LIGAND PHARMACEUTICALS INC
S-3, 2001-01-19
PHARMACEUTICAL PREPARATIONS
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    AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON JANUARY 19, 2001
                   REGISTRATION STATEMENT NO. 333-___________

================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                      ------------------------------------
                                    FORM S-3
                             REGISTRATION STATEMENT
                        UNDER THE SECURITIES ACT OF 1933
                      ------------------------------------

                       LIGAND PHARMACEUTICALS INCORPORATED
             (Exact Name of Registrant as Specified in its Charter)

         DELAWARE                                       77-0160744
(State or Other Jurisdiction             (I.R.S. Employer Identification Number)
of Incorporation or Organization)

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

          10275 Science Center Drive, San Diego, California 92121-1117
                                 (858) 550-7500
    (Address, Including Zip Code, and Telephone Number, Including Area Code,
                  of Registrant's Principal Executive Offices)

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

                                David E. Robinson
                      President and Chief Executive Officer
                       LIGAND PHARMACEUTICALS INCORPORATED

   10275 Science Center Drive, San Diego, California 92121-1117 (858) 550-7500
            (Name, Address, Including Zip Code, and Telephone Number,
                   Including Area Code, of Agent for Service)

                      ------------------------------------
                                   Copies to:
                              Faye H. Russell, Esq.
                               Carey J. Fox, Esq.
                         BROBECK, PHLEGER & HARRISON LLP
                              12390 El Camino Real
                           San Diego, California 92130
                                 (858) 720-2500

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

     Approximate date of commencement of proposed sale to the public: From time
to time 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, 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
<TABLE>
==========================================================================================================
         <S>                     <C>                 <C>                      <C>              <C>
                                                PROPOSED MAXIMUM      PROPOSED MAXIMUM
    TITLE OF SHARES          AMOUNT TO BE      AGGREGATE OFFERING    AGGREGATE OFFERING      AMOUNT OF
   TO BE REGISTERED         REGISTERED (1)     PRICE PER SHARE (2)        PRICE(2)        REGISTRATION FEE
-------------------------- --------------- ----------------------  --------------------- -----------------
Common Stock, par value       2,000,000           $12.16405            $24,328,100.00           $6,082.03
$.001 per share
========================== =============== ======================  ===================== =================
</TABLE>

(1)  This registration statement shall also cover any additional shares of
     common stock which become issuable in connection with the shares registered
     for sale hereby as a result of any stock dividend, stock split,
     recapitalization or other similar transaction effected without the receipt
     of consideration which results in an increase in the number of the
     Registrant's outstanding shares of common stock.

(2)  Estimated solely for the purpose of determining the registration fee and
     computed pursuant to Rule 457(c) based on the average of the high and low
     sales prices per share of the common stock on January 12, 2001 as reported
     on The Nasdaq Stock Market.

     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, AS AMENDED, OR UNTIL THE REGISTRATION STATEMENT
SHALL BECOME EFFECTIVE ON SUCH DATE AS THE SEC, ACTING PURSUANT TO SAID SECTION
8(A), MAY DETERMINE.

================================================================================
<PAGE>

                  SUBJECT TO COMPLETION, DATED JANUARY 19, 2001


                             PRELIMINARY PROSPECTUS


     The information in this preliminary 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 preliminary
prospectus is not an offer to sell our common stock and it is not soliciting an
offer to buy our common stock in any state where the offer or sale is not
permitted.


                       LIGAND PHARMACEUTICALS INCORPORATED

                        2,000,000 SHARES OF COMMON STOCK


     This prospectus relates to the public offering, which is not being
underwritten, of 2,000,000 shares of our common stock, which is held by some of
our current stockholders. These stockholders acquired the shares directly from
us in a private placement completed on January 10, 2001.

     Our common stock is traded on The Nasdaq Stock Market under the symbol
"LGND." On January 18, 2001, the average of the high and low sales prices for
our common stock was $13.0625.

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

     THE COMMON STOCK OFFERED INVOLVES A HIGH DEGREE OF RISK. SEE "RISK FACTORS"
COMMENCING ON PAGE [4] FOR A DISCUSSION OF SOME IMPORTANT RISKS YOU SHOULD
CONSIDER BEFORE BUYING ANY OF OUR COMMON STOCK.

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

     NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED THESE SECURITIES, OR PASSED UPON THE
ACCURACY OR ADEQUACY OF THIS PROSPECTUS. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.

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


                 The date of this prospectus is January 19, 2001

<PAGE>


                                TABLE OF CONTENTS

                                                                     PAGE
<TABLE>
<S>                                                                   <C>
LIGAND PHARMACEUTICALS INCORPORATED....................................1

RISK FACTORS...........................................................4

FORWARD-LOOKING STATEMENTS............................................12

WHERE YOU CAN FIND MORE INFORMATION...................................12

INFORMATION INCORPORATED BY REFERENCE.................................13

USE OF PROCEEDS.......................................................14

PLAN OF DISTRIBUTION..................................................14

SELLING STOCKHOLDERS..................................................16

LEGAL MATTERS.........................................................17

EXPERTS...............................................................17
</TABLE>



Our trademarks, trade names and service marks referenced in this document
include ONTAK(R), Panretin(R) and Targretin(R). Each other trademark, trade name
or service mark appearing in this document belongs to its holder.

Reference to Ligand Pharmaceuticals Incorporated, "Ligand", the "Company", "we"
or "our" include Ligand's wholly owned subsidiaries, Glycomed Incorporated,
Ligand Pharmaceuticals (Canada) Incorporated, Ligand Pharmaceuticals
International, Inc., and Seragen, Inc.

                                       i

<PAGE>

                       LIGAND PHARMACEUTICALS INCORPORATED

     We are a pharmaceutical company that discovers, develops and markets new
drugs that address critical unmet medical needs of patients. We have a diverse
product portfolio that includes four FDA approved drugs. Our pipeline includes
several product candidates in late stage development that address large market
indications, including non-small cell lung cancer, osteoporosis, cardiovascular
disease and diabetes. Our commercialization strategy includes developing
products internally, as well as establishing research and development
collaborations with global pharmaceutical companies using our proprietary
technology based on our leadership position in gene transcription technology.

     We have initially focused our approved products on niche oncology
indications, which we believe has allowed us to bring these products to market
relatively quickly. Revenues for these products totaled $16.2 million for the
nine months ended September 30, 2000. We are seeking to expand the markets for
these products by seeking additional indication approvals, approvals in
international markets and marketing and distribution agreements in select
international markets. Through our collaborative research and development
business with major pharmaceutical companies, we plan to develop and market
products with large market potential.

