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                                                                     Exhibit 3.1
 
                     RESTATED CERTIFICATE OF INCORPORATION

                             OF PHARMACOPEIA, INC.

           Pharmacopeia, Inc., a corporation organized and existing under the
laws of the State of Delaware, hereby certifies as follows:

     A.    The name of the corporation is Pharmacopeia, Inc. The original
Certificate of Incorporation of the corporation was filed with the Secretary of
State of the State of Delaware on March 26, 1993.
                   
     B.    Pursuant to Sections 228, 242 and 245 of the General Corporation Law
of the State of Delaware, this Restated Certificate of Incorporation restates
and integrates the provisions of the Certificate of Incorporation of this
corporation.

     C.    The text of the Certificate of Incorporation as heretofore amended or
supplemented is hereby amended and restated in its entirety to read as follows:

     ONE.  The name of this corporation is "Pharmacopeia, Inc."
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     TWO.  The address of the corporation's registered office in the State of
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Delaware is 1013 Centre Road, Wilmington, Delaware 19805-1297, New Castle
County. The name of its registered agent at such office is The Prentice-Hall
Corporation System, Inc.

     THREE.      The nature of the business or purposes to be conducted or
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promoted is to engage in any lawful act or activity for which corporations may
be organized under the General Corporation Law of Delaware.

     FOUR.       This corporation is authorized to issue two classes of stock to
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be designated, respectively, "Common Stock" and "Preferred Stock." The total
number of shares of Common Stock which the corporation is authorized to issue is
Forty Million (40,000,000) shares, par value $.0001. The total number of shares
of Preferred Stock which the corporation is authorized to issue is Two Million
(2,000,000), par value $.0001 per share.

     The Board of Directors is authorized, subject to limitations prescribed by
law and the provisions of this Article FOUR, to provide for the issuance of the
shares of Preferred Stock in series, and by filing a certificate pursuant to the
applicable law of the State of Delaware, to 
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establish from time to time the number of shares to be included in each such
series, and to fix the designation, powers, preferences, and rights of the
shares of each such series and the qualifications, limitations or restrictions
thereof.

     The authority of the Board with respect to each series shall include,
but not be limited to, determination of the following:

           (a)   The number of shares constituting that series and the
     distinctive designation of that series;

           (b)   The dividend rate on the shares of that series, whether
     dividends shall be cumulative, and, if so, from which date;

           (c)   Whether that series shall have voting rights, in addition to
     the voting rights provided by law, and, if so, the terms of such voting
     rights;

           (d)   Whether that series shall have conversion privileges, and, if
     so, the terms and conditions of such conversion, including provision for
     adjustment of the conversion rate in such events as the Board of Directors
     shall determine;

           (e)   Whether or not the shares of that series shall be redeemable,
     and, if so, the terms and conditions of such redemption, including the date
     or date upon or after which they shall be redeemable, and the amount per
     share payable in case of redemption, which amount may vary under different
     conditions and at different redemption dates;

           (f)   Whether that series shall have a sinking fund for the
     redemption or purchase of shares of that series, and, if so, the terms and
     amount of such sinking fund;

           (g)   The rights of the shares of that series in the event of
     voluntary or involuntary liquidation, dissolution or winding up of the
     corporation, and the relative rights or priority, if any, of payment of
     shares of that series; and

           (h)   Any other relative rights, preferences and limitations of that
     series.

     1.    Dividends. Dividends may be declared and paid upon the Common
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Stock in any fiscal year of the corporation only if dividends shall have been
paid to or declared and set apart for payment to all shares of Preferred Stock.
The holders of Preferred Stock and Common Stock shall be entitled, when, as and
if declared by the Board of Directors, to dividends out of the corporation's
assets legally available therefor; provided, however, that no such dividends may
be declared or paid on any shares of Common Stock or Preferred Stock unless at
the same time an equivalent dividend is declared and paid on all outstanding
shares of Common Stock and Preferred Stock. The right to dividends on shares of
the Common Stock or Preferred Stock shall not be cumulative, and no right shall
accrue to holders of Common Stock or Preferred Stock by reason of the fact that
dividends on said shares are not declared in any prior period.


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     2.    Voting Rights.
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           (a)   Common Stock. Each holder of shares of Common Stock shall be
     entitled to one vote for each share thereof held.

           (b)   Election by Ballot. The election of directors need not be by
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     written ballot unless the Bylaws of the corporation shall so provide.

     Two.  The corporation is to have perpetual existence.
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     Three.  In furtherance and not in limitation of the powers conferred by
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statute, the Board of Directors is expressly authorized to make, alter, amend or
repeal the Bylaws of the corporation.

     Four.  The number of directors of the corporation shall be fixed from time
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to time by a bylaw or amendment thereof duly adopted by the Board of Directors
or by the stockholders.

