinical studies and early clinical trials are often
different than the results that are obtained in large-scale testing. We cannot
be certain that we will show sufficient safety and effectiveness in our clinical
trials that would allow us to obtain the needed regulatory approval. A number of
companies in the pharmaceutical industry, including biotechnology companies,
have suffered significant setbacks in advanced clinical trials, even after
promising results in earlier trials.

     Any drug is likely to produce some level of toxicity or undesirable side
effects in animals and in humans when administered at sufficiently high doses
and/or for a long period of time. Unacceptable toxicities or side effects may
occur in the course of toxicity studies or clinical trials. If we observe
unacceptable toxicities or side effects, we, our collaborators or regulatory
authorities may interrupt, limit, delay or halt the development of the drug. In
addition, these unacceptable toxicities or side effects could prevent approval
by the FDA or foreign regulatory authorities for any or all indications.

     We currently have one compound, APC 2059, in clinical trials for
inflammatory bowel disease. We are performing clinical trials to determine the
safety and effectiveness of APC 2059 for the treatment of inflammatory bowel
disease. As these clinical trials are intended to establish proof-of-principle
in humans, we cannot be certain that we will be able to complete the clinical
trials successfully. Our collaboration partner Bayer is moving forward with
clinical development of a compound developed in our collaboration with them for
the treatment of asthma that would be taken as a pill. Phase I clinical trials
are being planned to commence in the first half of 2000 to establish the safety
and effectiveness of that compound in the treatment of asthma. We cannot be
certain that the clinical trials of this compound will be initiated or completed
successfully. Finally, we cannot be certain that any other drug candidates which
may enter clinical trials will successfully complete those trials or that we or
our collaborators will be able to show the safety and effectiveness of these
drug candidates.

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IF WE FAIL TO OBTAIN REGULATORY APPROVALS TO COMMERCIALLY MANUFACTURE OR SELL
ANY OF OUR PHARMACEUTICALS, OR IF APPROVAL IS DELAYED, WE WILL BE UNABLE TO
GENERATE REVENUE FROM THE SALE OF OUR PRODUCTS.

     We must obtain regulatory approval before marketing or selling our future
drug products. In the United States, we must obtain FDA approval for each drug
that we intend to commercialize. The FDA approval process is lengthy and
expensive, and approval is never certain. Products distributed abroad are also
subject to foreign government regulation. The process of obtaining FDA and other
required regulatory approvals can vary a great deal based upon the type,
complexity and novelty of the products involved. Delays or rejections may be
encountered based upon additional government regulation from future legislation
or administrative action or changes in FDA policy during the period of clinical
trials and FDA regulatory review. Similar delays also may be encountered in
foreign countries.

     None of our drug candidates has received regulatory approval. If we fail to
obtain this approval, we will be unable to commercially manufacture and sell our
drug products. We have several drugs in various stages of preclinical and
clinical development. These products are not expected to be available for
several more years. Because of the risks and uncertainties involved in
development of drug products, our drug candidates could take significantly
longer to gain approval than we expect or may never gain approval. If regulatory
approval is delayed, our management's credibility, the value of our company and
our operating results could be adversely affected. Even if regulatory approval
of a product is granted, we cannot be certain that we will be able to obtain the
labeling claims necessary or desirable for the successful promotion of those
products.

     Even if we obtain regulatory approval, we may be required to continue
clinical studies even after we have started selling a pharmaceutical. In
addition, identification of certain side effects after a drug is on the market
or the occurrence of manufacturing problems could cause subsequent withdrawal of
approval, reformulation of the drug, additional preclinical testing or clinical
trials and changes in labeling of the product. This could delay or prevent us
from generating revenues from the sale of that drug or cause our revenues to
decline.

     If regulatory approval is obtained, we will also be subject to ongoing
existing and future FDA regulations and guidelines and continued regulatory
review. In particular, we or any third party that we use to manufacturer the
drug or our collaborators will be required to adhere to regulations setting
forth current good manufacturing practices. The regulations require that we
manufacture our products and maintain our records in a particular way with
respect to manufacturing, testing and quality control activities. Furthermore,
we or our third party manufacturers or our collaborators must pass a
pre-approval inspection of our manufacturing facilities by the FDA before
obtaining marketing approval.

     Failure to comply with the FDA or other relevant regulatory requirements
may subject us to administrative or legally imposed restrictions. These include:
warning letters, civil penalties, injunctions, product seizure or detention,
product recalls, total or partial suspension of production and FDA refusal to
approve pending New Drug Applications, called NDAs, or supplements to approved
NDAs.

IF WE ARE UNABLE TO EFFECTIVELY PROTECT OUR INTELLECTUAL PROPERTY, WE MAY NOT BE
ABLE TO COMPETE EFFECTIVELY.

     Our success depends in large part on our ability to obtain patents,
maintain trade secrets and operate without infringing the rights of others, both
in the United States and in other countries.

     Patents may not issue from any of our pending or future applications.
Patent applications in the United States are maintained in secrecy until the
patent issues. As a result, we cannot be certain that

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others have not filed patent applications for technology covered by our pending
patent applications or that we were the first to invent the technology. In
addition, an issued patent may be challenged, invalidated or maneuvered around
or it may otherwise not be sufficient to protect our technology. The patent
positions of biotechnology and pharmaceutical companies can be highly uncertain
and involve complex legal and factual questions. As a result, it is difficult to
predict the broadness of claims allowed in biotechnology and pharmaceutical
patents or their enforceability.

     Our commercial success also depends, in part, on not infringing patents
issued to others and not breaching the technology licenses upon which any of our
potential products are based. Competitors may have filed applications for, or
may have received patents and may obtain additional patents and rights relating
to, genes, products or processes that block or compete with ours. A number of
third parties have filed patent applications or received patents in the areas of
our programs. Some of these applications or patents may limit or hinder our
patent applications, or conflict in certain ways with claims made under our
issued patents. Furthermore, in the past we have been, and we may from time to
time in the future be, notified of claims that we are infringing patents or
other intellectual property rights owned by third parties.

     We may have to participate in interference proceedings declared by the U.S.
Patent and Trademark Office. These proceedings determine the priority of
invention and the right to a patent for the technology in the U.S. In addition,
lawsuits may be necessary to enforce any patents issued to us or to determine
the scope and validity of the rights of third parties. Lawsuits and interference
proceedings, even if they are successful, are expensive to pursue, and we could
use a substantial amount of our limited financial resources in either case. An
adverse outcome could subject us to significant liabilities to third parties and
require us to license disputed rights from third parties or to cease using such
technology.

     It is also unclear whether our trade secrets will provide useful
protection. We protect our own technology and processes, in part, by
confidentiality agreements with our employees, consultants and certain
contractors. However, these agreements may be disregarded or breached, and we
may not have adequate remedies for any breach. In addition, it is possible that
our trade secrets will otherwise become known or be independently discovered by
competitors.

     Disputes may arise in the future with regards to the ownership of rights to
any technology developed with collaborators. These and other possible
disagreements with collaborators could lead to delays in the achievement of
milestones or receipt of royalty payments or in research, development and
commercialization of our pharmaceuticals. In addition, these disputes could
require or result in lawsuits or arbitration. Lawsuits and arbitration are
time-consuming and expensive. Even if we win, the cost of these proceedings
could adversely affect our business, financial condition and results of
operations. Furthermore, these proceedings could adversely affect our stock
price or our business reputation and may make the process of entering into
additional collaborative relationships more difficult.

BECAUSE WE DO NOT HAVE MANUFACTURING FACILITIES FOR OUR PROPOSED DRUG PRODUCTS
OR COMMERCIAL MANUFACTURING EXPERIENCE, WE COULD EXPERIENCE MANUFACTURING DELAYS
OR PROBLEMS THAT HURT OUR PRODUCT SALES.

     We have no manufacturing facilities for our proposed drug products, and our
potential products have never been commercially manufactured. We must currently
rely on our collaborators, such as Bayer, Merck, and Aventis, to manufacture
products created by our collaborations. We believe that our collaborators or
contract manufacturers or we will be able to manufacture our compounds at a cost
and in quantities necessary to make them commercially acceptable. However, we
cannot be certain that this will be the case. If we or our collaborators or
third party manufacturers are unable to

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manufacture or contract with others for a sufficient supply of our compounds on
acceptable terms, we may have to delay any of the following:

     - our preclinical and clinical testing schedule;

     - our submission of products for regulatory approval; or

     - the market introduction and subsequent sales of products.

     Any of these delays would adversely affect our financial condition and
results of operations.

     In addition to us, our collaborators and contract manufacturers must adhere
to current Good Manufacturing Practices regulations enforced by the FDA through
its facilities inspection program. If these facilities cannot pass a
pre-approval plant inspection, FDA approval of our products will not be granted
or will be delayed.

     With respect to our subsidiary, Axys Advanced Technologies, we are
developing new manufacturing processes to meet the expanding demand for our
combinatorial chemistry libraries. We have never had to manufacture the
quantities of libraries we are committed to delivering during this year. We have
experienced problems in manufacturing in the past that have delayed shipments of
libraries and we may experience manufacturing problems in the future as we
expand our manufacturing capabilities. Problems in manufacturing could delay
shipments of combinatorial chemistry compounds and this would have a material
adverse effect on our financial condition and results of operations.

IF WE ARE UNABLE TO ESTABLISH MARKETING AND DISTRIBUTION CAPABILITIES OR ENTER
INTO ARRANGEMENTS WITH THIRD PARTIES, OUR ABILITY TO GENERATE REVENUES WILL BE
HARMED.

     We currently have no sales, marketing or distribution capability. We will
rely on our collaborative relationships, such as those with Bayer, Merck and
Aventis, to market some of our future drug products. In addition, we may enter
into future collaborations in which we rely on our collaborator to market our
drug products. Revenues received under existing and future collaborations will
depend on the success of our collaborator in marketing our drugs. We cannot be
certain that collaborators will devote sufficient resources to the marketing and
sale of our drugs or that the efforts of our collaborators will be successful.

     We may also decide to market certain of our future pharmaceuticals by
ourselves. To market any pharmaceuticals ourselves, we must develop a marketing
and sales force with technical expertise and the necessary supporting
distribution capability. If we are unable to develop a marketing and sales
force, we may be unable to effectively sell any of our pharmaceuticals. We do
not know whether we will desire to or be able to establish our own sales and
distribution capabilities or whether we will be able to enter into the necessary
supporting relationships with third parties.

IF WE FAIL TO OBTAIN AN ADEQUATE LEVEL OF REIMBURSEMENT FOR OUR DRUGS, THERE MAY
BE NO COMMERCIALLY VIABLE MARKET FOR OUR PRODUCTS.