OUR PRODUCTS

     We currently market four oncology products in the United States. Panretin
gel, ONTAK and Targretin capsules were approved for marketing in 1999 and
Targretin gel was approved in 2000. In Europe, the European Commission granted
Marketing Authorization for Panretin gel in October 2000, and the Committee for
Proprietary Medicinal Products adopted a positive opinion recommending the grant
of Marketing Authorization for Targretin capsules in November 2000. Our current
marketed products, the diseases or conditions they address and additional
indications in development are shown below:

<TABLE>
<CAPTION>
------------------------- ------------- --------------- -------------------------- ------------------------------------
MARKETED
PRODUCTS                  INDICATION    U.S. STATUS     EUROPEAN STATUS            INDICATIONS IN DEVELOPMENT
------------------------- ------------- --------------- -------------------------- ------------------------------------
<S>                       <C>           <C>             <C>                        <C>
ONTAK                     Cutaneous     Marketed        Marketing Authorization    Non-Hodgkin's lymphoma,
                          T-cell                        Application (Europe) to    rheumatoid arthritis, and psoriasis
                          lymphoma                      be filed

Panretin gel              Kaposi's      Marketed        Approved                   Other skin diseases
                          sarcoma

Targretin capsules        Cutaneous     Marketed        Committee for Proprietary  Non-small cell lung cancer,
                          T-cell                        Medicinal Products         psoriasis, advanced breast
                          lymphoma                      recommendation received    cancer, and other cancers

Targretin gel             Cutaneous     Marketed        Marketing Authorization    Atopic dermatitis and psoriasis
                          T-cell                        Application (Europe) to
                          lymphoma                      be filed
------------------------- ------------- --------------- -------------------------- ------------------------------------
</TABLE>

In addition to our current products and collaborative product candidates, a new
application for market approval has been filed in the U.S. for Morphelan, a drug
for chronic pain that we license from Elan Corporation, plc.


OUR COLLABORATIVE PRODUCT CANDIDATES

     We have established research and development collaborations with numerous
global pharmaceutical companies, including: Bristol-Myers Squibb Company,
Organon Company, Warner-Lambert Company, Eli Lilly and Company, SmithKline
Beecham Corporation, American Home Products, Abbott Laboratories, Sankyo Company
Ltd., Glaxo-Wellcome plc, Allergan, Inc., and Pfizer Inc. Our corporate partner
products are being studied for the treatment of large market indications such as
osteoporosis, breast cancer, diabetes, cardiovascular

<PAGE>

disease, hormone replacement therapy and contraception. Selected product
candidates in our collaboration pipeline include the following:

<TABLE>
<CAPTION>
--------------------------- ---------------------- ------------------------------------- ------------------------
COLLABORATOR                PRODUCT CANDIDATE      INDICATION                            STAGE OF DEVELOPMENT
--------------------------- ---------------------- ------------------------------------- ------------------------
<S>                         <C>                    <C>                                   <C>

Pfizer                      Lasofoxifene           Osteoporosis                          Phase III

American Home Prod.         TSE 424                Osteoporosis                          Phase II/III
                            ERA 923                Breast Cancer                         Phase II
                            WAY 910/BU             Contraception                         IND Track

Glaxo                       GW 544                 Diabetes / Cardiovascular Disease     Phase I/II
                            GW 516                 Cardiovascular Disease                Phase I

Lilly                       LY 929                 Diabetes                              IND Track
                            LY YYY                 Cardiovascular Disease                Pre-clinical

Allergan                    AGN 4310               Psoriasis / Toxicity Modulator RA     Phase II
--------------------------- ---------------------- ------------------------------------- ------------------------
</TABLE>

OUR STRATEGY

     Our goal is to become a profitable pharmaceutical research, development and
marketing company. Building initially on our proprietary Intracellular Receptor
or IR, and Signal Transducer and Activator of Transcription or, STATs,
technologies, our strategy is to generate revenues primarily from:

o    the sale in the U.S. and Europe of specialty oncology and dermatology
     products developed, acquired or in-licensed by us; and

o    research, milestone and royalty revenues from the development and sale of
     products by our collaboration partners.

OUR ONCOLOGY FRANCHISE

     Our oncology strategy is to develop specialty cancer products and to market
these products initially with a specialized sales force in the U.S. and directly
or through marketing partners in selected international markets. We believe
focusing initially on niche oncology drugs that have the possibility of
expedited regulatory approval has allowed us to bring products to market
quickly. This strategy also allows us to market these products with a targeted
specialty oncology sales force, spreading the cost of our sales and marketing
infrastructure among multiple products. Our goal is to expand the markets for
our products through additional indication approvals, approvals in international
markets and marketing and distribution agreements in select international
markets where we will not market directly. To further derive value from our
specialty sales force, we intend to selectively license-in or acquire additional
complementary technology and product candidates in advanced stages of
development.

OUR COLLABORATION STRATEGY

     Our strategy in collaborative research and development is to share the
risks and benefits of discovering and developing drugs to treat diseases that
are beyond our strategic focus or resources. These diseases typically affect
large populations often treated by primary care physicians, and require
therapeutic treatments that may be costly to develop and/or to market
effectively. Despite these factors, drugs approved for these indications may
have large market potential.

     Since our inception, we have entered into 12 significant collaborations
with major pharmaceutical companies focusing on a broad range of disease
targets. In 2000, our corporate partners advanced three compounds into human
development track and an additional compound entered Phase III trials.

                                       2

<PAGE>

OUR INTELLECTUAL PROPERTY PORTFOLIO

     To date, we have filed or participated as a licensee in the filing of
approximately 108 currently pending patent applications in the United States
relating to our technology, as well as foreign counterparts of certain of these
applications in many countries. In addition, we own or are the exclusive
licensee to rights covered by approximately 190 patents issued, granted or
allowed worldwide. Subject to compliance with the terms of the respective
agreements, our rights under our licenses with our exclusive licensors extend
the life of the patents covering such developments.

HUMAN RESOURCES

     As of December 31, 2000, we had 384 full-time employees, of whom 219 were
involved directly in scientific research and development activities. Of these,
approximately 64 hold Ph.D. or M.D. degrees.

     Our executive offices are located at 10275 Science Center Drive, San Diego,
California 92121-1117, and our telephone number is (858) 550-7500.

                                       3

<PAGE>

                                  RISK FACTORS


     IN ADDITION TO THE OTHER INFORMATION IN THIS PROSPECTUS, YOU SHOULD
CAREFULLY CONSIDER THE FOLLOWING RISKS AND UNCERTAINTIES BEFORE PURCHASING
SHARES OF OUR COMMON STOCK. EACH OF THESE RISK AND UNCERTAINTIES COULD ADVERSELY
AFFECT OUR BUSINESS, OPERATING RESULTS AND FINANCIAL CONDITION, AS WELL AS
ADVERSELY AFFECTING THE VALUE OF AN INVESTMENT IN OUR COMMON STOCK


RISKS RELATED TO OUR BUSINESS


OUR PRODUCT DEVELOPMENT AND COMMERCIALIZATION INVOLVES A NUMBER OF UNCERTAINTIES
AND WE MAY NEVER GENERATE SUFFICIENT REVENUES FROM THE SALE OF PRODUCTS TO
BECOME PROFITABLE.


