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                                                                     Exhibit 3.1


                              AMENDED AND RESTATED
                         CERTIFICATE OF INCORPORATION OF
                        ARRIS PHARMACEUTICAL CORPORATION

      ARRIS PHARMACEUTICAL CORPORATION (the "Corporation"), a corporation
organized and existing under and by virtue of the General Corporation Law of the
State of Delaware, does hereby certify as follows:

      1.    That its Certificate of Incorporation, originally filed with the
Secretary of State of Delaware on April 19, 1989, and its Amended and Restated
Certificate of Incorporation, filed with the Secretary of State on December 17,
1993, is hereby amended and restated in its entirety to read as follows:

            "FIRST: The name of the corporation is AXYS PHARMACEUTICALS, INC.
(hereinafter referred to as the "Corporation").

            SECOND: The registered office of the Corporation is to be located at
1209 Orange Street, City of Wilmington, County of New Castle, State of Delaware
19801. The name of its registered agent is The Corporation Trust Company, whose
address is Corporation Trust Center, 1209 Orange Street, Wilmington, Delaware
19801.

            THIRD: The purpose of the Corporation is to engage in any lawful act
or activity for which corporations may be organized under the General
Corporation Law of the State of Delaware.

            FOURTH: The total number of shares of capital stock that the
Corporation shall have the authority to issue shall be 60,000,000 shares, all of
which shall be divided into two classes: Preferred Stock, to consist of
10,000,000 shares, par value $.001 per share, and Common Stock, to consist of
50,000,000 shares, par value $.001 per share.

            The Preferred Stock may be issued from time to time in one or more
series. The Board of Directors is hereby authorized, by filing a certificate (a
"Preferred Stock Designation") pursuant to the Delaware General Corporation Law,
to fix or alter from time to time the designation, powers, preferences and
rights of the shares of each such series and the qualifications, limitations or
restrictions of any wholly unissued series of Preferred Stock, and to establish
from time to time the number of shares constituting any such series or any of
them; and to increase or decrease the number of shares of any series subsequent
to the issuance of shares of that series, but not below the number of shares of
such series then outstanding. In case the number of shares of any series shall
be decreased in accordance with the foregoing sentence, the shares constituting
such decrease shall resume the status that they had prior to the adoption of the
resolution originally fixing the number of shares of such series.

            FIFTH: The election of directors need not be by written ballot
unless the Bylaws so provide.

            SIXTH: The Board of Directors of the Corporation is authorized and
empowered from time to time in its discretion to make, alter, amend or repeal
Bylaws of the Corporation,


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except as such power may be restricted or limited by the General Corporation Law
of the State of Delaware.

            SEVENTH: Whenever a compromise or arrangement is proposed between
the Corporation and its creditors or any class of them and/or between the
corporation and its stockholders or any class of them, any court of equitable
jurisdiction within the State of Delaware may, on the application in a summary
way of the Corporation or of any creditor or stockholder thereof, or on the
application of any receiver or receivers appointed for the Corporation under the
provision of Section 291 of Title 8 of the Delaware Code, or on the application
of trustees in dissolution or of any receiver or receivers appointed for the
Corporation under section 279 of Title 8 of the Delaware Code, order a meeting
of the creditors or class of creditors, and/or of the stockholders or class of
stockholders or the corporation, as the case may be, to be summoned in such
manner as the said court directs. If a majority in number representing
three-fourths (3/4) in value of the creditors or class of creditors, and/or of
the stockholders or class of stockholders of the Corporation, as the case may
be, agree to any compromise or arrangement and to any reorganization of the
Corporation as a consequence of such compromise arrangement, the said compromise
arrangement and the said reorganization shall, if sanctioned by the court to
which said application has been made, be binding on all the creditors or class
of creditors, and/or on all the stockholders or class of stockholders, of the
Corporation, as the case may be, and also on the Corporation.

            EIGHTH: No director shall be personally liable to the Corporation or
its stockholders for monetary damages for any breach or fiduciary duty by such
director as a director. Notwithstanding the foregoing sentence, a director shall
be liable to the extent provided by applicable law (i) for any breach of the
director's duty of loyalty to the Corporation or its stockholders, (ii) for acts
or omissions not in good faith or which involve intentional misconduct or a
knowing violation of law, (iii) under Section 174 of Title 8 of the Delaware
Code, or (iv) for any transaction from which the director derived an improper
personal benefit.