     The business and financial condition of pharmaceutical and biotechnology
companies will continue to be affected by the efforts of outside parties, such
as government health administrators, private health insurance companies and HMOs
seeking to contain or reduce the cost of health care. In some foreign markets,
pricing or profitability of prescription pharmaceuticals is subject to
governmental control. In the United States, there have been, and we expect that
there will continue to be, a number of federal and state proposals to adopt
similar governmental control. In addition, an increasing emphasis on managed
care in the United States has and will continue to increase the pressure on
price of prescription drugs. Third-party payors are increasingly challenging the
price and cost-effectiveness of medical products and services. Significant
uncertainty exists as to the

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reimbursement status of newly approved health care products. We cannot be
certain that third parties will pay for the costs of our drugs. Even if we
obtain third party reimbursement, we cannot be certain that reimbursement rates
will allow us to profit from the sale of our drugs.

     In addition, the announcement of cost containment proposals or efforts
could adversely affect our ability to raise capital and our stock price. In
addition, if these proposals or efforts adversely affect other pharmaceutical
companies that are prospective collaborators with Axys, our ability to establish
or maintain strategic alliances may be adversely affected.

IF PHYSICIANS, INSURERS AND PATIENTS DO NOT ACCEPT OUR PRODUCTS, WE MAY NOT
ACHIEVE SUFFICIENT REVENUE FROM SALE OF THOSE PRODUCTS.

     Even if our pharmaceuticals are approved for sale, we are not certain that
physicians, health insurance companies or patients will accept them. If the
medical community and patients do not accept our products, sales of these
products will be adversely affected. The degree of market acceptance will depend
upon a number of factors, including obtaining regulatory approvals,
demonstrating proof in the medical community of the clinical effectiveness and
safety of our product candidates and their potential advantages over existing
treatment methods and reimbursement policies of government and third-party
payors.

IF WE FAIL TO COMPETE SUCCESSFULLY, OUR REVENUES AND OPERATING RESULTS WILL BE
ADVERSELY AFFECTED.

     This is a highly competitive business and many of our competitors have
substantially greater resources than we have. In addition, some of these
companies have considerably more experience in preclinical testing, clinical
trials and other regulatory approval procedures than we have.

     Our competitors (including our collaborators) may develop, manufacture and
market products that are more effective or less expensive than ours. They may
also receive regulatory approval for their drugs faster than we can obtain them,
or may commercialize their drugs more quickly than we can. Many of our
competitors have greater financial and management resources than we do, and many
of them have significantly more experience in bringing drugs to market. If our
competitors successfully commercialize drugs to treat the indications that we
are working on before we do, or if their products are less expensive or more
effective than ours, demand for our drugs may suffer and our revenues may be
reduced.

     Additionally, certain colleges and universities, governmental agencies and
other research organizations are conducting research in the same areas in which
we are working. These institutions are becoming increasingly aware of the
commercial value of their findings and are becoming more active in seeking
patent protection and licensing arrangements to collect royalties for the use of
technology that they have developed. These institutions also may market
competitive commercial products on their own or through joint ventures.
Currently, they compete with us in recruiting highly qualified scientific
personnel.

IF WE FAIL TO RECRUIT AND RETAIN PROFESSIONAL STAFF, OUR PRODUCT DEVELOPMENT
PROGRAMS WILL BE DELAYED.

     We are highly dependent on the senior members of our scientific and
management staff. Retaining and attracting qualified personnel, consultants and
advisors is critical to our success. If we fail to recruit and retain qualified
personnel, our product development efforts will be delayed. We face intense
competition for qualified individuals from numerous pharmaceutical and
biotechnology companies, universities and other research institutions. We are
currently seeking to hire additional qualified scientific personnel to perform
research and development. In addition, we expect that we will need to add
management personnel and develop additional expertise by existing management
personnel in order to expand product development and clinical testing. We cannot
be certain that we will be able to attract and retain such individuals on
acceptable terms or at all.

                                        8
<PAGE>   12

     In addition, our academic collaborators are not our employees. As a result,
we have limited control over their activities and can expect that only limited
amounts of their time will be dedicated to our activities. These academic
collaborators may also have relationships with other commercial entities, some
of whom may compete with Axys.

OUR STOCK MAY BE VOLATILE AND YOUR INVESTMENT COULD SUFFER A DECLINE IN VALUE.

     Stock prices and trading volumes for biotechnology companies often
fluctuate widely for reasons which may be unrelated to their businesses. Our
stock price could decline as a result of many factors, including:

     - announcements of technological innovations or new products by Axys or
       other companies;

     - developments or disputes concerning patents or other rights;

     - publicity regarding actual or potential medical results from products
       under development by Axys or other companies;

     - regulatory developments in both the United States and foreign countries;

     - public concern regarding the safety of biopharmaceutical products;

     - any shortfall in our revenues or net income from that expected by
       securities analysts;

     - changes in analyst's estimates of our financial performance, the
       financial performance or our competitors or the financial performance of
       biotechnology companies in general;

     - sales of large blocks of our common stock; or

     - conditions in the financial markets or economy in general or the
       biotechnology industry in particular.

     In the past, following large price declines in the public market price of a
company's securities, securities litigation has often been initiated against
that company. Litigation of this type could result in substantial costs and
diversion of management's attention and resources. Any adverse determination in
litigation could subject us to substantial liabilities.

IF PRODUCT LIABILITY CLAIMS ARE BROUGHT AGAINST US, WE MAY INCUR SUBSTANTIAL
LIABILITIES.

     We may be exposed to liability claims resulting from the use of our
products in clinical trials, or the manufacturing, marketing and sale of any
approved products. These claims may be made directly by consumers,
pharmaceutical companies or others. We maintain product liability insurance
coverage for claims arising from the use of our products which are still in the
developmental phase. However, this insurance coverage is becoming increasingly
expensive. We and our collaborative partners may not be able to obtain and
maintain commercially reasonable product liability insurance. Furthermore, even
if we maintain insurance, the amount may not be enough to protect us against
losses due to a lawsuit. A successful product liability claim against Axys or
series of claims in excess of our insurance could adversely affect our results
of operations and our need for additional financing.

ANTI-TAKEOVER PROVISIONS UNDER DELAWARE LAW AND IN OUR CHARTER DOCUMENTS AND OUR
STOCKHOLDER RIGHTS PLAN COULD MAKE AN ACQUISITION OF AXYS MORE DIFFICULT.

     In 1998, we adopted a stockholder rights plan, which may have the effect of
delaying or preventing an unsolicited takeover of the company. Our certificate
of incorporation and bylaws state that any action taken by stockholders must be
conducted at an annual or special meeting of stockholders and may not be
conducted by written consent. Only the board of directors, the Chairman of the
Board or the President may call special meetings of the stockholders. In
addition,

                                        9
<PAGE>   13

our board of directors has the authority to issue additional shares of preferred
stock and to determine the rights of those shares without any further action by
the stockholders. Those rights could be senior to those of the common
stockholders. The issuance of preferred stock may make it more difficult for a
third party to acquire Axys. These and other charter provisions may discourage
certain types of transactions involving an actual or potential change in control
of Axys. In fact, these provisions may discourage transactions in which the
stockholders might otherwise receive a premium for their shares over then
current prices, and may limit the stockholders' ability to approve transactions
that they think are in their best interests.

     Delaware law also prohibits corporations from engaging in a business
combination with any holders of 15% or more of their capital stock until the
holder has held the stock for three years unless, among other things, the board
approves the transaction. Also, under Delaware law, our board of directors may
adopt additional anti-takeover measures in the future.

                                       10
<PAGE>   14

              CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS

     Some of the statements in this prospectus and the documents incorporated by
reference are forward-looking statements. These statements are based on our
current expectations, assumptions, estimates and projections about our business
and industry and involve known and unknown risks, uncertainties and other
factors that may cause our results, levels of activity, performance or
achievement to be materially different from any future results, levels of
activity, performance or achievements expressed or implied in or contemplated by
the forward-looking statements.

     In some cases, you can identify forward-looking statements by words such as
"believe", "anticipate", "expect", "intend", "plan", "will", "may", "should",
"estimate", "predict", "potential", "continue", or the negative of such terms or
other similar expressions. In addition, any statements that refer to
expectations, projections or other characterizations of future events or
circumstances are forward-looking statements.

     Although we believe that the expectations reflected in the forward-looking
statements are reasonable, we cannot guarantee future results, events, levels of
activity, performance, or achievements. Our actual results could differ
materially from those anticipated in such forward-looking statements as a result
of several factors more fully described under the caption "Risk Factors" and the
documents incorporated by reference. You are cautioned not to place undue
reliance on these forward-looking statements.

     The forward-looking statements made in this prospectus relate only to
events as of the date on which the statements are made. We do not intend to
update publicly any of the forward-looking statements for any reason, even if
new information becomes available or other events occur in the future.

        WHERE YOU CAN FIND MORE INFORMATION ABOUT AXYS AND THIS OFFERING

     We have filed with the SEC a registration statement on Form S-3 to register
the common stock offered by this prospectus. However, this prospectus does not
contain all of the information contained in the registration statement and the
exhibits and schedules to the registration statement. We strongly encourage you
to carefully read the registration statement and the exhibits and schedules to
the registration statement.

     We file annual, quarterly and special reports, proxy statements and other
information with the SEC. You may read and copy any document we file at the
SEC's public reference rooms in Washington, D.C., New York, New York and
Chicago, Illinois. You can request copies of these documents by contacting the
SEC and paying a fee for the copying cost. Please call the SEC at 1-800-SEC-0330
for further information on the public reference rooms. Our SEC filings are also
available to the public from the SEC's website at www.sec.gov.

     The SEC allows us to "incorporate by reference" the information contained
in documents that we file with them, which means that we can disclose important
information to you by referring you to those documents. The information
incorporated by reference is considered to be part of this prospectus.
Information in this prospectus supersedes information incorporated by reference
which we filed with the SEC prior to the date of this prospectus, while
information that we file later with the SEC will automatically update and
supersede this information. We incorporate by reference the documents listed
below:

     1. Our Annual Report on Form 10-K for the year ended December 31, 1999,
        filed with the Commission on March 7, 2000;

     2. Our Current Report of Form 8-K filed with the Commission on February 22,
        2000;

                                       11
<PAGE>   15

     3. Our Definitive Proxy Statement filed with the Commission on April 23,
        1999 in connection with our 1999 Annual Meeting of Stockholders;

     4. The description of the common stock contained in our Registration
        Statement on Form 8-A filed under the Securities Exchange Act of 1934,
        as amended, including any amendment or report filed for the purpose of
        updating such description.

     In addition, we incorporate by reference any future filings we will make
with the SEC under Sections 13(a), 13(c), 14 or 15(d) of the Securities Exchange
Act of 1934, as amended.

     You may request a copy of these filings, at no cost to you, by writing or
telephoning us at:

                           Axys Pharmaceuticals, Inc.
                               Investor Relations
                                180 Kimball Way
                         South San Francisco, CA 94080
                                 (650) 829-1000

                                USE OF PROCEEDS

     The proceeds from the sale of the common stock offered pursuant to this
prospectus are solely for the account of the selling stockholders. We will not
receive any proceeds from the sale of these shares of common stock.