     We were founded in 1987. We have incurred significant losses since our
inception. At September 30, 2000, our accumulated deficit was $516.7 million. To
date, we have received the majority of our revenues from our collaborative
arrangements and only began receiving revenues from the sale of pharmaceutical
products in 1999. To become profitable, we must successfully develop, clinically
test, market and sell our products. Even if we achieve profitability, we cannot
predict the level of that profitability or whether we will be able to sustain
profitability. We expect that our operating results will fluctuate from period
to period as a result of differences in when we incur expenses and receive
revenues from product sales, collaborative arrangements and other sources. Some
of these fluctuations may be significant.

     Most of our products in development will require extensive additional
development, including preclinical testing and human studies, as well as
regulatory approvals, before we can market them. We do not expect that any
products resulting from our product development efforts or the efforts of our
collaborative partners, other than those for which marketing approval has
already been received, will be available for sale until the second half of the
2001 calendar year at the earliest, if at all. There are many reasons that we or
our collaborative partners may fail in our efforts to develop our other
potential products, including the possibility that:

o    preclinical testing or human studies may show that our potential products
     are ineffective or cause harmful side effects,

o    the products may fail to receive necessary regulatory approvals from the
     FDA or foreign authorities in a timely manner or at all,

o    the products, if approved, may not be produced in commercial quantities or
     at reasonable costs,

o    the products once approved, may not achieve commercial acceptance, or

o    the proprietary rights of other parties may prevent us or our partners from
     marketing the products.

WE ARE BUILDING MARKETING AND SALES FORCES IN THE UNITED STATES AND EUROPE WHICH
IS AN EXPENSIVE AND TIME-CONSUMING PROCESS.

     Developing the sales force to market and sell products is a difficult,
expensive and time-consuming process. We have developed a 40 person U.S. sales
force and rely on another company to distribute our products. The distributor is
responsible for providing many marketing support services, including customer
service, order entry, shipping and billing, and customer reimbursement
assistance. In Europe, we will rely initially on other companies to distribute
and market our products. In 1999, we entered into agreements for the marketing
and distribution of our products in Spain, Portugal, Greece, Italy, and Central
and South America and we established a subsidiary, Ligand Pharmaceuticals
International, Inc., with a branch in London, England, to prepare for our
European marketing and operations. We may not be able to continue to establish
and maintain the sales and marketing capabilities necessary to successfully
commercialize our products in the territories where they receive

                                       4

<PAGE>

marketing approval. To the extent we enter into co-promotion or other
licensing arrangements, any revenues we receive will depend on the marketing
efforts of others, which may or may not be successful.

SOME OF OUR KEY TECHNOLOGIES HAVE NOT BEEN USED TO PRODUCE MARKETED PRODUCTS AND
MAY NOT BE CAPABLE OF PRODUCING SUCH PRODUCTS.

     To date, we have dedicated most of our resources to the research and
development of potential drugs based upon our expertise in our IR and STATs
technologies. Even though there are marketed drugs that act through IRs, some
aspects of our IR technologies have not been used to produce marketed products.
In addition, we are not aware of any drugs that have been developed and
successfully commercialized that interact directly with STATs. Much remains to
be learned about the location and function of IRs and STATs. If we are unable to
apply our IR and STAT technologies to the development of our potential products,
we will not be successful in developing new products.

OUR DRUG DEVELOPMENT PROGRAMS WILL REQUIRE SUBSTANTIAL ADDITIONAL FUTURE
CAPITAL.

     Our drug development programs require substantial additional capital to
successfully complete them, arising from costs to:

o    conduct research, preclinical testing and human studies,

o    establish pilot scale and commercial scale manufacturing processes and
     facilities, and

o    establish and develop quality control, regulatory, marketing, sales and
     administrative capabilities to support these programs.


     Our future operating and capital needs will depend on many factors,
including:

o    the pace of scientific progress in our research and development programs
     and the magnitude of these programs,

o    the scope and results of preclinical testing and human studies,

o    the time and costs involved in obtaining regulatory approvals,

o    the time and costs involved in preparing, filing, prosecuting, maintaining
     and enforcing patent claims,

o    competing technological and market developments,

o    our ability to establish additional collaborations,

o    changes in our existing collaborations,

o    the cost of manufacturing scale-up, and

o    the effectiveness of our commercialization activities.


     For example, we are required under the terms of our agreement with Elan to
spend not less than $7 million through May 2003 to undertake additional clinical
activities related to the commercialization of Morphelan. In the

                                       5

<PAGE>

event we do not spend this amount, any shortfall would have to be paid to
Elan. If additional funds are required to support our operations and we are
unable to obtain them on terms favorable to us, we may be required to cease or
reduce further commercialization of our products, to sell some or all of our
technology or assets or to merge with another entity.

OUR PRODUCTS MUST CLEAR SIGNIFICANT REGULATORY HURDLES PRIOR TO MARKETING.

     Before we obtain the approvals necessary to sell any of our potential
products, we must show through preclinical studies and human testing that each
product is safe and effective. Our failure to show any product's safety and
effectiveness would delay or prevent regulatory approval of the product and
could adversely affect our business. The clinical trials process is complex and
uncertain. The results of preclinical studies and initial clinical trials may
not necessarily predict the results from later large-scale clinical trials. In
addition, clinical trials may not demonstrate a product's safety and
effectiveness to the satisfaction of the regulatory authorities. A number of
companies have suffered significant setbacks in advanced clinical trials or in
seeking regulatory approvals, despite promising results in earlier trials. The
FDA may also require additional clinical trials after regulatory approvals are
received, which could be expensive and time-consuming, and failure to
successfully conduct those trials could jeopardize continued commercialization.

     The rate at which we complete our clinical trials depends on many factors,
including our ability to obtain adequate supplies of the products to be tested
and patient enrollment. Patient enrollment is a function of many factors,
including the size of the patient population, the proximity of patients to
clinical sites and the eligibility criteria for the trial. Delays in patient
enrollment may result in increased costs and longer development times. In
addition, our collaborative partners have rights to control product development
and clinical programs for products developed under the collaborations. As a
result, these collaborators may conduct these programs more slowly or in a
different manner than we had expected. Even if clinical trials are completed, we
or our collaborative partners still may not apply for FDA approval in a timely
manner or the FDA still may not grant approval.

WE MAY NOT BE ABLE TO PAY AMOUNTS DUE ON OUR OUTSTANDING INDEBTEDNESS WHEN DUE
WHICH WOULD CAUSE DEFAULTS UNDER THESE ARRANGEMENTS.

     We and our subsidiaries may not have sufficient funds to make required
payments due under existing debt. If we or our subsidiaries do not have adequate
funds, we will be forced to refinance the existing debt and may not be
successful in doing so. Our subsidiary, Glycomed, is obligated to make payments
under convertible subordinated debentures in the total principal amount of $50
million. The debentures incur interest semi-annually at a rate of 7 1/2% per
annum, are due in 2003 and convertible into our common stock at $26.52 per
share. In addition, at September 30, 2000, we had outstanding a $2.5 million
convertible note to SmithKline Beecham Corporation due in 2002 with interest at
prime and convertible into our common stock at $13.56 per share. At September
30, 2000, we also had outstanding $68.4 million in zero coupon convertible
senior notes to Elan, due 2008 with an 8% per annum yield to maturity and
convertible into our common stock at $14 per share. On December 29, 2000, we
issued $10 million of zero coupon convertible notes to Elan due 2008, accruing
interest at 8% per annum, compounding semi-annually, convertible at $14.16 per
share and callable at accreted value beginning in November 2001. Glycomed's
failure to make payments when due under its debentures would cause us to default
under the outstanding notes to Elan.

