AGOURON PHARMACEUTICALS INC
424B3, 1998-11-16
PHARMACEUTICAL PREPARATIONS
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PROSPECTUS SUPPLEMENT                          FILED PURSUANT TO RULE 424(b)(3)
TO PROSPECTUS DATED NOVEMBER 6, 1998                 REGISTRATION NO. 333-61317


                           PROXY STATEMENT/PROSPECTUS
                         ANNUAL MEETING OF SHAREHOLDERS
                         TO BE HELD ON DECEMBER 16, 1998

         This Proxy  Statement/Prospectus  ("Proxy  Statement")  is furnished in
connection  with the  solicitation  of  Proxies by and on behalf of the Board of
Directors  (the  "Board")  of  Agouron   Pharmaceuticals,   Inc.,  a  California
corporation  ("Agouron"  or the  "Company"),  for  use at the  Company's  Annual
Meeting of Shareholders  for the fiscal year ended June 30, 1998 (the "Meeting")
to be held at the Sheraton  Grande Torrey Pines,  10950 North Torrey Pines Road,
La Jolla,  California 92037, on Wednesday,  December 16, 1998 at 10:00 a.m., San
Diego time, and at any  adjournments or postponements  thereof.  At the Meeting,
shareholders  will be asked (i) to elect nine  directors  of the Company to hold
office until the 1999 Annual Meeting of Shareholders  and until their successors
are elected and  qualified,  (ii) to increase the number of shares of authorized
Common Stock to 150,000,000  shares,  of which 75,000,000 shares would initially
be designated as Agouron Pharmaceuticals Common Stock ("Agouron  Pharmaceuticals
Stock") and 25,000,000  shares would initially be designated as Agouron Oncology
Division Common Stock ("Oncology Division Stock"),  to provide  authorization to
the  Board  to  designate  and  issue  any  undesignated  shares  in one or more
additional  series of Common  Stock,  determine  the number of  shares,  rights,
preferences,  privileges and  restrictions  of any such series,  and increase or
decrease the number of shares of any existing series,  and to convert each share
of the Company's  existing Common Stock ("Existing Common Stock") into one share
of Agouron  Pharmaceuticals Stock and 0.5 shares of Oncology Division Stock (the
"Divisional Stock  Proposal"),  (iii) to increase the number of shares available
for issuance  under the  Company's  1996 Stock Option Plan by 1,000,000  shares,
(iv) to increase the number of shares available for purchase under the Company's
Employee Stock Purchase Plan by 200,000  shares,  (v) to ratify the selection of
the Company's independent accountants,  and (vi) to transact such other business
as may properly be presented to the Meeting or any adjournments or postponements
thereof.  This Proxy  Statement also  constitutes  the Prospectus of the Company
with  respect  to the  shares of  Agouron  Pharmaceuticals  Stock  and  Oncology
Division Stock to be issued  pursuant to the Divisional  Stock  Proposal.  It is
anticipated that this Proxy Statement and the accompanying  Proxy will be mailed
to the Company's shareholders on or about November 12, 1998. An Index of Defined
Terms showing the pages on which certain terms used in this Proxy  Statement are
defined is included as Annex I.

     SEE "RISK FACTORS" BEGINNING ON PAGE 23 FOR CERTAIN INFORMATION THAT SHOULD
BE CONSIDERED IN CONNECTION WITH AN EVALUATION OF THE DIVISIONAL STOCK PROPOSAL.

         The Existing Common Stock is traded on the Nasdaq National Market under
the symbol AGPH. There has been no prior market for the Agouron  Pharmaceuticals
Stock or the Oncology  Division  Stock.  Application  will be made to The Nasdaq
Stock  Market,  Inc.  to  redesignate  the  Existing  Common  Stock  as  Agouron
Pharmaceuticals  Stock,  to be quoted on the Nasdaq  National  Market  under the
symbol AGPH, and for the quotation of the Oncology  Division Stock on the Nasdaq
National Market under a separate symbol to be determined.

         Shareholders  should  note that if the  Divisional  Stock  Proposal  is
approved,  holders  will  NOT have to send in  their  certificates  representing
shares of Existing  Common Stock to be exchanged for  certificates  representing
shares of Agouron  Pharmaceuticals Stock. DO NOT MAIL YOUR EXISTING COMMON STOCK
CERTIFICATES  TO EITHER THE COMPANY OR ITS  TRANSFER  AGENT IN  CONNECTION  WITH
THESE TRANSACTIONS.

     THE BOARD HAS CAREFULLY  CONSIDERED THE DIVISIONAL  STOCK PROPOSAL AND EACH
OF THE OTHER PROPOSALS SET FORTH IN THE NOTICE OF ANNUAL MEETING OF SHAREHOLDERS
AND BELIEVES THAT THE APPROVAL OF THESE PROPOSALS BY THE  SHAREHOLDERS IS IN THE
BEST  INTERESTS  OF THE COMPANY  AND THE  SHAREHOLDERS.  ACCORDINGLY,  THE BOARD
UNANIMOUSLY  RECOMMENDS  THAT THE  SHAREHOLDERS  APPROVE  THE  DIVISIONAL  STOCK
PROPOSAL AND EACH OF THE OTHER  PROPOSALS  WHICH ARE DESCRIBED IN MORE DETAIL IN
THIS PROXY STATEMENT.