                              SELLING STOCKHOLDERS

     We are registering the shares covered by this prospectus on behalf of the
selling stockholders named in the table below. We issued all of the shares to
the selling stockholders in a private placement transaction. We have registered
the shares to permit the selling stockholders and their pledgees, donees,
transferees or other successors-in-interest that receive their shares from a
selling stockholder as a gift, partnership distribution or other non-sale
related transfer after the date of this prospectus to resell the shares.

     The following table sets forth the name of each selling stockholder, the
number of shares owned by each selling stockholder, the number of shares that
may be offered under this prospectus and the number of shares of our common
stock owned by each selling stockholder after this offering is completed. Except
as set forth in the table below, none of the selling stockholders has had a
material relationship with us within the past three years. The number of shares
in the column "Number of Shares Being Offered" represent all of the shares that
each selling stockholder may offer under this prospectus. The selling
stockholders may sell some, all or none of their shares. We do not know how long
the selling stockholders will hold the shares before selling them and we
currently have no agreements, arrangements or understandings with any of the
selling stockholders regarding the sale of any of the shares. The shares offered
by this prospectus may be offered from time to time by the selling stockholders.

                                       12
<PAGE>   16

     The percentages of shares owned prior to the offering are based on
34,946,051 shares of our common stock outstanding, after giving effect to the
sale of 3,497,778 shares to the selling stockholders in the Company's February
2000 private placement.

<TABLE>
<CAPTION>
                                               SHARES BENEFICIALLY               SHARES BENEFICIALLY
                                                 OWNED PRIOR TO      NUMBER OF       OWNED AFTER
                                                    OFFERING          SHARES         OFFERING**
                                               -------------------     BEING     -------------------
                    NAME                        NUMBER    PERCENT     OFFERED     NUMBER    PERCENT
                    ----                       --------   --------   ---------   --------   --------
<S>                                            <C>        <C>        <C>         <C>        <C>
Deutsche Vermogensbildungsgesellschaft m.b.H.
  (DVG)......................................  600,000      1.72%     600,000          0         *
Franklin Biotechnology Discovery Fund........  600,000      1.72%     600,000          0         *
Deutsche Asset Management (NAVAP)............  300,000         *      300,000          0         *
Chelsey Capital..............................  250,000         *      250,000          0         *
ProQuest Investments, L.P....................  219,378         *      219,378          0         *
KMF Partners, L.P............................  200,000         *      200,000          0         *
Special Situations Private Equity Fund,
  L.P........................................  166,667         *      166,667          0         *
The Aries Master Fund........................  128,759         *      128,759          0         *
Delta Opportunity Fund, Ltd..................  123,555         *      123,555          0         *
Activest Management SA.......................  120,000         *      120,000          0         *
Merlin BioMed Int'l Ltd......................  120,000         *      120,000          0         *
Deutsche Asset Management (Dirfonds-AP)......  100,000         *      100,000          0         *
Merlin BioMed L.P............................  100,000         *      100,000          0         *
Aeolus Capital...............................  100,000         *      100,000          0         *
Delta Opportunity Fund (Institutional),
  LLC........................................   98,667         *       98,667          0         *
Activest American Performance LTD............   80,000         *       80,000          0         *
Aries Domestic Fund, L.P.....................   60,964         *       60,964          0         *
Bradley N. Rotter............................   50,000         *       50,000          0         *
Lodestone Capital Fund, LLC..................   50,000         *       50,000          0         *
Douglas and Laurie Moore, Trustees FBO
  The Moore '89 Family Trust dtd 3-9-89......   16,667         *       16,667          0         *
Aries Domestic Fund II, L.P..................   10,277         *       10,277          0         *
ProQuest Companion Fund, L.P.................    2,844         *        2,844          0         *
</TABLE>

- -------------------------
 * Represents less than 1%.

** Assuming the sale of all the offered shares

                              PLAN OF DISTRIBUTION

     The selling stockholders may sell the shares from time to time. The selling
stockholders will act independently of us in making decisions regarding the
timing, manner and size of each sale. The sales may be made on one or more
exchanges or in the over-the-counter market or otherwise, at prices and at terms
then prevailing or at prices related to the then current market price, or in
privately negotiated transactions. The selling stockholders may effect these
transactions by selling the shares to or through broker-dealers. The selling
stockholders may sell their shares in one or more of, or a combination of:

     - a block trade in which the broker-dealer will attempt to sell the shares
       as agent but may position and resell a portion of the block as principal
       to facilitate the transaction,

     - purchases by a broker-dealer as principal and resale by a broker-dealer
       for its account under this prospectus,

     - an exchange distribution in accordance with the rules of an exchange,

                                       13
<PAGE>   17

     - ordinary brokerage transactions and transactions in which the broker
       solicits purchasers, and

     - privately negotiated transactions.

     To the extent required, this prospectus may be amended or supplemented from
time to time to describe a specific plan of distribution. If the plan of
distribution involves an arrangement with a broker-dealer for the sale of shares
through a block trade, special offering, exchange distribution or secondary
distribution or a purchase by a broker or dealer, the amendment or supplement
will disclose:

     - the name of each selling stockholder and of the participating
       broker-dealer(s),

     - the number of shares involved,

     - the price at which the shares were sold,

     - the commissions paid or discounts or concessions allowed to the
       broker-dealer(s), where applicable,

     - that a broker-dealer(s) did not conduct any investigation to verify the
       information set out or incorporated by reference in this prospectus, and

     - other facts material to the transaction.

     From time to time, a selling stockholder may transfer, pledge, donate or
assign its shares of common stock to lenders or others and each of such persons
will be deemed to be a "selling stockholder" for purposes of this prospectus.
The number of shares of common stock beneficially owned by the selling
stockholder will decrease as and when it takes such actions. The plan of
distribution for the selling stockholders' shares of common stock sold under
this prospectus will otherwise remain unchanged, except that the transferees,
pledgees, donees or other successors will be selling stockholders hereunder.
Upon being notified by a selling stockholder that a donee or pledgee intends to
sell more than 500 shares, we will file a supplement to this prospectus.

     The selling stockholders may enter into hedging transactions with
broker-dealers in connection with distributions of the shares or otherwise. In
these transactions, broker-dealers may engage in short sales of the shares in
the course of hedging the positions they assume with selling stockholders. The
selling stockholders also may sell shares short and redeliver the shares to
close out short positions. The selling stockholders may enter into option or
other transactions with broker-dealers which require the delivery to the
broker-dealer of the shares. The broker-dealer may then resell or otherwise
transfer the shares under this prospectus. The selling stockholders also may
loan or pledge the shares to a broker-dealer. The broker-dealer may sell the
loaned shares, or upon a default the broker-dealer may sell the pledged shares
under this prospectus.

     In effecting sales, broker-dealers engaged by the selling stockholders may
arrange for other broker-dealers to participate in the resales. Broker-dealers
or agents may receive compensation in the form of commissions, discounts or
concessions from selling stockholders. Broker-dealers or agents may also receive
compensation from the purchasers of the shares for whom they act as agents or to
whom they sell as principals, or both. Compensation as to a particular
broker-dealer might be in excess of customary commissions and will be in amounts
to be negotiated in connection with the sale. Broker-dealers or agents and any
other participating broker-dealers or the selling stockholders may be deemed to
be "underwriters" within the meaning of Section 2(11) of the Securities Act of
1933, as amended, in connection with sales of the shares. Accordingly, any
commission, discount or concession received by them and any profit on the resale
of the shares purchased by them may be deemed to be underwriting discounts or
commissions under the Securities Act. Because selling stockholders may be deemed
to be "underwriters" within the meaning of Section 2(11) of the Securities Act,
the selling stockholders will be subject to the prospectus delivery requirements
of the Securities Act. In addition,

                                       14
<PAGE>   18

any securities covered by this prospectus that qualify for sale under Rule 144
promulgated under the Securities Act may be sold under Rule 144 rather than
under this prospectus. The selling stockholders have advised that they have not
entered into any agreements, understandings or arrangements with any
underwriters or broker-dealers regarding the sale of their securities. There is
no underwriter or coordinating broker acting in connection with the proposed
sale of shares by the selling stockholders.

     The shares will be sold only through registered or licensed brokers or
dealers if required under applicable state securities laws. In addition, in some
states the shares may not be sold unless they have been registered or qualified
for sale in the applicable state or an exemption from the registration or
qualification requirement is available and is complied with.

     Under applicable rules and regulations under the Securities Exchange Act of
1934, as amended, any person engaged in the distribution of the shares may not
simultaneously engage in market making activities with respect to our common
stock for a period of two business days prior to the commencement of the
distribution. In addition, each selling stockholder will be subject to
applicable provisions of the Exchange Act and the associated rules and
regulations under the Exchange Act, including Regulation M, which provisions may
limit the timing of purchases and sales of shares of our common stock by the
selling stockholders.

     We will make copies of this prospectus available to the selling
stockholders and have informed them of the need to deliver copies of this
prospectus to purchasers at or prior to the time of any sale of the shares.

     We will bear all costs, expenses and fees in connection with the
registration of the shares. The selling stockholders will bear all commissions
and discounts, if any, attributable to the sales of the shares. The selling
stockholders may agree to indemnify any broker-dealer or agent that participates
in transactions involving sales of the shares against specific liabilities,
including liabilities arising under the Securities Act. The selling stockholders
have agreed to indemnify specific persons, including broker-dealers and agents,
against specific liabilities in connection with the offering of the shares,
including liabilities arising under the Securities Act.

     We have agreed to maintain the effectiveness of this registration statement
until each selling stockholder can sell all of the shares it holds under Rule
144(k) promulgated under the Securities Act. The selling stockholders may sell
all, some or none of the shares offered by this prospectus.

                                 LEGAL MATTERS

     The legality of the shares of common stock offered hereby is being passed
upon by Cooley Godward LLP, Palo Alto, California. Cooley Godward LLP and
attorneys in the firm own an aggregate of approximately 5,000 shares of the
Axys' common stock. Alan C. Mendelson, a partner at Cooley Godward LLP, is a
director of Axys and also owns approximately 18,329 shares of Axys' common
stock.

                                    EXPERTS

     Ernst & Young LLP, independent auditors, have audited our consolidated
financial statements included in our Annual Report on Form 10-K for the year
ended December 31, 1999, as set forth in their report, which is incorporated by
reference in this prospectus and elsewhere in the registration statement. Our
financial statements are incorporated by reference in reliance on Ernst & Young
LLP's report, given on their authority as experts in accounting and auditing.

                                       15
<PAGE>   19

                                    PART II

                   INFORMATION NOT REQUIRED IN THE PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

     The following table sets forth the costs and expenses in connection with
the sale and distribution of the securities being registered, other than
underwriting discounts and commissions. All of the amounts shown are estimates
except the Securities and Exchange Commission registration fees and Nasdaq
filing fee.