WE MAY REQUIRE ADDITIONAL MONEY TO RUN OUR BUSINESS AND MAY BE REQUIRED TO RAISE
THIS MONEY ON TERMS WHICH ARE NOT FAVORABLE TO OUR EXISTING STOCKHOLDERS.

     We have incurred losses since our inception and do not expect to generate
positive cash flow to fund our operations for one or more years. As a result, we
may need to complete additional equity or debt financings to fund our
operations. Our inability to obtain additional financing could adversely affect
our business. Financings may not be available on acceptable terms. In addition,
these financings, if completed, still may not meet our capital needs and could
result in substantial dilution to our stockholders. For instance, the zero
coupon convertible senior notes

                                       6
<PAGE>

outstanding to Elan are convertible into common stock at the option of
Elan, subject to some limitations. If adequate funds are not available, we may
be required to delay, reduce the scope of or eliminate one or more of our drug
development programs. Alternatively, we may be forced to attempt to continue
development by entering into arrangements with collaborative partners or others
that require us to relinquish some or all of our rights to technologies or drug
candidates that we would not otherwise relinquish.

WE FACE SUBSTANTIAL COMPETITION.

     Some of the drugs that we are developing and marketing will compete with
existing treatments. In addition, several companies are developing new drugs
that target the same diseases that we are targeting and are taking IR-related
and STAT-related approaches to drug development. Many of our existing or
potential competitors, particularly large drug companies, have greater
financial, technical and human resources than us and may be better equipped to
develop, manufacture and market products. Many of these companies also have
extensive experience in preclinical testing and human clinical trials, obtaining
FDA and other regulatory approvals and manufacturing and marketing
pharmaceutical products. In addition, academic institutions, governmental
agencies and other public and private research organizations are developing
products that may compete with the products we are developing. These
institutions are becoming more aware of the commercial value of their findings
and are seeking patent protection and licensing arrangements to collect payments
for the use of their technologies. These institutions also may market
competitive products on their own or through joint ventures and will compete
with us in recruiting highly qualified scientific personnel.

OUR SUCCESS WILL DEPEND ON THIRD-PARTY REIMBURSEMENT AND MAY BE IMPACTED BY
HEALTH CARE REFORM.

     Sales of prescription drugs depend significantly on the availability of
reimbursement to the consumer from third party payors, such as government and
private insurance plans. These third party payors frequently require drug
companies to provide predetermined discounts from list prices, and they are
increasingly challenging the prices charged for medical products and services.
Our current and potential products may not be considered cost-effective and
reimbursement to the consumer may not be available or sufficient to allow us to
sell our products on a competitive basis.

     In addition, the efforts of governments and third party payors to contain
or reduce the cost of health care will continue to affect the business and
financial condition of drug companies such as us. A number of legislative and
regulatory proposals to change the health care system have been discussed in
recent years. In addition, an increasing emphasis on managed care in the United
States has and will continue to increase pressure on drug pricing. We cannot
predict whether legislative or regulatory proposals will be adopted or what
effect those proposals or managed care efforts may have on our business. The
announcement and/or adoption of such proposals or efforts could adversely affect
our profit margins and business.

WE RELY HEAVILY ON COLLABORATIVE RELATIONSHIPS AND TERMINATION OF ANY OF THESE
PROGRAMS COULD REDUCE THE FINANCIAL RESOURCES AVAILABLE TO US.

     Our strategy for developing and commercializing many of our potential
products includes entering into collaborations with corporate partners,
licensors, licensees and others. To date, we have entered into collaborations
with Bristol-Myers Squibb Company, Organon Company, Warner-Lambert Company, Eli
Lilly and Company, SmithKline Beecham Corporation, American Home Products,
Abbott Laboratories, Sankyo Company Ltd., Glaxo-Wellcome plc, Allergan, Inc.,
and Pfizer Inc. These collaborations provide us with funding and research and
development resources for potential products for the treatment or control of
metabolic diseases, hematopoiesis, women's health disorders, inflammation,
cardiovascular disease, cancer and skin disease, and osteoporosis. These
agreements also give our collaborative partners significant discretion when
deciding whether or not to pursue any development program. Our collaborations
may not continue or be successful.

                                       7
<PAGE>

     In addition, our collaborators may develop drugs, either alone or with
others, that compete with the types of drugs they currently are developing with
us. This would result in less support and increased competition for our
programs. If products are approved for marketing under our collaborative
programs, any revenues we receive will depend on the manufacturing, marketing
and sales efforts of our collaborators, who generally retain commercialization
rights under the collaborative agreements. Our current collaborators also
generally have the right to terminate their collaborations under specified
circumstances. If any of our collaborative partners breach or terminate their
agreements with us or otherwise fail to conduct their collaborative activities
successfully, our product development under these agreements will be delayed or
terminated.

     We may have disputes in the future with our collaborators, including
disputes concerning which of us owns the rights to any technology developed. For
instance, we were involved in litigation with Pfizer, which we settled in April
1996, concerning our right to milestones and royalties based on the development
and commercialization of droloxifene. These and other possible disagreements
between us and our collaborators could delay our ability and the ability of our
collaborators to achieve milestones or our receipt of other payments. In
addition, any disagreements could delay, interrupt or terminate the
collaborative research, development and commercialization of certain potential
products, or could result in litigation or arbitration. The occurrence of any of
these problems could be time-consuming and expensive and could adversely affect
our business.

OUR SUCCESS DEPENDS ON OUR ABILITY TO OBTAIN AND MAINTAIN OUR PATENTS AND OTHER
PROPRIETARY RIGHTS.

     Our success will depend on our ability and the ability of our licensors to
obtain and maintain patents and proprietary rights for our potential products
and to avoid infringing the proprietary rights of others, both in the United
States and in foreign countries. Patents may not be issued from any of these
applications currently on file or, if issued, may not provide sufficient
protection. In addition, disputes with licensors under our license agreements
may arise which could result in additional financial liability or loss of
important technology and potential products.

     Our patent position, like that of many pharmaceutical companies, is
uncertain and involves complex legal and technical questions for which important
legal principles are unresolved. We may not develop or obtain rights to products
or processes that are patentable. Even if we do obtain patents, they may not
adequately protect the technology we own or have licensed. In addition, others
may challenge, seek to invalidate, infringe or circumvent any patents we own or
license, and rights we receive under those patents may not provide competitive
advantages to us. Further, the manufacture, use or sale of our products may
infringe the patent rights of others.

