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                  NINTH RESTATED CERTIFICATE OF INCORPORATION

                                      OF

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

     3-DIMENSIONAL PHARMACEUTICALS, INC. (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.  The name of the Corporation is 3-Dimensional Pharmaceuticals, Inc.  The
Certificate of Incorporation of the Corporation was originally filed by the
Corporation with the Secretary of State of the State of Delaware on March 11,
1993, a Certificate of Amendment to the Certificate of Incorporation was filed
by the Corporation with the Secretary of State of Delaware on September 29, 1993
and a Restated Certificate of Incorporation (the "First Restated Certificate of
Incorporation") was filed by the Corporation with the Secretary of State of
Delaware on October 13, 1993.  Certificates of Amendment to the First Restated
Certificate of Incorporation were filed with the Secretary of State of Delaware
on December 13, 1993, April 21, 1994, December 12, 1994, May 16, 1995, May 26,
1995, August 14, 1995, December 12, 1995, December 27, 1995, February 8, 1996,
June 20, 1996 and September 25, 1996.  A Second Restated Certificate of
Incorporation was filed by the Corporation with the Secretary of State of
Delaware on October 11, 1996.  A Third Restated Certificate of Incorporation was
filed by the Corporation with the Secretary of State of Delaware on March 12,
1997.  A Fourth Restated Certificate of Incorporation was filed by the
Corporation with the Secretary of State of Delaware on June 12, 1997.
Certificates of Amendment to the Fourth Restated Certificate of Incorporation
were filed with the Secretary of State of Delaware on August 6, 1997 and
November 14, 1997.  The Fifth Restated Certificate of Incorporation was filed by
the Corporation with the Secretary of State of Delaware on December 31, 1997.
Certificates of Amendment to the Fifth Restated Certificate of Incorporation
were filed on October 12, 1999 and November 18, 1999.  The Sixth Restated
Certificate of Incorporation was filed by the Corporation with the Secretary of
State of Delaware on March 31, 2000.  The Seventh Restated Certificate of
Incorporation was filed by the Corporation with the Secretary of State of
Delaware on May 17, 2000. The Eighth Restated Certificate of Incorporation was
filed by the Corporation with the Secretary of State of Delaware on _______,
2000.

     2.   This Ninth Restated Certificate of Incorporation  restates and
integrates and further amends the Eighth Restated Certificate of Incorporation
of the Corporation.  This Certificate of Incorporation was duly adopted in
accordance with the provisions of Sections 242 and 245 and was approved by
written consent of the stockholders of the Corporation given in accordance with
the provisions of Section 228 of the General Corporation Law (prompt notice of
such action having been given to those stockholders who did not consent in
writing).

     3.   This Ninth Restated Certificate of Incorporation shall not become
effective upon its filing date, but rather, shall become effective at [closing
date and time to be inserted].

     3.  The text of the Certificate of Incorporation of the Corporation is
hereby restated
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and amended to read in its entirety, as of the effective time, as follows:

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<PAGE>

          FIRST:  The name of the Corporation is 3-Dimensional Pharmaceuticals,
Inc.

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

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

          FOURTH:  The aggregate number of shares of all classes of capital
stock which the Corporation shall have authority to issue is fifty million
(50,000,000) shares, consisting of forty-five million (45,000,000) shares of
Common Stock, par value $.001 per share ("Common Stock"), and five million
(5,000,000) shares of Preferred Stock, par value $.001 per share ("Preferred
Stock").

   (A) Common Stock.
       ------------

          1.  General.  The voting, dividend and liquidation rights of the
              -------
holders of the Common Stock are subject to and qualified by the rights of the
holders of the Preferred Stock of any series as may be designated by the Board
of Directors upon any issuance of the Preferred Stock of any series.

          2.  Voting.  The holders of the Common Stock are entitled to one vote
              ------
for each share held at all meetings of stockholders. The number of authorized
shares of Common Stock may be increased or decreased (but not below the number
of shares thereof then outstanding) by the affirmative vote of the holders of a
majority of the stock of the Corporation entitled to vote, irrespective of the
provisions of Section 242(b)(2) of the General Corporation Law of the State of
Delaware.

          3.  Dividends.  Dividends may be declared and paid on the Common
              ---------
Stock from funds lawfully available therefor as and when determined by the Board
of Directors and subject to any preferential dividend rights of any then
outstanding Preferred Stock.

          4.  Liquidation.  Upon the dissolution or liquidation of the
              -----------
Corporation, whether voluntary or involuntary, holders of Common Stock will be
entitled to receive all assets of the Corporation available for distribution to
its stockholders, subject to any preferential rights of any then outstanding
Preferred Stock.