<TABLE>
<S>                                                           <C>
SEC Registration Fee........................................  $ 14,500
Nasdaq filing fee...........................................  $ 17,500
Accounting fees and expenses................................  $  5,000
Legal fees and expenses.....................................  $ 75,000
Printing expenses...........................................  $  6,000
Miscellaneous expenses......................................  $  5,000
                                                              --------
  Total.....................................................  $123,000
                                                              --------
</TABLE>

ITEM 15. INDEMNIFICATION OF DIRECTORS AND OFFICERS.

     Section 145 of the Delaware General Corporation Law permits a corporation
to include in its charter documents and in agreements with its directors and
officers provisions expanding the scope of indemnification beyond that
specifically provided by the Delaware law. The Registrant's Bylaws provide that
the Registrant shall indemnify to the full extent authorized by law each of its
directors and officers against expenses (including attorney fees), judgments,
fines, settlements and other amounts actually and reasonable incurred in
connection with any proceeding arising by reason of the fact that such person is
or was an agent of the Registrant or any predecessor of the Registrant or serves
or served any other enterprise as a director or officer at the request of the
Registrant or a predecessor of the Registrant. The Registrant's Bylaws also
provide that the Registrant may similarly indemnify each of its employees or
agents. The Registrant has entered into indemnification agreements with each of
our directors and officers that provide for indemnification greater than that
provided in the Bylaws.

     The Registrant maintains insurance on behalf of any person who is a
director or officer against any loss arising from any claim asserted against him
or her and incurred by him or her in any such capacity, subject to certain
exclusions. At present, there is no pending litigation or proceeding involving a
director or officer of the Registrant as to which indemnification is being
sought nor is the Registrant aware of any threatened litigation that may result
in claims for indemnification by any officer or director.

     See also the undertakings set out in response to Item 17 herein.

                                      II-1
<PAGE>   20

ITEM 16. EXHIBITS.

     The following exhibits are filed with this Registration Statement:

<TABLE>
<CAPTION>
EXHIBIT
NUMBER                       DESCRIPTION OF EXHIBIT
- -------                      ----------------------
<C>       <S>
  5.1     Opinion of Cooley Godward LLP.
 10.1     Form of Stock Purchase Agreement by and between Axys
          Pharmaceuticals, Inc. and each of the selling stockholders.
 23.1     Consent of Ernst & Young LLP, independent auditors.
 23.2     Consent of Cooley Godward LLP (included in Exhibit 5.1).
 24.1     Power of Attorney (included in the Signature Page contained
          in Part II of the Registration Statement).
</TABLE>

ITEM 17. UNDERTAKINGS.

     The undersigned registrant hereby undertakes:

          (1) To file, during any period in which offers or sales are being
     made, a post-effective amendment to this registration statement to include
     any material information with respect to the plan of distribution not
     previously disclosed in the registration statement or any material change
     to that information in the registration statement.

          (2) That, for the purpose of determining any liability under the
     Securities Act, each post-effective amendment shall be deemed to be a new
     registration statement relating to the securities it offers, and the
     offering of the securities at that time shall be deemed to be the initial
     bona fide offering thereof.

          (3) To remove from registration by means of a post-effective amendment
     any of the securities being registered which remain unsold at the
     termination of this offering.

          (4) That, for purposes of determining any liability under the
     Securities Act, each filing of the registrant's annual report pursuant to
     Section 13(a) or Section 15(d) of the Exchange Act that is incorporated by
     reference in the registration statement shall be deemed to be a new
     registration statement relating to the securities offered therein, and the
     offering of the securities at that time shall be deemed to be the initial
     bona fide offering thereof.

     Insofar as indemnification for liabilities arising under the Securities Act
may be permitted to directors, officers and controlling persons of the
registrant pursuant to the foregoing provisions, or otherwise, the registrant
has been advised that in the opinion of the SEC this form of indemnification is
against public policy as expressed in the Securities Act and is, therefore,
unenforceable. In the event that a claim for indemnification against these
liabilities (other than the payment by the registrant of expenses incurred or
paid by a director, officer or controlling person of the registrant in the
successful defense of any action, suit or proceeding) is asserted by a director,
officer or controlling person in connection with the securities being
registered, the registrant will, unless in the opinion of its counsel the matter
has been settled by controlling precedent, submit to a court of appropriate
jurisdiction the question whether such indemnification by it is against public
policy as expressed in the Securities Act and will be governed by the final
adjudication of this issue.

                                      II-2
<PAGE>   21

                                   SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-3 and has duly caused this registration
statement to be signed on its behalf by the undersigned, thereunto duly
authorized in the City of South San Francisco, State of California on February
24, 2000.

                                          AXYS PHARMACUETICALS, INC.

                                          By:      /s/ JOHN P. WALKER
                                            ------------------------------------
                                                       John P. Walker
                                                Chief Executive Officer and
                                                   Chairman of the Board

     KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints John P. Walker and Kathleen Stafford, and
each of them, as his or her true and lawful attorneys-in-fact and agents, with
full power of substitution and resubstitution, for him or her and in his or her
name, place and stead, in any and all capacities, to sign any and all amendments
(including post-effective amendments) to this Registration Statement on Form
S-3, and to file the same, with all exhibits thereto, and other documents in
connection therewith, with the Securities and Exchange Commission, granting unto
said attorneys-in-fact and agents, and each of them, full power and authority to
do and perform each and every act and thing requisite and necessary to be done
in connection therewith, as fully to all intents and purposes as he or she might
or could do in person, hereby ratifying and confirming all that said
attorney-in-facts and agents, or either of them, or their or his substitute or
substitutes, may lawfully do or cause to be done by virtue hereof. Pursuant to
the requirements of the Securities Act of 1933, this Registration Statement has
been signed by the following persons in the capacities and on the dates
indicated:

<TABLE>
<CAPTION>
                      SIGNATURE                                    TITLE                    DATE
                      ---------                                    -----                    ----
<C>                                                    <C>                            <S>

                 /s/ JOHN P. WALKER                      Chief Executive Officer,     February 24, 2000
- -----------------------------------------------------     Chairman of the Board,
                   John P. Walker                      Director (Principal Executive
                                                                 Officer)

                /s/ KATHLEEN STAFFORD                    Senior Vice President and    February 24, 2000
- -----------------------------------------------------     Chief Financial Officer
                  Kathleen Stafford                      (Principal Financial and
                                                            Accounting Officer)

                  /s/ ANN M. ARVIN                               Director             March 6, 2000
- -----------------------------------------------------
                  Ann M. Arvin, MD

                /s/ VAUGHN M. KAILIAN                            Director             February 24, 2000
- -----------------------------------------------------
                  Vaughn M. Kailian

                 /s/ DONALD KENNEDY                              Director             February 24, 2000
- -----------------------------------------------------
                Donald Kennedy, Ph.D.

                                                                 Director
- -----------------------------------------------------
                    Irwin Lerner

                /s/ ALAN C. MENDELSON                            Director             February 24, 2000
- -----------------------------------------------------
                  Alan C. Mendelson

                /s/ J. LEIGHTON READ                             Director             February 24, 2000
- -----------------------------------------------------
               J. Leighton Read, M.D.
</TABLE>

                                      II-3
<PAGE>   22

                               INDEX TO EXHIBITS

<TABLE>
<CAPTION>
EXHIBIT
NUMBER                             DESCRIPTION
- -------                            -----------
<C>        <S>
  5.1      Opinion of Cooley Godward LLP.
 10.1      Form of Stock Purchase Agreement by and between Axys
           Pharmaceuticals, Inc. and each of the selling stockholders.
 23.1      Consent of Ernst & Young LLP, independent auditors.
 23.2      Consent of Cooley Godward LLP (included in Exhibit 5.1).
 24.1      Power of Attorney (included in the Signature Page contained
           in Part II of the Registration Statement).
</TABLE>

<PAGE>   1
                                                                     EXHIBIT 5.1



March 9, 2000

Axys Pharmaceuticals, Inc.
180 Kimball Way
South San Francisco, CA  94080

Dear Ladies and Gentlemen:

You have requested our opinion with respect to certain matters in connection
with the filing by Axys Pharmaceuticals, Inc. (the "Company") of a Registration
Statement on Form S-3 (the "Registration Statement") with the Securities and
Exchange Commission covering the offering for resale of 3,497,778 shares of the
Company's Common Stock (the "Shares"), with a par value of $0.001, issued in
connection with that certain Purchase Agreement by and between the Company and
the purchasers named therein.

In connection with this opinion, we have examined the Registration Statement,
the Company's Certificate of Incorporation and Bylaws, as amended, the
resolutions adopted by the Board of Directors of the Company on February 11,
2000, and such other documents, records, certificates, memoranda and other
instruments as we deem necessary as a basis for this opinion. We have assumed
the genuineness and authenticity of all documents submitted to us as originals,
the conformity to originals of all documents submitted to us as copies thereof,
and the due execution and delivery of all documents where due execution and
delivery are a prerequisite to the effectiveness thereof.

On the basis of the foregoing, and in reliance thereon, we are of the opinion
that the Shares are validly issued, fully paid and nonassessable.

We consent to the filing of this opinion as an exhibit to the Registration
Statement and to the reference to our firm under the caption "Legal Matters" in
the Prospectus included in the Registration Statement.

Sincerely,

/s/ Alan C. Mendelson

Alan C. Mendelson


<PAGE>   1
                                                                    EXHIBIT 10.1
                            STOCK PURCHASE AGREEMENT

Axys Pharmaceuticals, Inc.
180 Kimball Way
South San Francisco, CA 94080

Ladies & Gentlemen:

        The undersigned, _________________________________(the "Investor"),
hereby confirms its agreement with you as follows:

1. This Stock Purchase Agreement (the "Agreement") is made as of _______ __,
2000 between Axys Pharmaceuticals, Inc., a Delaware corporation (the "Company"),
and the Investor.

2. The Company has authorized the sale and issuance of up to ________ shares
(the "Shares") of common stock of the Company, $0.001 par value per share (the
"Common Stock"), subject to adjustment by the Company's Board of Directors, to
certain investors in a private placement (the "Offering").

3. The Company and the Investor agree that the Investor will purchase from the
Company and the Company will issue and sell to the Investor ___________ Shares,
for a purchase price of $_______ per share, or an aggregate purchase price of
$_______________, pursuant to the Terms and Conditions for Purchase of Shares
attached hereto as Annex I and incorporated herein by reference as if fully set
forth herein. Unless otherwise requested by the Investor, certificates
representing the Shares purchased by the Investor will be registered in the
Investor's name and address as set forth below.