     Several drug companies and research and academic institutions have
developed technologies, filed patent applications or received patents for
technologies that may be related to our business. Others have filed patent
applications and received patents that conflict with patents or patent
applications we have licensed for our use, either by claiming the same methods
or compounds or by claiming methods or compounds that could dominate those
licensed to us. In addition, we may not be aware of all patents or patent
applications that may impact our ability to make, use or sell any of our
potential products. For example, United States patent applications may be kept
confidential while pending in the Patent and Trademark Office, and patent
applications filed in foreign countries are often first published six months or
more after filing. Any conflicts resulting from the patent rights of others
could significantly reduce the coverage of our patents and limit our ability to
obtain meaningful patent protection. If other companies obtain patents with
conflicting claims, we may be required to obtain licenses to those patents or to
develop or obtain alternative technology. We may not be able to obtain any such
license on acceptable terms or at all. Any failure to obtain such licenses could
delay or prevent us from pursuing the development or commercialization of our
potential products.

     We have had and will continue to have discussions with our current and
potential collaborators regarding the scope and validity of our patent and other
proprietary rights. If a collaborator or other party successfully establishes
that our patent rights are invalid, we may not be able to continue our existing
collaborations beyond their expiration. Any determination that our patent rights
are invalid also could encourage our collaborators to terminate their agreements
where contractually permitted. Such a determination could also adversely affect
our ability to enter into new collaborations.

     We may also need to initiate litigation, which could be time-consuming and
expensive, to enforce our proprietary rights or to determine the scope and
validity of others' rights. If litigation results, a court may find our

                                       8
<PAGE>

patents or those of our licensors invalid or may find that we have infringed on
a competitor's rights. If any of our competitors have filed patent applications
in the United States which claim technology we also have invented, the Patent
and Trademark Office may require us to participate in expensive interference
proceedings to determine who has the right to a patent for the technology.

     We have learned that Hoffmann-La Roche Inc. has received a United States
patent and has made patent filings in foreign countries that relate to our
Panretin capsules and gel products. We filed a patent application with an
earlier filing date than Hoffmann-La Roche's patent, which we believe is broader
than, but overlaps in part with, Hoffmann-La Roche's patent. We currently are
investigating the scope and validity of Hoffmann-La Roche's patent to determine
its impact upon our products. The Patent and Trademark Office has informed us
that the overlapping claims are patentable to us and has initiated a proceeding
to determine whether we or Hoffmann-La Roche are entitled to a patent. We may
not receive a favorable outcome in the proceeding. In addition, the proceeding
may delay the Patent and Trademark Office's decision regarding our earlier
application. If we do not prevail, the Hoffmann-La Roche patent might block our
use of Panretin capsules and gel in specified cancers.

     We also rely on unpatented trade secrets and know-how to protect and
maintain our competitive position. We require our employees, consultants,
collaborators and others to sign confidentiality agreements when they begin
their relationship with us. These agreements may be breached and we may not have
adequate remedies for any breach. In addition, our competitors may independently
discover our trade secrets.

WE RELY ON THIRD-PARTY MANUFACTURERS TO SUPPLY OUR PRODUCTS AND THUS HAVE LITTLE
CONTROL OVER OUR MANUFACTURING RESOURCES.

     We currently have no manufacturing facilities and we rely on others for
clinical or commercial production of our marketed and potential products. To be
successful, we will need to manufacture our products, either directly or through
others, in commercial quantities, in compliance with regulatory requirements and
at acceptable cost. Any extended and unplanned manufacturing shutdowns could be
expensive and could result in inventory and product shortages. If we are unable
to develop our own facilities or contract with others for manufacturing
services, our revenues could be adversely affected. In addition, if we are
unable to supply products in development, our ability to conduct preclinical
testing and human clinical trials will be adversely affected. This in turn could
also delay our submission of products for regulatory approval and our initiation
of new development programs. In addition, although other companies have
manufactured drugs acting through IRs and STATs on a commercial scale, we may
not be able to do so at costs or in quantities to make marketable products.

     The manufacturing process also may be susceptible to contamination, which
could cause the affected manufacturing facility to close until the contamination
is identified and fixed. In addition, problems with equipment failure or
operator error also could cause delays in filling our customers' orders.

OUR BUSINESS EXPOSES US TO PRODUCT LIABILITY RISKS OR OUR PRODUCTS MAY NEED TO
BE RECALLED AND WE MAY NOT HAVE SUFFICIENT INSURANCE TO COVER ANY CLAIMS.

     Our business exposes us to potential product liability risks. Our products
also may need to be recalled to address regulatory issues. A successful product
liability claim or series of claims brought against us could result in payment
of significant amounts of money and divert management's attention from running
the business. Some of the compounds we are investigating may be harmful to
humans. For example, retinoids as a class are known to contain compounds which
can cause birth defects. We may not be able to maintain our insurance on
acceptable terms, or our insurance may not provide adequate protection in the
case of a product liability claim. To the extent that product liability
insurance, if available, does not cover potential claims, we will be required to
self-insure the risks associated with such claims.

                                       9

<PAGE>

WE ARE DEPENDENT ON OUR KEY EMPLOYEES, THE LOSS OF WHOSE SERVICES COULD
ADVERSELY AFFECT US.

     We depend on our key scientific and management staff, the loss of whose
services could adversely affect our business. Furthermore, we may need to hire
new scientific, management and operational personnel. Recruiting and retaining
qualified management, operations and scientific personnel is also critical to
our success. We may not be able to attract and retain such personnel on
acceptable terms given the competition among numerous drug companies,
universities and other research institutions for such personnel.

WE USE HAZARDOUS MATERIALS WHICH REQUIRES US TO INCUR SUBSTANTIAL COSTS TO
COMPLY WITH ENVIRONMENTAL REGULATIONS.

     In connection with our research and development activities, we handle
hazardous materials, chemicals and various radioactive compounds. To properly
dispose of these hazardous materials in compliance with environmental
regulations, we are required to contract with third parties at substantial cost
to us. We cannot completely eliminate the risk of accidental contamination or
injury from the handling and disposing of hazardous materials, whether by us or
by our third-party contractors. In the event of any accident, we could be held
liable for any damages that result, which could be significant.

OUR SHAREHOLDER RIGHTS PLAN AND CHARTER DOCUMENTS MAY PREVENT TRANSACTIONS THAT
COULD BE BENEFICIAL TO YOU.

     Our shareholder rights plan and provisions contained in our certificate of
incorporation and bylaws may discourage transactions involving an actual or
potential change in our ownership, including transactions in which you might
otherwise receive a premium for your shares over then-current market prices.
These provisions also may limit your ability to approve transactions that you
deem to be in your best interests. In addition, our board of directors may issue
shares of preferred stock without any further action by you. Such issuances may
have the effect of delaying or preventing a change in our ownership.

RISKS RELATING TO AN INVESTMENT IN OUR COMMON STOCK

THE MARKET PRICE OF OUR STOCK IS HIGHLY VOLATILE, AND, AS A RESULT, YOUR
INVESTMENT IN US COULD RAPIDLY LOSE ITS VALUE.