            NINTH: For the management of the business and for the conduct of the
affairs of the corporation, and in further definition, limitation and regulation
of the powers of the corporation, of its directors and of its stockholders or
any class thereof, as the case may be, it is further provided that:

            (a)   (i) The management of the business and the conduct of the
affairs of the corporation shall be vested in its Board of Directors. The number
of directors which shall constitute the whole Board of Directors shall be fixed
exclusively by one or more resolutions adopted by the Board of Directors.

                  (ii)  Subject to the rights of the holders of any series of
Preferred Stock to elect additional directors under specified circumstances,
directors shall be elected at each annual meeting of stockholders for a term of
one year. Each director shall serve until his or her successor is duly elected
and qualified or until his or her death, resignation or removal. No decrease in
the number of directors constituting the Board of Directors shall shorten the
term of any incumbent director.


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                  (iii) Subject to the rights of the holders of any series of
Preferred Stock, no director shall be removed without cause. Subject to any
limitations imposed by law, the Board of Directors or any individual director
may be removed from office at any time with cause by the affirmative vote of the
holders of an majority of the voting power of all the then-outstanding shares of
voting stock of the corporation, entitled to vote at an election of directors
(the "Voting Stock").

                  (iv)  Subject to the rights of the holders of any series of
Preferred Stock, any vacancies on the board of Directors resulting from death,
resignation, disqualification, removal or other causes and any newly created
directorships resulting from any increase in the number of directors, shall,
unless the Board of Directors determines by resolution that any such vacancies
or newly created directorships shall be filled by the stockholders, except as
otherwise provided by law, be filled only by the affirmative vote of a majority
of the directors then in office, even though less than a quorum of the Board of
Directors, and not by the stockholders. Any director elected in accordance with
the preceding sentence shall hold office for the remainder of the full term of
the director for which the vacancy was created or occurred and until such
director's successor shall have been elected and qualified.

            (b)   (i) Subject to Article IX of the Bylaws, the Bylaws may be
altered or amended or new Bylaws adopted by the affirmative vote of at least
sixty-six and two-thirds percent (66-2/3%) of the voting power of all of the
ten-outstanding shares of the Voting Stock. The Board of Directors shall also
have the power to make, alter, amend, or repeal Bylaws pursuant to Article
Sixth.

                  (ii)  No action shall be taken by the stockholders of the
corporation except at an annual or special meeting of stockholders called in
accordance with the Bylaws and no action shall be taken by the stockholders by
written consent.

                  (iii) Special meetings of the stockholders of the corporation
may be called, for any purpose or purposes, by (i) the Chairman of the Board of
Directors, (ii) the Chief Executive Officer, or (iii) the Board of Directors
pursuant to a resolution adopted by a majority of the total number of authorized
directors (whether or not there exist any vacancies in previously authorized
directorships at the time any such resolution presented to the Board of
Directors for adoption), and shall be held at such place, on such date, and at
such time as the Board of Directors shall fix.

                  (iv)  Advance notice of stockholder nominations for the
election of directors and of business to be brought by stockholders before any
meeting of the stockholders of the corporation shall be given in the manner
provided in the Bylaws of the corporation.

            TENTH: Subject to the limitations set forth herein, the corporation
reserves the right to amend, alter, change or repeal any provision contained in
this Certificate of Incorporation, in the manner now or hereafter prescribed by
law, and all rights and powers conferred herein on stockholders, directors and
officers are subject to this reserved power."


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      IN WITNESS WHEREOF, the Corporation has caused this Certificate to be
executed by its President and attested to by its Secretary this 8th day of
January, 1998.


                                       ARRIS PHARMACEUTICAL CORPORATION



                                       /s/  JOHN P. WALKER
                                       -----------------------------------------
                                       John P. Walker
                                       President


ATTEST:



/s/  ALAN C. MENDELSON
-------------------------------------
Alan C. Mendelson
Secretary


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