     THESE  SECURITIES  HAVE NOT BEEN APPROVED OR  DISAPPROVED BY THE SECURITIES
AND EXCHANGE COMMISSION OR ANY STATE SECURITIES COMMISION NOR HAS THE SECURITIES
AND  EXCHANGE  COMMISSION  OR ANY STATE  SECURITIES  COMMISSION  PASSED UPON THE
ACCURACY OR ADEQUACY OF THIS PROXY STATEMENT. ANY REPRESENTATION TO THE CONTRARY
IS A CRIMINAL OFFENSE.

Dated:  November 6, 1998


<PAGE>


         SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

         The  following  table sets forth  information  as of October  19,  1998
relating to the  beneficial  ownership of the Existing  Common Stock by (i) each
person known by the Company to beneficially  own more than 5% of the outstanding
shares of the Company's  Common  Stock,  (ii) each  director,  (iii) each of the
executive  officers named in the Summary  Compensation Table below, and (iv) all
executive officers and directors as a group.
<TABLE>
<CAPTION>

                                                                                  BENEFICIAL OWNERSHIP(1)

                                                                   Number of Percentage of
         BENEFICIAL OWNER                                                 SHARES(9)                  TOTAL
- ------------------------------                                        ---------------              ---------
<S>                                                                      <C>                         <C>   
 
    Wellington Management Co.                                         4,264,000*                   13.63%*
         75 State Street, Boston, MA 02109
     Peter Johnson(2)                                                    706,533                     2.22%
     Gary E. Friedman(2) Family Trust(8)                                 294,123                        **
     John N. Abelson(2)(3)(6)                                            102,943                        **
     Patricia M. Cloherty(2)                                              27,659                        **
     A. E. Cohen(2)                                                       73,333                        **
     Michael E. Herman(2)(4)                                              83,333                        **
     Irving S. Johnson(2)                                                 41,933                        **
     Antonie T. Knoppers(2)                                               51,533                        **
     Melvin I. Simon(2)(3) and Linda F. Simon Living Trust(5)            122,843                        **
     Marvin R. Brown                                                     194,995                        **
     Barry D. Quart                                                      152,481                        **
     R. Kent Snyder(7)                                                   175,035                        **
All executive officers and directors as a group (19 persons)           2,706,671                     8.14%
</TABLE>

*    Based upon June 1998 Form 13-F filing.
**   less than 1%.
(1)  Unless otherwise  indicated,  the persons named in the above table exercise
     sole voting and investment  powers with respect to all shares  beneficially
     owned by them, subject to applicable community property laws. The number of
     shares  beneficially owned includes the following number of shares issuable
     upon  exercise of stock options  exercisable  within 60 days of October 19,
     1998: Mr.  Johnson,  596,923 shares;  Mr.  Friedman,  241,599  shares;  Dr.
     Abelson,  33,333 shares;  Ms. Cloherty,  13,333 shares;  Mr. Cohen,  43,333
     shares;  Mr.  Herman,  39,333  shares;  Dr.  Johnson,  15,833  shares;  Dr.
     Knoppers,  43,333  shares;  Dr. Simon,  33,333  shares;  Dr. Brown,  23,077
     shares;  Dr. Quart,  117,266 shares;  Mr. Snyder,  168,932 shares;  and all
     executive officers and directors as a group, 1,952,280 shares.
(2)  Director.
(3)  Does not include 1,106,000 shares held by The Agouron  Institute,  of which
     Drs. Abelson and Simon are directors.  As directors,  they share voting and
     investment powers as to the shares held by The Agouron Institute.
(4)  Includes 20,000 shares held by the Herman Family Trading Company,  a family
     partnership of which Mr. Herman is the general partner,  10,000 shares held
     by Vail  Fishing  Partners in which Mr.  Herman has a 50%  general  partner
     interest  and  2,000  shares  held by Mrs.  Herman,  of  which  Mr.  Herman
     disclaims any beneficial ownership.
(5)  Shared voting and investment power.
(6)  Includes  2,350  shares  held by Dr.  Abelson  as  custodian  for his minor
     children, of which Dr. Abelson disclaims any beneficial ownership.
(7)  Includes 800 shares held by immediate  family  members,  of which
     Mr. Snyder disclaims any  beneficial  ownership.  
(8)  Includes 5,408 shares held by wife as custodian for minor children of which
     Mr. Friedman disclaims any beneficial ownership.
(9)  Adjusted to reflect the two-for-one stock split in the form of a stock 
     dividend in August 1997.




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