     The market prices and trading volumes for our securities, and the
securities of emerging companies like us, have historically been highly volatile
and have experienced significant fluctuations unrelated to operating
performance. Future announcements concerning us or our competitors may impact
the market price of our common stock. These announcements might include:

o    the results of research or development testing of ours or our competitors'
     products,

o    technological innovations related to diseases we are studying,

o    new commercial products introduced by our competitors,

o    government regulation of our industry,

o    receipt of regulatory approvals by competitors,

o    our failure to receive regulatory approvals for products under development,

o    developments concerning proprietary rights, or

                                       10
<PAGE>

o    litigation or public concern about the safety of our products.


YOU MAY NOT RECEIVE A RETURN ON YOUR SHARES OTHER THAN THROUGH THE SALE OF YOUR
SHARES OF COMMON STOCK

     We have not paid any cash dividends on our common stock to date. We intend
to retain any earnings to support the expansion of our business and we do not
anticipate paying cash dividends in the foreseeable future. Accordingly, other
than through a sale of your shares, you will not receive a return on your
investment in our common stock.

WE MAY INCUR SIGNIFICANT COSTS FROM CLASS ACTION LITIGATION DUE TO OUR EXPECTED
STOCK VOLATILITY

     As described above, our stock price is highly volatile. Recently, when the
market price of a stock has been volatile as our stock price has been, holders
of that stock have occasionally instituted securities class action litigation
against the company that issued the stock. If any of our stockholders were to
bring a lawsuit of this type against us, even if the lawsuit is without merit,
we could incur substantial costs defending the lawsuit. The lawsuit could also
divert the time and attention of our management.

FUTURE SALES OF OUR COMMON STOCK MAY DEPRESS OUR STOCK PRICE

     Future sales of substantial amounts of our common stock in the public
market could seriously harm prevailing market prices for our common stock. These
sales might make it difficult or impossible for us to sell additional securities
when we need to raise capital.

                                       11

<PAGE>


                           FORWARD-LOOKING STATEMENTS

     This prospectus includes "forward-looking statements" regarding future
events or our future performance within the meaning of Section 27A of the
Securities Act of 1933, as amended and Section 21E of the Securities Exchange
Act of 1934, as amended. All statements other than statements of historical
facts included in this prospectus or incorporated by reference regarding our
financial position and business strategy may constitute forward-looking
statements. Although we believe that the expectations reflected in these
forward-looking statements are reasonable, we can not guarantee that these
expectations will prove to be correct. Important factors that could cause actual
results to differ materially from our expectations are listed in this
prospectus, and they include the forward-looking statements under "Risk
Factors." All subsequent written and oral forward-looking statements
attributable to us or persons acting on our behalf are expressly qualified in
their entirety by these statements.


                       WHERE YOU CAN FIND MORE INFORMATION

     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 at 450 Fifth Street, N.W., Washington, D.C. 20549,
and also at the SEC's public reference rooms in New York, New York and Chicago,
Illinois. 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 on the
SEC's website at http://www.sec.gov.


                                       12

<PAGE>


                      INFORMATION INCORPORATED BY REFERENCE

     The SEC allows us to incorporate by reference the information 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, and later information filed with the SEC will
update and supersede this information. We incorporate by reference the documents
listed below and any future filings we make with the SEC under Section 13(a),
13(c), 14, or 15(d) of the Securities Exchange Act of 1934 until our offering is
completed:

o    Our annual report on Form 10-K for the fiscal year ended December 31, 1999,
     including specified information in our definitive proxy statement in
     connection with our 2000 annual meeting of stockholders.

o    Our quarterly reports on Form 10-Q for the quarterly periods ended March
     31, 2000, June 30, 2000 and September 30, 2000.

o    Our current reports on Form 8-K filed November 6, 2000, January 4, 2001 and
     January 8, 2001.

o    The description of our common stock, contained in our registration
     statement on Form 8-A filed on November 21, 1994, including any amendments
     or reports filed for the purpose of updating such descriptions.


     The reports and other documents that we file after the date of this
prospectus will update and supersede the information in this prospectus.

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

                   Ligand Pharmaceuticals Incorporated
                   Attn:  Investor Relations
                   10275 Science Center Road
                   San Diego, California 92121-1117
                   (858) 550-7500

     YOU SHOULD RELY ONLY ON THE INFORMATION PROVIDED OR INCORPORATED BY
REFERENCE IN THIS PROSPECTUS. WE HAVE NOT AUTHORIZED ANYONE TO PROVIDE YOU WITH
DIFFERENT INFORMATION. THE SELLING STOCKHOLDERS ARE NOT AUTHORIZED TO MAKE AN
OFFER OF THESE SECURITIES IN ANY STATE WHERE THE OFFER IS NOT PERMITTED. YOU
SHOULD NOT ASSUME THAT THE INFORMATION IN THIS PROSPECTUS IS ACCURATE AS OF ANY
DATE OTHER THAN THE DATE ON THE FRONT OF THE DOCUMENT.

                                       13

<PAGE>


                                 USE OF PROCEEDS

     We will not receive any of the proceeds from the sale of the shares of our
common stock by the selling stockholders.

                              PLAN OF DISTRIBUTION

     We are registering all 2,000,000 shares on behalf of the selling
stockholders. We issued all of the shares to the selling stockholders in a
private placement transaction. The selling stockholders named in the table below
or pledgees, donees, transferees or other successors-in-interest selling shares
received from a named selling stockholder as a gift, partnership distribution or
other non-sale related transfer after the date of this prospectus 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 The Nasdaq Stock Market 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 negotiated transactions. The selling
stockholders may effect these transactions by selling the shares to or through
broker-dealers. The shares may be sold by one or more of, or a combination of,
the following:

o    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,

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

o    an exchange distribution in accordance with the rules of the respective
     exchange,

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

o    in 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. In effecting sales,
broker-dealers engaged by the selling stockholders may arrange for other
broker-dealers to participate in the resales.

     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 such 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 such shares covered by this prospectus. The selling stockholders also
may loan or pledge the shares to a broker-dealer. The broker-dealer may sell the
shares so loaned, or upon a default the broker-dealer may sell the pledged
shares under this prospectus. 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 in connection with sales of the
shares. Accordingly, any such 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, any
securities covered by this prospectus which qualify for sale in compliance with
Rule 144 promulgated under the Securities Act may be sold under Rule 144 rather
than under this prospectus. The selling stockholders have advised us that they

                                       14
<PAGE>

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
certain 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, 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 such
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 file a supplement to this prospectus, if required, to comply with
Rule 424(b) under the Securities Act, upon being notified by a selling
stockholder that any material arrangements have been entered into 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. Such supplement will disclose:

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

o    the number of shares involved,

o    the price at which such shares were sold,

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

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

o    other facts material to the transaction.


     In addition, 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.

     We will bear all costs, expenses and fees in connection with the
registration of the shares, other than fees and expenses, if any, of counsel or
other advisers to the selling stockholders. In addition, 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 various liabilities, including liabilities arising under the
Securities Act. The selling stockholders have agreed to indemnify us, our
directors and officers who sign the registration statement of which this
prospectus forms a part, and control persons against various liabilities in
connection with the offering of the shares, including liabilities arising under
the Securities Act.