4. The Investor represents that, except as set forth below, (a) it has had no
position, office or other material relationship within the past three years with
the Company or persons known to it to be affiliates of the Company, (b) neither
it, nor any group of which it is a member or to which it is related,
beneficially owns (including the right to acquire or vote) any securities of the
Company and (c) it has no direct or indirect affiliation or association with any
NASD member as of the date hereof. Exceptions:

- --------------------------------------------------------------------------------

- -------------------------------------------------------------------------------
                 (If no exceptions, write "none." If left blank,
                     response will be deemed to be "none.")

        Please confirm that the foregoing correctly sets forth the agreement
between us by signing in the space provided below for that purpose. By executing
this Agreement, you acknowledge that the Company may use the information in
paragraph 4 above and the name and address information below in preparation of
the Registration Statement (as defined in Annex 1).

AGREED AND ACCEPTED:
Axys Pharmaceuticals, Inc.             "INVESTOR"


                                       By:
- ----------------------------------
By:
Title:                                 Print Name:
                                                  ------------------------------
                                       Title:
                                             -----------------------------------
                                       Address:
                                               ---------------------------------

                                       Tax ID No.:
                                                  ------------------------------
                                       Contact name:
                                                    ----------------------------
                                       Telephone:
                                                 -------------------------------

                                       Name in which shares should registered
                                       (if different):
                                                      --------------------------

<PAGE>   2
                                     ANNEX I

                   TERMS AND CONDITIONS FOR PURCHASE OF SHARES


        1. Authorization and Sale of the Shares. Subject to the terms and
conditions of this Agreement, the Company has authorized the sale of up to
________ Shares. The Company reserves the right to increase or decrease this
number.

        2. Agreement to Sell and Purchase the Shares; Subscription Date.

               2.1 At the Closing (as defined in Section 3), the Company will
sell to the Investor, and the Investor will purchase from the Company, upon the
terms and conditions hereinafter set forth, the number of Shares set forth on
the signature page hereto at the purchase price set forth on such signature
page.

               2.2 The Company may enter into this same form of Stock Purchase
Agreement with certain other investors (the "Other Investors") and expects to
complete sales of Shares to them. (The Investor and the Other Investors are
hereinafter sometimes collectively referred to as the "Investors," and this
Agreement and the Stock Purchase Agreements executed by the Other Investors are
hereinafter sometimes collectively referred to as the "Agreements.") The Company
may accept executed Agreements from Investors for the purchase of Shares
commencing upon the date on which the Company provides the Investors with the
proposed purchase price per Share and concluding upon the date (the
"Subscription Date") on which the Company has (i) executed Agreements with
Investors for the purchase of at least _______ Shares, and (ii) notified the
Investors in writing that it is no longer accepting Agreements from Investors
for the purchase of Shares. The Company may not enter into any Agreements after
the Subscription Date.

        3. Delivery of the Shares at Closing. The completion of the purchase and
sale of the Shares (the "Closing") shall occur (the "Closing Date") on ________
__, 2000, at the offices of the Company's counsel. At the Closing, the Company
shall deliver to the Investor one or more stock certificates representing the
number of Shares set forth on the signature page hereto, each such certificate
to be registered in the name of the Investor or, if so indicated on the
signature page hereto, in the name of a nominee designated by the Investor.

        The Company's obligation to issue the Shares to the Investor shall be
subject to the following conditions, any one or more of which may be waived by
the Company: (a) receipt by the Company of a certified or official bank check or
wire transfer of funds in the full amount of the purchase price for the Shares
being purchased hereunder as set forth on the signature page hereto; (b)
completion of the purchases and sales under the Agreements with the Other
Investors; and (c) the accuracy of the representations and warranties made by
the Investors and the fulfillment of those undertakings of the Investors to be
fulfilled prior to the Closing.

        The Investor's obligation to purchase the Shares shall be subject to the
following conditions, any one or more of which may be waived by the Investor:
(a) Investors shall have executed Agreements for the purchase of at least
_______ Shares, (b) the representations and warranties of the Company set forth
herein shall be true and correct as of the Closing Date in all material respects
and (c) the Investor shall have received such documents as such Investor shall
reasonably have requested, including, a standard opinion of Company Counsel as
to the matters set forth in Section 4.2 and as to exemption from the
registration requirements of the Securities Act of 1933, as amended, of the sale
of the Shares.

        4. Representations, Warranties and Covenants of the Company. The Company
hereby represents and warrants to, and covenants with, the Investor, as follows:

               4.1 Organization. The Company is duly organized and validly
existing in good standing under the laws of the jurisdiction of its
organization. Each of the Company and its Subsidiaries (as defined in Rule 405
under the Securities Act of 1933, as amended (the "Securities Act")) has full
power and authority to own, operate and occupy its properties and to conduct its
business as presently conducted and as described in the confidential offering
memorandum, dated February 11, 2000 distributed in connection with the sale of
the Shares (including the documents incorporated by reference therein, the
"Placement Memorandum") and is registered or qualified to do business and in
good standing in each jurisdiction in which it owns or leases property or
transacts business and where the failure to be so qualified would have a
material adverse effect upon the business, financial

<PAGE>   3
condition, properties or operations of the Company and its Subsidiaries,
considered as one enterprise, and no proceeding has been instituted in any such
jurisdiction, revoking, limiting or curtailing, or seeking to revoke, limit or
curtail, such power and authority or qualification.

               4.2 Due Authorization and Valid Issuance. The Company has all
requisite power and authority to execute, deliver and perform its obligations
under the Agreements, and the Agreements have been duly authorized and validly
executed and delivered by the Company and constitute legal, valid and binding
agreements of the Company enforceable against the Company in accordance with
their terms, except as rights to indemnity and contribution may be limited by
state or federal securities laws or the public policy underlying such laws,
except as enforceability may be limited by applicable bankruptcy, insolvency,
reorganization, moratorium or similar laws affecting creditors' and contracting
parties' rights generally and except as enforceability may be subject to general
principles of equity (regardless of whether such enforceability is considered in
a proceeding in equity or at law). The Shares being purchased by the Investor
hereunder will, upon issuance pursuant to the terms hereof, be duly authorized,
validly issued, fully-paid and nonassessable.

               4.3 Non-Contravention. The execution and delivery of the
Agreements, the issuance and sale of the Shares to be sold by the Company under
the Agreements, the fulfillment of the terms of the Agreements and the
consummation of the transactions contemplated thereby will not (A) conflict with
or constitute a violation of, or default (with the passage of time or otherwise)
under, (i) any material bond, debenture, note or other evidence of indebtedness,
lease, contract, indenture, mortgage, deed of trust, loan agreement, joint
venture or other agreement or instrument to which the Company or any Subsidiary
is a party or by which it or any of its Subsidiaries or their respective
properties are bound, which individually, or in the aggregate, would have a
material adverse effect upon the business or financial condition of the Company
and its Subsidiaries, considered as one enterprise, (ii) the charter, by-laws or
other organizational documents of the Company or any Subsidiary, or (iii) any
law, administrative regulation, ordinance or order of any court or governmental
agency, arbitration panel or authority applicable to the Company or any
Subsidiary or their respective properties, or (B) result in the creation or
imposition of any lien, encumbrance, claim, security interest or restriction
whatsoever upon any of the material properties or assets of the Company or any
Subsidiary or an acceleration of indebtedness pursuant to any obligation,
agreement or condition contained in any material bond, debenture, note or any
other evidence of indebtedness or any material indenture, mortgage, deed of
trust or any other agreement or instrument to which the Company or any
Subsidiary is a party or by which any of them is bound or to which any of the
property or assets of the Company or any Subsidiary is subject, which
individually, or in the aggregate, would have a material adverse effect upon the
business or financial condition of the Company and its Subsidiaries, considered
as one enterprise. No consent, approval, authorization or other order of, or
registration, qualification or filing with, any regulatory body, administrative
agency, or other governmental body in the United States or any other person is
required for the execution and delivery of the Agreements and the valid issuance
and sale of the Shares to be sold pursuant to the Agreements, other than such as
have been made or obtained, and except for any post-closing securities filings
or notifications required to be made under federal or state securities laws.

               4.4 Capitalization. The capitalization of the Company as of
September 30, 1999 is as set forth in the Placement Memorandum (excluding
unvested options and treasury shares). The Company has not issued any capital
stock since that date other than pursuant to (i) employee benefit plans
disclosed in the Placement Memorandum, or (ii) outstanding warrants or options
disclosed in the Placement Memorandum. The Shares to be sold pursuant to the
Agreements have been duly authorized, and when issued and paid for in accordance
with the terms of the Agreements will be duly and validly issued, fully paid and
nonassessable. The outstanding shares of capital stock of the Company have been
duly and validly issued and are fully paid and nonassessable, have been issued
in compliance with all federal and state securities laws, and were not issued in
violation of any preemptive rights or similar rights to subscribe for or
purchase securities. Except as set forth in or contemplated by the Placement
Memorandum and except for certain registration rights, certain rights of first
refusal and certain time-limited prohibitions on sales without the consent of a
third party applicable to one Subsidiary (PPGx, Inc.), there are no outstanding
rights (including, without limitation, preemptive rights), warrants or options
to acquire, or instruments convertible into or exchangeable for, any unissued
shares of capital stock or other equity interest in the Company or any
Subsidiary, or any contract, commitment, agreement, understanding or arrangement
of any kind to which the Company is a party or of which the Company has
knowledge and relating to the issuance or sale of any capital stock of the
Company or any Subsidiary, any such convertible or exchangeable securities or
any such rights, warrants or options. Without limiting the foregoing, no
preemptive right, co-sale right, right of first refusal, registration right, or
other similar right exists with respect to the Shares or the issuance and sale
thereof. No further approval or authorization of any stockholder, the Board of
Directors of the Company or others is required for the issuance and sale of the
Shares. The Company owns the entire equity interest in each of its Subsidiaries,
free and clear of any pledge, lien, security interest, encumbrance, claim or
equitable interest, other than as described in the Placement Memorandum. Except
as disclosed in

<PAGE>   4
the Placement Memorandum, there are no stockholders agreements, voting
agreements or other similar agreements with respect to the Common Stock to which
the Company is a party or, to the knowledge of the Company, between or among any
of the Company's stockholders.

               4.5 Legal Proceedings. There is no material legal or governmental
proceeding pending or, to the knowledge of the Company, threatened to which the
Company or any Subsidiary is or may be a party or of which the business or
property of the Company or any Subsidiary is subject that is not disclosed in
the Placement Memorandum.

               4.6 No Violations. Neither the Company nor any Subsidiary is in
violation of its charter, bylaws, or other organizational document, or in
violation of any law, administrative regulation, ordinance or order of any court
or governmental agency, arbitration panel or authority applicable to the Company
or any Subsidiary, which violation, individually or in the aggregate, would be
reasonably likely to have a material adverse effect on the business or financial
condition of the Company and its Subsidiaries, considered as one enterprise, or
is in default (and there exists no condition which, with the passage of time or
otherwise, would constitute a default) in any material respect in the
performance of any bond, debenture, note or any other evidence of indebtedness
in any indenture, mortgage, deed of trust or any other material agreement or
instrument to which the Company or any Subsidiary is a party or by which the
Company or any Subsidiary is bound or by which the properties of the Company or
any Subsidiary are bound, which would be reasonably likely to have a material
adverse effect upon the business or financial condition of the Company and its
Subsidiaries, considered as one enterprise.