           The Board of Directors shall be and is divided into three classes:
Class I, Class II and Class III, which shall be as nearly equal in number as
possible. Each director shall serve for a term ending on the date of the third
annual meeting of stockholders following the annual meeting at which the
director was elected; provided, however, that each initial director in Class I
shall hold office until the annual meeting of stockholders in 1996; each initial
director in Class II shall hold office until the annual meeting of stockholders
in 1997; and each initial director in Class III shall hold office until the
annual meeting of stockholders in 1998. Notwithstanding the foregoing provisions
of this Article, each director shall serve until his successor is duly elected
and qualified or until his death, resignation or removal.

           In the event of any increase or decrease in the authorized number of
directors, (1) each director then serving as such shall nevertheless continue as
a director of the class of which he is a member until the expiration of his
current term, or his earlier resignation, removal from office or death, and (2)
the newly created or eliminated directorship resulting from such increase or
decrease shall be apportioned by the Board of Directors among the three classes
of directors so as to maintain such classes as nearly equal as possible.

     Five. Meetings of stockholders may be held within or without the State of
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Delaware, as the Bylaws may provide. The books of the corporation may be kept
(subject to any provisions contained in the statutes) outside the State of
Delaware at such place or places as may be designated from time to time by the
Board of Directors or in the Bylaws of the corporation.

     Six.
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           (a)   The corporation shall indemnify each of the corporation's
     directors and officers in each and every situation where, under Section 145
     of the General Corporation


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     Law of the State of Delaware, as amended from time to time ("Section 145"),
     the corporation is permitted or empowered to make such indemnification. The
     corporation may, in the sole discretion of the Board of Directors of the
     corporation, indemnify any other person who may be indemnified pursuant to
     Section 145 to the extent the Board of Directors deems advisable, as
     permitted by Section 145. The corporation shall promptly make or cause to
     be made any determination required to be made pursuant to Section 145.

           (b)   No person shall be personally liable to the corporation or its
     stockholders for monetary damages for breach of fiduciary duty as a
     director, provided, however, that the foregoing shall not eliminate or
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     limit the liability of a director (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 the General
     Corporation Law of the State of Delaware or (iv) for any transaction from
     which the director derived an improper personal benefit. If the General
     Corporation Law of the State of Delaware is subsequently amended to further
     eliminate or limit the liability of a director, then a director of the
     corporation, in addition to the circumstances in which a director is not
     personally liable as set forth in the preceding sentence, shall not be
     liable to the fullest extent permitted by the amended General Corporation
     Law of the State of Delaware. For purposes of this Article NINE, "fiduciary
     duty as a director" shall include any fiduciary duty arising out of serving
     at the corporation's request as a director of another corporation,
     partnership, joint venture or other enterprise, and "personal liability to
     the corporation or its stockholders" shall include any liability to such
     other corporation, partnership, joint venture, trust or other enterprise,
     and any liability to the corporation in its capacity as a security holder,
     joint venturer, partner, beneficiary, creditor or investor of or in any
     such other corporation, partnership, joint venture, trust or other
     enterprise.

           (c)   Neither any amendment nor repeal of this Article NINE, nor the
     adoption of any provision of this Certificate of Incorporation inconsistent
     with this Article NINE, shall eliminate or reduce the effect of this
     Article NINE in respect of any matter occurring, or any cause of action,
     suit or claim that, but for this repeal or adoption of an inconsistent
     provision.

     Seven.  Advance notice of new business and stockholder nominations for the
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election of directors shall be given in the manner and to the extent provided in
the Bylaws of the corporation.

     Eight.  Whenever a compromise or arrangement is proposed between this
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corporation and its creditors or any class of them and/or between this
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 this corporation or of any creditor or stockholder thereof or on the
application of any receiver or receivers appointed for this corporation under
the provisions 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 this corporation under the provisions of Section 279 of 


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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 of this
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 in value of the
creditors or class of creditors, and/or of the stockholders or class of
stockholders of this corporation, as the case may be, agree to any compromise or
arrangements and to any reorganization of this corporation as consequence of
such compromise or arrangement, the said compromise or arrangement and the said
reorganization shall, if sanctioned by the court to which the 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 this corporation, as the case
may be, and also on this corporation.

     Nine.  The corporation reserves the right to amend, alter, change or repeal
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any provisions contained in this Certificate, in the manner now or hereafter
prescribed by statute, and all rights conferred upon stockholders herein are
granted subject to this reservation.


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           IN WITNESS WHEREOF, the corporation has caused this Certificate to be
signed by Joseph A. Mollica, its Chief Executive Officer, and attested by Lewis
J. Shuster, its Assistant Secretary, this 8th day of December 1995.


                                            PHARMACOPEIA, INC.


                                            By:
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                                            Joseph A. Mollica
                                            Chief Executive Officer

         ATTEST:


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         Lewis J. Shuster
         Assistant Secretary