                                       15

<PAGE>

                              SELLING STOCKHOLDERS

     The following table sets forth the number of shares owned by each of the
selling stockholders. This registration statement also shall cover any
additional shares of common stock which become issuable in connection with the
shares registered for sale hereby by reason of any stock dividend, stock split,
recapitalization or other similar transaction effected without the receipt of
consideration which results in an increase in the number of our outstanding
shares of common stock.

     Other than Elan Corporation and its affiliates, none of the selling
stockholders has had a material relationship with us within the past three years
other than as a result of the ownership of the shares or other securities of
ours.

An affiliate of Elan Corporation is participating in this offering as a selling
stockholder. In 1998, we entered into a strategic alliance with Elan and one of
its affiliates, which we collectively refer to as Elan, to license exclusive
rights to market Elan's proprietary product Morphelan in the U.S. and Canada for
pain management in cancer and HIV patients. We also have an option to co-promote
Morphelan in continental Europe for the same indications. Since September 1998,
as part of our strategic alliance and under related securities purchase
agreements, we have issued to Elan an aggregate of 3,011,549 shares of our
common stock and $110 million issue price of notes convertible into shares of
our common stock. In December 1999 and March 2000, Elan converted an aggregate
of $40 million issue price of these convertible notes plus accrued interest,
together with conversion incentives, for which it received an aggregate of
4,033,155 additional shares of our common stock.

     In addition, under the strategic alliance, Elan has the right to maintain
its proportionate level of ownership of our stock in connection with specified
offerings of our common stock. In 1999, in connection with this right, Elan
purchased 52,742 additional shares of our common stock and warrants to purchase
91,406 additional shares of our common stock. Elan also purchased 416,667
additional shares of our common stock in connection with the sale of
unregistered shares of our common stock completed on January 10, 2001, which
shares are being registered in connection with this registration statement. As a
result, as of the date of this prospectus, and prior to any sales under this
prospectus, Elan beneficially owns an aggregate of 12,886,408 shares of our
common stock, assuming conversion of all outstanding warrants and notes,
representing approximately 18.6% of our common stock on a fully diluted basis.

     We do not know when or in what amounts the selling stockholders may offer
shares for sale. The selling stockholders may decide not to sell all or any of
the shares that this prospectus covers. The shares offered by this prospectus
may be offered from time to time by the selling stockholders named below.
Because the selling stockholders may offer all or some of the shares pursuant to
this offering, and because there are currently no agreements, arrangements or
understandings with respect to the sale of any of the shares that the selling
stockholders will hold after completion of the offering, we cannot estimate the
number of shares that the selling stockholders will hold after completion of the
offering.

<TABLE>
<CAPTION>
                                                       SHARES BENEFICIALLY
                                                   OWNED PRIOR TO THIS OFFERING
                                          ---------------------------------------------
                                                                   PERCENTAGE OF COMMON       NUMBER OF SHARES OF
                NAME OF                                             STOCK OUTSTANDING             COMMON STOCK
          SELLING STOCKHOLDER                    NUMBER                                        REGISTERED HEREBY
-----------------------------------       --------------------     --------------------       --------------------
<S>                                            <C>                        <C>                      <C>
Baystar Capital LLP                            93,750                      *                        93,750

Baystar International                          31,250                      *                        31,250

Domain Public Equity Partners L.P.            200,000                      *                       200,000

Elan International Services, LTD            7,514,113                    12.8%                     416,667

Merlin BioMed II, L.P.                         34,500                      *                        34,500

Merlin BioMed INT'L LTD                       156,000                      *                       156,000
</TABLE>

                                       16

<PAGE>


<TABLE>
<S>                                            <C>                        <C>                      <C>
Merlin BioMed LP                              102,000                      *                       102,000

Narragansett I, LP                            119,000                      *                        85,000

Narragansett Offshore Ltd.                    231,000                      *                       165,000

Royal Bank of Canada                          250,000                      *                       250,000

S.A.C. Capital Associates, LLC                375,000                      *                       375,000

TAIB Funds, LTD                                 7,500                      *                         7,500

United Capital Management, Inc.                83,333                      *                        83,333
                                           ----------                                         ------------
                                 TOTAL:     9,197,446                                            2,000,000
                                           ==========                                         ============
</TABLE>
* Indicates less than 1%


                                  LEGAL MATTERS

     The validity of the securities offered hereby will be passed upon by
Brobeck, Phleger & Harrison LLP, San Diego, California. Members of Brobeck,
Phleger & Harrison LLP own a total of 1,375 shares of our class B common stock
and 5,781 shares of our 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. Our financial statements are incorporated by
reference in reliance upon Ernst & Young LLP's reports, given on their authority
as experts in accounting and auditing.

WE HAVE NOT AUTHORIZED ANY PERSON TO MAKE A STATEMENT THAT DIFFERS FROM WHAT IS
IN THIS PROSPECTUS. IF ANY PERSON DOES MAKE A STATEMENT THAT DIFFERS FROM WHAT
IS IN THIS PROSPECTUS, YOU SHOULD NOT RELY ON IT. THIS PROSPECTUS IS NOT AN
OFFER TO SELL, NOR IS IT AN OFFER TO BUY, THESE SECURITIES IN ANY STATE IN WHICH
THE OFFER OR SALE IS NOT PERMITTED. THE INFORMATION IN THIS PROSPECTUS IS
COMPLETE AND ACCURATE AS OF ITS DATE, BUT THE INFORMATION MAY CHANGE AFTER THAT
DATE.


                                       17

<PAGE>




                                2,000,000 SHARES


                       LIGAND PHARMACEUTICALS INCORPORATED


                                  COMMON STOCK



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

                                   Prospectus

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



                                JANUARY 19, 2001




<PAGE>

                                     PART II
                     INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14.  OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

     The following table sets forth all expenses, other than underwriting
discounts and commissions, payable by the registrant in connection with the sale
of the common stock being registered. All the amounts shown are estimates,
except for the SEC registration fee.

<TABLE>
<S>                                                            <C>
SEC registration fee.................................          $   6,100
                                                               ---------
Printing and engraving expenses......................              5,000
                                                               ---------
Nasdaq additional listing fee........................             17,500
                                                               ---------
Legal fees and expenses..............................             50,000
                                                               ---------
Accounting fees and expenses.........................             25,000
                                                               ---------
Transfer agent and registrar fee.....................              5,000
                                                               ---------
Miscellaneous expenses...............................             10,000
                                                               ---------
        TOTAL                                                  $ 118,600
                                                               =========
</TABLE>

ITEM 15.  INDEMNIFICATION OF OFFICERS AND DIRECTORS.

     Under Section 145 of the Delaware General Corporation Law, we have broad
powers to indemnify our directors and officers against liabilities they may
incur in such capacities, including liabilities under the Securities Act.

     Our amended and restated certificate of incorporation provides for the
indemnification of all persons to the fullest extent permissible under Delaware
law.

     Our amended and restated by-laws provides for the indemnification of
officers, directors and third parties acting on our behalf if such person acted
in good faith and in a manner reasonably believed to be in and not opposed to
our best interest, and, with respect to any criminal action or proceeding, the
indemnified party had no reason to believe his or her conduct was unlawful.