               4.7 Governmental Permits, Etc. With the exception of the matters
which are dealt with separately in Section 4.1, 4.12, 4.13, and 4.14, each of
the Company and its Subsidiaries has all necessary franchises, licenses,
certificates and other authorizations from any foreign, federal, state or local
government or governmental agency, department, or body that are currently
necessary for the operation of the business of the Company and its Subsidiaries
as currently conducted and as described in the Placement Memorandum except where
the failure to currently possess could not reasonably be expected to have a
material adverse effect upon the business or financial condition of the Company
and its Subsidiaries, considered as one enterprise.

               4.8 Intellectual Property. Except as specifically disclosed under
"Risk Factors" in the Placement Memorandum (i) each of the Company and its
Subsidiaries owns or possesses sufficient rights to use all material patents,
patent rights, trademarks, copyrights, licenses, inventions, trade secrets,
trade names and know-how (collectively, "Intellectual Property") described or
referred to in the Placement Memorandum as owned or possessed by it or that are
necessary for the conduct of its business as now conducted or, to the Company's
knowledge, as proposed to be conducted as described in the Placement Memorandum
except where the failure to currently own or possess would not have a material
adverse effect on the condition (financial or otherwise), earnings, operations,
business or business prospects of the Company and its Subsidiaries considered as
one enterprise, (ii) neither the Company nor any of its Subsidiaries has
received any notice of, or has any knowledge of, any infringement of asserted
rights of a third party with respect to any Intellectual Property that,
individually or in the aggregate, would have a material adverse effect on the
financial condition or business of the Company and its Subsidiaries considered
as one enterprise and (iii) neither the Company nor any of its Subsidiaries has
received any notice of any infringement of rights of a third party with respect
to any Intellectual Property that, individually or in the aggregate, would have
a material adverse effect upon the business or financial condition of the
Company and its Subsidiaries, considered as one enterprise.

               4.9 Financial Statements. The financial statements of the Company
and the related notes contained in the Placement Memorandum present fairly, in
accordance with generally accepted accounting principles, the financial position
of the Company and its Subsidiaries as of the dates indicated, and the results
of its operations and cash flows for the periods therein specified. Such
financial statements (including the related notes) have been prepared in
accordance with generally accepted accounting principles applied on a consistent
basis throughout the periods therein specified, except as disclosed in the
Placement Memorandum. The other financial information contained in the Placement
Memorandum has been prepared on a basis consistent with the financial statements
of the Company.

               4.10 No Material Adverse Change. Except as disclosed in the
Placement Memorandum, since September 30, 1999, there has not been (i) any
material adverse change in the financial condition or earnings of the Company
and its Subsidiaries considered as one enterprise nor has any material adverse
event occurred to the Company or its Subsidiaries, (ii) any material adverse
event affecting the Company, (iii) any obligation, direct or contingent, that is
material to the Company and its Subsidiaries considered as one enterprise,
incurred by the Company, except obligations incurred in the ordinary course of
business, (iv) any dividend or distribution of any kind declared, paid or made
on the capital stock of the Company or, in the case

<PAGE>   5
of any of its Subsidiaries, payable to any party other than the Company, or (v)
any loss or damage (whether or not insured) to the physical property of the
Company or any of its Subsidiaries which has been sustained which has a material
adverse effect on the condition (financial or otherwise), earnings, operations,
business or business prospects of the Company and its Subsidiaries considered as
one enterprise.

               4.11 Disclosure. The information contained in the Placement
Memorandum as of the date hereof and as of the Closing Date, did not and shall
not contain an untrue statement of a material fact or omit to state a material
fact required to be stated therein or necessary to make the statements therein,
in light of the circumstances under which they were made, not misleading.

               4.12 NASDAQ Compliance. The Company's Common Stock is registered
pursuant to Section 12(g) of the Exchange Act and is listed on The Nasdaq Stock
Market, Inc. National Market (the "Nasdaq National Market"), and the Company has
taken no action designed to, or likely to have the effect of, terminating the
registration of the Common Stock under the Exchange Act or de-listing the Common
Stock from the Nasdaq National Market, nor has the Company received any
notification that the Securities and Exchange Commission (the "SEC") or the
National Association of Securities Dealers, Inc. ("NASD") is contemplating
terminating such registration or listing.

               4.13 Reporting Status. The Company has filed in a timely manner
all documents that the Company was required to file under the Securities
Exchange Act of 1934, as amended (the "Exchange Act") during the 12 months
preceding the date of this Agreement. The following documents complied in all
material respects with the SEC's requirements as of their respective filing
dates, and the information contained therein as of the date thereof did not
contain an untrue statement of a material fact or omit to state a material fact
required to be stated therein or necessary to make the statements therein in
light of the circumstances under where they were made not misleading:

                        (a) Annual Report on Form 10-K for the year ended
                        December 31, 1998, filed with the SEC on March 31, 1999;

                        (b) Definitive Proxy Statement filed with the SEC on
                        April 23, 1999 in connection with the 1999 Annual
                        Meeting of Stockholders;

                        (c) Quarterly Reports on Form 10-Q filed with the SEC on
                        May 17, 1999, August 14, 1999 and November 16, 1999; and

                        (d) All other documents, if any, filed by the Company
                        with the SEC since the date of the Placement Memorandum
                        pursuant to the reporting requirements of the Exchange
                        Act.

               4.14 Listing. The Company shall comply with all requirements of
the National Association of Securities Dealers, Inc. with respect to the
issuance of the Shares and the listing thereof on the Nasdaq National Market.

               4.15 No Manipulation of Stock. The Company has not taken and will
not, in violation of applicable law, take, any action designed to or that might
reasonably be expected to cause or result in stabilization or manipulation of
the price of the Common Stock to facilitate the sale or resale of the Shares.

        5. Representations, Warranties and Covenants of the Investor.

               5.1 The Investor represents and warrants to, and covenants with,
the Company that: (i) the Investor is an "accredited investor" as defined in
Regulation D under the Securities Act and the Investor is also knowledgeable,
sophisticated and experienced in making, and is qualified to make decisions with
respect to investments in shares presenting an investment decision like that
involved in the purchase of the Shares, including investments in securities
issued by the Company and investments in comparable companies, and has
requested, received, reviewed and considered all information it deemed relevant
in making an informed decision to purchase the Shares; (ii) the Investor is
acquiring the number of Shares set forth on the signature page hereto in the
ordinary course of its business and for its own account for investment only and
with no present intention of distributing any of such Shares or any arrangement
or understanding with any other persons regarding the distribution of such
Shares; (iii) the Investor will not, directly or indirectly, offer, sell,
pledge, transfer or otherwise dispose of (or solicit any offers to

<PAGE>   6
buy, purchase or otherwise acquire or take a pledge of) any of the Shares except
in compliance with the Securities Act, applicable state securities laws and the
respective rules and regulations promulgated thereunder; (iv) the Investor has
answered all questions on the signature page hereto for use in preparation of
the Registration Statement and the answers thereto are true and correct as of
the date hereof and will be true and correct as of the Closing Date; (v) the
Investor will notify the Company immediately of any change in any of such
information until such time as the Investor has sold all of its Shares or until
the Company is no longer required to keep the Registration Statement effective;
and (vi) the Investor has, in connection with its decision to purchase the
number of Shares set forth on the signature page hereto, relied only upon the
Placement Memorandum and the representations and warranties of the Company
contained herein. Investor understands that its acquisition of the Shares has
not been registered under the Securities Act or registered or qualified under
any state securities law in reliance on specific exemptions therefrom, which
exemptions may depend upon, among other things, the bona fide nature of the
Investor's investment intent as expressed herein. Investor has completed or
caused to be completed and delivered to the Company the Investor Questionnaire
attached as Exhibit B to the Placement Memorandum, which questionnaire is true
and correct in all material respects.

               5.2 The Investor acknowledges, represents and agrees that no
action has been or will be taken in any jurisdiction outside the United States
by the Company that would permit an offering of the Shares, or possession or
distribution of offering materials in connection with the issue of the Shares,
in any jurisdiction outside the United States where legal action by the Company
for that purpose is required. Each Investor outside the United States will
comply with all applicable laws and regulations in each foreign jurisdiction in
which it purchases, offers, sells or delivers Shares or has in its possession or
distributes any offering material, in all cases at its own expense.

               5.3 The Investor hereby covenants with the Company not to make
any sale of the Shares without complying with the provisions of this Agreement
and without causing the prospectus delivery requirement under the Securities Act
to be satisfied, and the Investor acknowledges that the certificates evidencing
the Shares will be imprinted with a legend that prohibits their transfer except
in accordance therewith. The Investor acknowledges that there may occasionally
be times when the Company determines that it must suspend the use of the
Prospectus forming a part of the Registration Statement, as set forth in Section
7.2(c).

               5.4 The Investor further represents and warrants to, and
covenants with, the Company that (i) the Investor has full right, power,
authority and capacity to enter into this Agreement and to consummate the
transactions contemplated hereby and has taken all necessary action to authorize
the execution, delivery and performance of this Agreement, and (ii) this
Agreement constitutes a valid and binding obligation of the Investor enforceable
against the Investor in accordance with its terms, except as enforceability may
be limited by applicable bankruptcy, insolvency, reorganization, moratorium or
similar laws affecting creditors' and contracting parties' rights generally and
except as enforceability may be subject to general principles of equity
(regardless of whether such enforceability is considered in a proceeding in
equity or at law) and except as the indemnification agreements of the Investors
herein may be legally unenforceable.

               5.5 Investor will not use any of the restricted Shares acquired
pursuant to this Agreement to cover any short position in the Common Stock of
the Company if doing so would be in violation of applicable securities laws.

               5.6 The Investor understands that nothing in the Placement
Memorandum, this Agreement or any other materials presented to the Investor in
connection with the purchase and sale of the Shares constitutes legal, tax or
investment advice. The Investor has consulted such legal, tax and investment
advisors as it, in its sole discretion, has deemed necessary or appropriate in
connection with its purchase of Shares.

        6. Survival of Representations, Warranties and Agreements.
Notwithstanding any investigation made by any party to this Agreement, all
covenants, agreements, representations and warranties made by the Company and
the Investor herein shall survive the execution of this Agreement, the delivery
to the Investor of the Shares being purchased and the payment therefor.

        7. Registration of the Shares; Compliance with the Securities Act.

               7.1 Registration Procedures and Other Matters. The Company shall:

                      (a) subject to receipt of necessary information from the
Investors after prompt request from the Company to the Investors to provide such
information, use its best efforts to prepare and file with the SEC, within 10
days after

<PAGE>   7
the Closing Date, a registration statement (the "Registration Statement") to
enable the resale of the Shares by the Investors from time to time through the
automated quotation system of the Nasdaq National Market or in
privately-negotiated transactions;

                      (b) use its reasonable best efforts, subject to receipt of
necessary information from the Investors after prompt request from the Company
to the Investors to provide such information, to cause the Registration
Statement to become effective within 30 days after the Registration Statement is
filed by the Company, such efforts to include, without limiting the generality
of the foregoing, preparing and filing with the SEC on or prior to the filing of
the Registration Statement, but in any case, within ten (10) days of the Closing
Date any financial statements that are required to be filed prior to the
effectiveness of such Registration Statement;

                      (c) use its reasonable efforts to prepare and file with
the SEC such amendments and supplements to the Registration Statement and the
Prospectus used in connection therewith as may be necessary to keep the
Registration Statement current and effective for a period not exceeding, with
respect to each Investor's Shares purchased hereunder, the earlier of (i) the
second anniversary of the Closing Date, (ii) the date on which the Investor may
sell all Shares then held by the Investor without restriction by the volume
limitations of Rule 144(e) of the Securities Act, or (iii) such time as all
Shares purchased by such Investor in this Offering have been sold pursuant to a
registration statement.

                      (d) furnish to the Investor with respect to the Shares
registered under the Registration Statement such number of copies of the
Registration Statement, Prospectuses and Preliminary Prospectuses in conformity
with the requirements of the Securities Act and such other documents as the
Investor may reasonably request, in order to facilitate the public sale or other
disposition of all or any of the Shares by the Investor; provided, however, that
the obligation of the Company to deliver copies of Prospectuses or Preliminary
Prospectuses to the Investor shall be subject to the receipt by the Company of
reasonable assurances from the Investor that the Investor will comply with the
applicable provisions of the Securities Act and of such other securities or blue
sky laws as may be applicable in connection with any use of such Prospectuses or
Preliminary Prospectuses;

                      (e) file documents required of the Company for normal blue
sky clearance in states specified in writing by the Investor; provided, however,
that the Company shall not be required to qualify to do business or consent to
service of process in any jurisdiction in which it is not now so qualified or
has not so consented;

                      (f) bear all expenses in connection with the procedures in
paragraph (a) through (f) of this Section 7.1 and the registration of the Shares
pursuant to the Registration Statement; and

                      (g) advise the Investor, promptly after it shall receive
notice or obtain knowledge of the issuance of any stop order by the SEC delaying
or suspending the effectiveness of the Registration Statement or of the
initiation or threat of any proceeding for that purpose; and it will promptly
use its reasonable efforts to prevent the issuance of any stop order or to
obtain its withdrawal at the earliest possible moment if such stop order should
be issued.

        The Company understands that the Investor disclaims being an
underwriter, but the Investor being deemed an underwriter by the SEC shall not
relieve the Company of any obligations it has hereunder; provided, however that
if the Company receives notification from the SEC that the Investor is deemed an
underwriter, then the period by which the Company is obligated to submit an
acceleration request to the SEC shall be extended to the earlier of (i) the 90th
day after such SEC notification, or (ii) 120 days after the initial filing of
the Registration Statement with the SEC.

               7.2 Transfer of Shares After Registration; Suspension.

                      (a) The Investor agrees that it will not effect any
disposition of the Shares or its right to purchase the Shares that would
constitute a sale within the meaning of the Securities Act except as
contemplated in the Registration Statement referred to in Section 7.1 and as
described below or as otherwise permitted by law, and that it will promptly
notify the Company of any changes in the information set forth in the
Registration Statement regarding the Investor or its plan of distribution.

                      (b) Except in the event that paragraph (c) below applies,
the Company shall (i) if deemed necessary by the Company, prepare and file from
time to time with the SEC a post-effective amendment to the Registration

<PAGE>   8
Statement or a supplement to the related Prospectus or a supplement or amendment
to any document incorporated therein by reference or file any other required
document so that such Registration Statement will not contain an untrue
statement of a material fact or omit to state a material fact required to be
stated therein or necessary to make the statements therein not misleading, and
so that, as thereafter delivered to purchasers of the Shares being sold
thereunder, such Prospectus will not contain an untrue statement of a material
fact or omit to state a material fact required to be stated therein or necessary
to make the statements therein, in light of the circumstances under which they
were made, not misleading; (ii) provide the Investor copies of any documents
filed pursuant to Section 7.2(b)(i); and (iii) inform each Investor that the
Company has complied with its obligations in Section 7.2(b)(i) (or that, if the
Company has filed a post-effective amendment to the Registration Statement which
has not yet been declared effective, the Company will notify the Investor to
that effect, will use its reasonable efforts to secure the effectiveness of such
post-effective amendment as promptly as possible and will promptly notify the
Investor pursuant to Section 7.2(b)(i) hereof when the amendment has become
effective).

                      (c) Subject to paragraph (d) below, in the event (i) of
any request by the SEC or any other federal or state governmental authority
during the period of effectiveness of the Registration Statement for amendments
or supplements to a Registration Statement or related Prospectus or for
additional information; (ii) of the issuance by the SEC or any other federal or
state governmental authority of any stop order suspending the effectiveness of a
Registration Statement or the initiation of any proceedings for that purpose; or
(iii) of the receipt by the Company of any notification with respect to the
suspension of the qualification or exemption from qualification of any of the
Shares for sale in any jurisdiction or the initiation or threatening of any
proceeding for such purpose; or (iv) of any event or circumstance which, upon
the advice of its counsel, necessitates the making of any changes in the
Registration Statement or Prospectus, or any document incorporated or deemed to
be incorporated therein by reference, so that, in the case of the Registration
Statement, it will not contain any untrue statement of a material fact or any
omission to state a material fact required to be stated therein or necessary to
make the statements therein not misleading, and that in the case of the
Prospectus, it will not contain any untrue statement of a material fact or any
omission to state a material fact required to be stated therein or necessary to
make the statements therein, in the light of the circumstances under which they
were made, not misleading; then the Company shall, deliver a certificate in
writing to the Investor (the "Suspension Notice") to the effect of the foregoing
and, upon receipt of such Suspension Notice, the Investor will refrain from
selling any Shares pursuant to the Registration Statement (a "Suspension") until
the Investor's receipt of copies of a supplemented or amended Prospectus
prepared and filed by the Company, or until it is advised in writing by the
Company that the current Prospectus may be used, and has received copies of any
additional or supplemental filings that are incorporated or deemed incorporated
by reference in any such Prospectus. In the event of any Suspension, the Company
will use its reasonable efforts to cause the use of the Prospectus so suspended
to be resumed as soon as reasonably practicable within 20 business days after
the delivery of a Suspension Notice to the Investor. In addition to and without
limiting any other remedies (including, without limitation, at law or at equity)
available to the Investor, the Investor shall be entitled to specific
performance in the event that the Company fails to comply with the provisions of
this Section 7.2(c).

                      (d) Notwithstanding the foregoing paragraphs of this
Section 7.2, the Investor shall not be prohibited from selling Shares under the
Registration Statement as a result of Suspensions on more than two occasions of
not more than 30 days each in any twelve month period, unless, in the good faith
judgment of the Company's Board of Directors, upon advice of counsel, the sale
of Shares under the Registration Statement in reliance on this paragraph 7.2(e)
would be reasonably likely to cause a violation of the Securities Act or the
Exchange Act and result in liability to the Company directly or under Section
7.3.

                      (e) Provided that a Suspension is not then in effect the
Investor may sell Shares under the Registration Statement, provided that it
arranges for delivery of a current Prospectus to the transferee of such Shares.
Upon receipt of a request therefor, the Company has agreed to provide an
adequate number of current Prospectuses to the Investor and to supply copies to
any other parties requiring such Prospectuses in order for the Investor to
effect sales thereunder.

                      (f) In the event of a sale of Shares by the Investor
pursuant to the Registration Statement, the Investor must also deliver to the
Company's transfer agent, with a copy to the Company, a Certificate of
Subsequent Sale substantially in the form attached hereto as Exhibit A, so that
the Shares may be properly transferred.

               7.3 Indemnification.  For the purpose of this Section 7.3:

               (i) the term "Selling Stockholder" shall include the Investor and
any affiliate of such Investor;


<PAGE>   9
               (ii) the term "Registration Statement" shall include any final
Prospectus, exhibit, supplement or amendment included in or relating to the
Registration Statement referred to in Section 7.1; and

               (iii) the term "untrue statement" shall include any untrue
statement or alleged untrue statement, or any omission or alleged omission to
state in the Registration Statement a material fact required to be stated
therein or necessary to make the statements therein, in the light of the
circumstances under which they were made, not misleading.

                       (a) The Company agrees to indemnify and hold harmless
each Selling Stockholder from and against any losses, claims, damages or
liabilities to which such Selling Stockholder may become subject (under the
Securities Act or otherwise) insofar as such losses, claims, damages or
liabilities (or actions or proceedings in respect thereof) arise out of, or are
based upon (i) any untrue statement of a material fact contained in the
Registration Statement, or (ii) any failure by the Company to fulfill any
undertaking included in the Registration Statement, and the Company will
reimburse such Selling Stockholder for any reasonable legal or other expenses
reasonably incurred in investigating, defending or preparing to defend any such
action, proceeding or claim, or preparing to defend any such action, proceeding
or claim, provided, however, that the Company shall not be liable in any such
case to the extent that such loss, claim, damage or liability arises out of, or
is based upon, an untrue statement made in such Registration Statement in
reliance upon and in conformity with written information furnished to the
Company by or on behalf of such Selling Stockholder specifically for use in
preparation of the Registration Statement or the failure of such Selling
Stockholder to comply with its covenants and agreements contained in Section 7.2
hereof respecting sale of the Shares or any statement or omission in any
Prospectus that is corrected in any subsequent Prospectus that was delivered to
the Investor prior to the pertinent sale or sales by the Investor. The Company
shall reimburse each Selling Stockholder for the amounts provided for herein on
demand as such expenses are incurred.

                       (b) The Investor agrees to indemnify and hold harmless
the Company (and each person, if any, who controls the Company within the
meaning of Section 15 of the Securities Act, each officer of the Company who
signs the Registration Statement and each director of the Company) from and
against any losses, claims, damages or liabilities to which the Company (or any
such officer, director or controlling person) may become subject (under the
Securities Act or otherwise), insofar as such losses, claims, damages or
liabilities (or actions or proceedings in respect thereof) arise out of, or are
based upon, (i) any failure to comply with the covenants and agreements
contained in Section 7.2 hereof respecting sale of the Shares, or (ii) any
untrue statement of a material fact contained in the Registration Statement if
such untrue statement was made in reliance upon and in conformity with written
information furnished by or on behalf of the Investor specifically for use in
preparation of the Registration Statement, and the Investor will reimburse the
Company (or such officer, director or controlling person), as the case may be,
for any legal or other expenses reasonably incurred in investigating, defending
or preparing to defend any such action, proceeding or claim; provided that the
Investor's obligation to indemnify the Company shall be limited to the net
amount received by the Investor from the sale of the Shares.