     We maintain directors and officers insurance providing indemnification for
certain of our directors and officers for certain liabilities.

     We also entered into indemnification agreements between us and our
directors and officers, which may be sufficiently broad to permit
indemnification of our officers and directors for liabilities arising under the
1933 Act.

     In connection with the January 2001 private placement, the Company agreed
to indemnify the selling stockholders and its controlling persons, as defined in
the Securities Act of 1933, against liabilities, including legal fees, that the
selling stockholders or their controlling persons may incur under the Securities
Act, the Exchange Act, or any other federal or state statutory law or
regulation, or at common law or otherwise in connection with this registration
statement, including the prospectus, financial statements and schedules, and
amendments and supplements to those documents, except liabilities related to
misstatements or omissions made in the registration statement in conformity with
written information furnished to the Company by or on behalf of the selling
stockholders expressly for use in the registration statement or prospectus or
any breach or violation of the representations and warranties of the selling
stockholders under the purchase agreement between the Company and the selling
stockholder dated as of January 5, 2001.

     Insofar as indemnification for liabilities arising under the Securities Act
of 1933 may be permitted to directors, officers or persons controlling us
pursuant to the foregoing provisions, we have been informed that in the opinion
of the Securities and Exchange Commission such indemnification is against public
policy as expressed in the Act and is therefore unenforceable.

                                      II-1

<PAGE>

ITEM 16.  EXHIBITS.

         (a) EXHIBITS.
<TABLE>
<CAPTION>
EXHIBIT NO.   DESCRIPTION
-----------   -----------
<S>           <C>
4.1           Instruments defining the rights of stockholders.
              Reference is made to our Form 8-A registration
              statement filed on November 21, 1994 (incorporated
              into this registration statement by reference), the
              Amended and Restated Certificate of Incorporation
              (incorporated into this registration statement by
              reference to Exhibit 3.2 to our Form S-4 registration
              statement filed on July 9, 1998), the Bylaws
              (incorporated into this registration statement by
              reference to Exhibit 3.3 of our Form S-4 registration
              statement, filed on July 9, 1998), the Amended
              Certificate of Designation of Rights, Preferences and
              Privileges of Series A Participating Preferred Stock
              (incorporated into this registration statement by
              reference to Exhibit 3.3 to our quarterly report on
              Form 10-Q for the period ended March 31, 1999) and
              our Forms 8-A registration statements filed on
              December 24, 1998, November 10, 1998 and September
              30, 1996.

5.1           Opinion of Brobeck, Phleger & Harrison LLP

23.1          Consent of Ernst & Young LLP, Independent Auditors

23.2          Consent of Brobeck, Phleger & Harrison LLP.  Included in the
              Opinion of Brobeck, Phleger & Harrison LLP filed as Exhibit 5.1

24.1          Power of Attorney.  Included on page II-5 of this 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 such
information in the registration statement;

          (2) That, for the purpose of determining any liability under the
Securities Act of 1933, each such post-effective amendment shall be deemed to be
a new registration statement relating to the securities offered therein, and the
offering of such 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
the offering.

     The undersigned registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act of 1933, each filing of the
registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Securities Exchange Act of 1934 (and, where applicable, each filing of an
employee benefit plan's annual report pursuant to Section 15(d) of the
Securities Exchange Act of 1934) 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 such 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
of 1933 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 Securities and Exchange Commission
such indemnification is against public policy as expressed in the Act and is,
therefore, unenforceable. In the event that a claim for indemnification against
such 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 such
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 of whether such indemnification by it is against
public policy as expressed in the Act and will be governed by the final
adjudication of such issue.

                                     II-2

<PAGE>

                                   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 San Diego, State of California, on January 19, 2001.


LIGAND PHARMACEUTICALS INCORPORATED


                                  By: /s/ David E. Robinson
                                  ---------------------------------------
                                      David E. Robinson, President
                                      and Chief Executive Officer


                                POWER OF ATTORNEY


     KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below hereby constitutes and appoints David E. Robinson and Paul V.
Maier and each of them acting individually, as his or her attorney-in-fact, each
with full power of substitution and resubstitution, for him or her in any and
all capacities, to sign any and all amendments to this Registration Statement
(including post-effective amendments), and to file the same, with exhibits
thereto and other documents in connection therewith, with the Securities and
Exchange Commission, granting unto said attorneys-in-fact 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
attorneys-in-fact, or their 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
         ---------                                   -----                                 ----
<S>                                                  <C>                                   <C>
/s/ David E. Robsinson                                                                 January 19, 2001
---------------------------------
    David E. Robinson                   President and Chief Executive Officer
                                           (Principal Executive Officer)

/s/ Paul V. Maier                                                                      January 19, 2001
---------------------------------
    Paul V. Maier                             Senior Vice President
                                            and Chief Financial Officer
                                    (Principal Financial and Accounting Officer)

/s/ Henry F. Blissenbach                                                               January 12, 2001
---------------------------------
    Henry F. Blissenbach                              Director


/s/                                                                                    January ___, 2001
---------------------------------
   Alexander D. Cross                                 Director


/s/ Michael A. Rocca                                                                   January 12, 2001
---------------------------------
    Michael A. Rocca                                  Director


/s/ John Groom                                                                         January 15, 2001
---------------------------------
    John Groom                                        Director


/s/ Irving S. Johnson                                                                  January 19, 2001
---------------------------------
    Irving S. Johnson, Ph.D.                          Director


/s/ Carl C. Peck                                                                       January 12, 2001
---------------------------------
    Carl C. Peck                                      Director
</TABLE>



                                     II-3

<PAGE>

                                  EXHIBIT INDEX
<TABLE>
<CAPTION>
EXHIBIT NO.      DESCRIPTION
-----------      -----------
<S>              <C>
4.1              Instruments defining the rights of stockholders.
                 Reference is made to our Form 8-A registration
                 statement filed on November 21, 1994 (incorporated
                 into this registration statement by reference), the
                 Amended and Restated Certificate of Incorporation
                 (incorporated into this registration statement by
                 reference to Exhibit 3.2 to our Form S-4 registration
                 statement filed on July 9, 1998), the Bylaws
                 (incorporated into this registration statement by
                 reference to Exhibit 3.3 of our Form S-4 registration
                 statement, filed on July 9, 1998), the Amended
                 Certificate of Designation of Rights, Preferences and
                 Privileges of Series A Participating Preferred Stock
                 (incorporated into this registration statement by
                 reference to Exhibit 3.3 to our quarterly report on
                 Form 10-Q for the period ended March 31, 1999) and
                 our Forms 8-A registration statements filed on
                 December 24, 1998, November 10, 1998 and September
                 30, 1996.

5.1              Opinion of Brobeck, Phleger & Harrison LLP

23.1             Consent of Ernst & Young, LLP, Independent Auditors

23.2             Consent of Brobeck, Phleger & Harrison LLP.  Included in the
                 Opinion of Brobeck, Phleger & Harrison LLP filed as Exhibit 5.1

24.1*            Power of Attorney.  Included on page II-5 of this registration
                 statement
</TABLE>

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


                                     II-4


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