                       (c) Promptly after receipt by any indemnified person of a
notice of a claim or the beginning of any action in respect of which indemnity
is to be sought against an indemnifying person pursuant to this Section 7.3,
such indemnified person shall notify the indemnifying person in writing of such
claim or of the commencement of such action, but the omission to so notify the
indemnifying party will not relieve it from any liability which it may have to
any indemnified party under this Section 7.3 (except to the extent that such
omission materially and adversely affects the indemnifying party's ability to
defend such action) or from any liability otherwise than under this Section 7.3.
Subject to the provisions hereinafter stated, in case any such action shall be
brought against an indemnified person, the indemnifying person shall be entitled
to participate therein, and, to the extent that it shall elect by written notice
delivered to the indemnified party promptly after receiving the aforesaid notice
from such indemnified party, shall be entitled to assume the defense thereof,
with counsel reasonably satisfactory to such indemnified person. After notice
from the indemnifying person to such indemnified person of its election to
assume the defense thereof, such indemnifying person shall not be liable to such
indemnified person for any legal expenses subsequently incurred by such
indemnified person in connection with the defense thereof, provided, however,
that if there exists or shall exist a conflict of interest that would make it
inappropriate, in the opinion of counsel to the indemnified person, for the same
counsel to represent both the indemnified person and such indemnifying person or
any affiliate or associate thereof, the indemnified person shall be entitled to
retain its own counsel at the expense of such indemnifying person; provided,
however, that no indemnifying person shall be responsible for the fees and
expenses of more than one separate counsel (together with appropriate local
counsel) for all indemnified parties. In no event shall any indemnifying person
be liable in respect of any amounts paid in settlement of any action unless the
indemnifying person shall have approved the terms of such settlement; provided
that such consent shall not be

<PAGE>   10
unreasonably withheld. No indemnifying person shall, without the prior written
consent of the indemnified person, effect any settlement of any pending or
threatened proceeding in respect of which any indemnified person is or could
have been a party and indemnification could have been sought hereunder by such
indemnified person, unless such settlement includes an unconditional release of
such indemnified person from all liability on claims that are the subject matter
of such proceeding.

                       (d) If the indemnification provided for in this Section
7.3 is unavailable to or insufficient to hold harmless an indemnified party
under subsection (a) or (b) above in respect of any losses, claims, damages or
liabilities (or actions or proceedings in respect thereof) referred to therein,
then each indemnifying party shall contribute to the amount paid or payable by
such indemnified party as a result of such losses, claims, damages or
liabilities (or actions in respect thereof) in such proportion as is appropriate
to reflect the relative fault of the Company on the one hand and the Investor,
as well as any other Selling Shareholders under such registration statement on
the other in connection with the statements or omissions or other matters which
resulted in such losses, claims, damages or liabilities (or actions in respect
thereof), as well as any other relevant equitable considerations. The relative
fault shall be determined by reference to, among other things, in the case of an
untrue statement, whether the untrue statement relates to information supplied
by the Company on the one hand or an Investor or other Selling Shareholder on
the other and the parties' relative intent, knowledge, access to information and
opportunity to correct or prevent such untrue statement. The Company and the
Investor agree that it would not be just and equitable if contribution pursuant
to this subsection (d) were determined by pro rata allocation (even if the
Investor and other Selling Shareholders were treated as one entity for such
purpose) or by any other method of allocation which does not take into account
the equitable considerations referred to above in this subsection (d). The
amount paid or payable by an indemnified party as a result of the losses,
claims, damages or liabilities (or actions in respect thereof) referred to above
in this subsection (d) shall be deemed to include any legal or other expenses
reasonably incurred by such indemnified party in connection with investigating
or defending any such action or claim. Notwithstanding the provisions of this
subsection (d), the Investor shall not be required to contribute any amount in
excess of the amount by which the net amount received by the Investor from the
sale of the Shares to which such loss relates exceeds the amount of any damages
which such Investor has otherwise been required to pay by reason of such untrue
statement. No person guilty of fraudulent misrepresentation (within the meaning
of Section 11(f) of the Securities Act) shall be entitled to contribution from
any person who was not guilty of such fraudulent misrepresentation. The
Investor's obligations in this subsection to contribute shall be in proportion
to its Investor sale of Shares to which such loss relates and shall not be joint
with any other Selling Shareholders.

                       (e) The parties to this Agreement hereby acknowledge that
they are sophisticated business persons who were represented by counsel during
the negotiations regarding the provisions hereof including, without limitation,
the provisions of this Section 7.3, and are fully informed regarding said
provisions. They further acknowledge that the provisions of this Section 7.3
fairly allocate the risks in light of the ability of the parties to investigate
the Company and its business in order to assure that adequate disclosure is made
in the Registration Statement as required by the Act and the Exchange Act. The
parties are advised that federal or state public policy as interpreted by the
courts in certain jurisdictions may be contrary to certain of the provisions of
this Section 7.3, and the parties hereto hereby expressly waive and relinquish
any right or ability to assert such public policy as a defense to a claim under
this Section 7.3 and further agree not to attempt to assert any such defense.

               7.4 Termination of Conditions and Obligations. The conditions
precedent imposed by Section 5 or this Section 7 upon the transferability of the
Shares shall cease and terminate as to any particular number of the Shares when
such Shares shall have been effectively registered under the Securities Act and
sold or otherwise disposed of in accordance with the intended method of
disposition set forth in the Registration Statement covering such Shares or at
such time as an opinion of counsel satisfactory to the Company shall have been
rendered to the effect that such conditions are not necessary in order to comply
with the Securities Act.

               7.5 Information Available. So long as the Registration Statement
is effective covering the resale of Shares owned by the Investor, the Company
will furnish to the Investor:

                       (a) as soon as practicable after it is available, one
copy of (i) its Annual Report to Stockholders (which Annual Report shall contain
financial statements audited in accordance with generally accepted accounting
principles by a national firm of certified public accountants), (ii) its Annual
Report on Form 10-K and (iii) its Quarterly Reports on Form 10-Q (the foregoing,
in each case, excluding exhibits);



<PAGE>   11
                       (b) upon the request of the Investor, all exhibits
excluded by the parenthetical to subparagraph (a) of this Section 7.5 as filed
with the SEC and all other information that is made available to shareholders;
and

                       (c) upon the reasonable request of the Investor, an
adequate number of copies of the Prospectuses to supply to any other party
requiring such Prospectuses in order for the Investor to effect sales
thereunder; and the Company, upon the reasonable request of the Investor, will
meet with the Investor or a representative thereof at the Company's headquarters
to discuss all information relevant for disclosure in the Registration Statement
covering the Shares and will otherwise cooperate with any Investor conducting an
investigation for the purpose of reducing or eliminating such Investor's
exposure to liability under the Securities Act, including the reasonable
production of information at the Company's headquarters; provided, that the
Company shall not be required to disclose any confidential information to or
meet at its headquarters with any Investor until and unless the Investor shall
have entered into a confidentiality agreement in form and substance reasonably
satisfactory to the Company with the Company with respect thereto.

        8. Notices. All notices, requests, consents and other communications
hereunder shall be in writing, shall be mailed (A) if within domestic United
States by first-class registered or certified airmail, or nationally recognized
overnight express courier, postage prepaid, or by facsimile, or (B) if delivered
from outside the United States, by International Federal Express or facsimile,
and shall be deemed given (i) if delivered by first-class registered or
certified mail domestic, three business days after so mailed, (ii) if delivered
by nationally recognized overnight carrier, one business day after so mailed,
(iii) if delivered by International Federal Express, two business days after so
mailed, (iv) if delivered by facsimile, upon electronic confirmation of receipt
and shall be delivered as addressed as follows:

               (a)     if to the Company, to:

                             Axys Pharmaceuticals, Inc.
                             180 Kimball Way
                             South San Francisco, CA 94080
                             Attn:  William J. Newell
                             Fax:  (650) 829-1067

               (b)     with a copy to:

                             Cooley Godward LLP
                             5 Palo Alto Square
                             Palo Alto, CA 94306
                             Attn:  Alan C. Mendelson
                             Fax:  (650) 857-0663


               (c)    if to the Investor, at its address on the signature page
                      hereto, or at such other address or addresses as may have
                      been furnished to the Company in writing.

        9. Changes. This Agreement may not be modified or amended except
pursuant to an instrument in writing signed by the Company and the Investor.

        10. Headings. The headings of the various sections of this Agreement
have been inserted for convenience of reference only and shall not be deemed to
be part of this Agreement.

        11. Severability. In case any provision contained in this Agreement
should be invalid, illegal or unenforceable in any respect, the validity,
legality and enforceability of the remaining provisions contained herein shall
not in any way be affected or impaired thereby.

        12. Governing Law. This Agreement shall be governed by, and construed in
accordance with, the internal laws of the State of Delaware, without giving
effect to the principles of conflicts of law.

<PAGE>   12
        13. Counterparts. This Agreement may be executed in two or more
counterparts, each of which shall constitute an original, but all of which, when
taken together, shall constitute but one instrument, and shall become effective
when one or more counterparts have been signed by each party hereto and
delivered to the other parties.

        14. Rule 144. The Company covenants that it will file the reports
required to be filed by it under the Securities Act and the Exchange Act and the
rules and regulations adopted by the SEC thereunder (or, if the Company is not
required to file such reports, it will, upon the request of any Investor holding
Shares purchased hereunder made after the first anniversary of the Closing Date,
make publicly available such information as necessary to permit sales pursuant
to Rule 144 under the Securities Act), and it will take such further action as
any such Investor may reasonably request, all to the extent required from time
to time to enable such Investor to sell Shares purchased hereunder without
registration under the Securities Act within the limitation of the exemptions
provided by (a) Rule 144 under the Securities Act, as such Rule may be amended
from time to time, or (b) any similar rule or regulation hereafter adopted by
the SEC. Upon the request of the Investor, the Company will deliver to such
holder a written statement as to whether it has complied with such information
and requirements.

<PAGE>   1
                                                                    EXHIBIT 23.1

               CONSENT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS


We consent to the reference to our firm under the caption "Experts" in the
Registration Statement (Form S-3) and related prospectus of Axys
Pharmaceuticals, Inc. for the registration of 3,497,778 shares of its common
stock and to the incorporation by reference therein of our report dated February
18, 2000, with respect to the consolidated financial statements of Axys
Pharmaceuticals, Inc. included in its Annual Report (Form 10-K) for the year
ended December 31, 1999, filed with the Securities and Exchange Commission.



                                                 Ernst & Young LLP

March 7, 2000
Palo Alto, California



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