   (B)  Preferred Stock.
        ---------------

          Shares of Preferred Stock may be issued from time to time in one or
more series as may from time to time be determined by the Board of Directors,
each of said series to be distinctly designated in one or more certificates of
designation (each a "Certificate of Designation").  The voting powers,
preferences and relative, optional and other special rights, and the
qualifications, limitations or restrictions thereof, if any, of each such series
may differ from those of any and all other series of Preferred Stock at any time
outstanding, and the Board

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of Directors is hereby expressly granted authority to fix, by resolution or
resolutions and filing of a Certificate of Designation, or alter the
designation, number, voting powers, preferences and relative, participating,
optional and other special rights, and the qualifications, limitations and
restrictions thereof, of each series, including but without limiting the
generality of the foregoing, the following:

          1.  The distinctive designation of such series and the number of
shares to constitute such series, which number (except as set forth in the
Certificate of Designation with respect to such series) may be increased or
decreased (but not below the number of shares of such series then outstanding)
from time to time by the Board of Directors;

          2.  The rights in respect of dividends, if any, on the shares of such
series, the extent of the preference or relation, if any, of such dividends to
the dividends payable on any other class or series of stock of the Corporation,
and whether such dividends shall be cumulative or accruing;

          3.  The right or obligation, if any, of the Corporation to redeem
shares of the particular series of Preferred Stock and, if redeemable, the
price, terms, conditions and manner of such redemption;

          4.  The special and relative rights and preferences, if any, and the
amount or amounts per share, which the shares of such series of Preferred Stock
shall be entitled to receive upon any voluntary or involuntary liquidation,
dissolution or winding up of the Corporation or in the event of any merger or
consolidation of or sale of assets by the Corporation;

          5.  The right, if any, of the holders of such series of Preferred
Stock to convert the same into, or exchange the same for, shares of any other
class or series of stock of the Corporation, and the terms and conditions of
such conversion or exchange, including the price or prices or the rate or rates
of conversion or exchange and the terms of adjustment, if any;

          6.  The terms of any sinking fund or redemption or repurchase or
purchase account, if any, the obligation, if any, of the Corporation to retire,
redeem, repurchase or purchase shares of such series pursuant to such fund or
account, and the terms and conditions of such obligation;

          7.  The voting powers, if any, of the holders of such series of
Preferred Stock generally or with respect to any particular matter, which may be
less than, equal to or greater than one vote per share, and which may, without
limiting the generality of the foregoing, include the right, voting as a series
by itself or together with the holders of any other series of Preferred Stock or
all series of Preferred Stock as a class, to elect one or more directors of the
Corporation generally or under such specific circumstances and on such
conditions as shall be provided in the Certificate of Designation, including,
without limitation, in the event there shall have been a default in the payment
of dividends on or redemption of any one or more series of Preferred Stock;

          8.  Limitations, if any, on the issuance of additional shares of such
series or any shares of any other class or series of stock of the Corporation;
and

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          9.  Such other preferences, powers, and special, participating,
optional, relative or other rights, and the qualifications, limitations and
restrictions thereof, as the Board of Directors shall determine.

          The number of authorized shares of Preferred Stock may be increased
but not decreased (but not below the number of shares then outstanding) by the
affirmative vote of the holders of a majority of the voting power of all of the
then outstanding shares of capital stock of the Corporation entitled to vote
generally in the election of directors (the "Voting Stock"), voting together as
a single class, without a separate vote of the holders of the Preferred Stock,
or any series thereof, unless a vote of any such holders is required pursuant to
any Certificate of Designation for such series.

          FIFTH:  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)  Number of Directors.  Subject to the rights of the holders of any
        -------------------
series of Preferred Stock to elect additional directors under specified
circumstances, the number of directors shall be fixed from time to time
exclusively by the Board of Directors pursuant to a resolution adopted by a
majority of the total number of directors which the Corporation would have if
there were no vacancies (the "Whole Board").

   (B)  Election and Term of Directors.  Elections of directors need not be by
        ------------------------------
written ballot, except as and to the extent provided in the Bylaws of the
Corporation. Stockholders of the Corporation shall not have the right to
cumulate their votes for the election of directors of the Corporation.  Subject
to the rights of the holders of any series of Preferred Stock to elect
additional directors under specified circumstances, the Board of Directors shall
be classified, with respect to the time for which the directors severally hold
office, into three classes, as nearly equal as possible in number of directors,
as determined by the Board of Directors, one class to be originally elected in
2000 for a term expiring at the annual meeting of stockholders to be held in
2001, another class to be originally elected in 2000 for a term expiring at the
annual meeting of stockholders to be held in 2002, and another class to be
originally elected in 2000 for a term expiring at the annual meeting of
stockholders to be held in 2003, with each class to hold office until its
successors is elected and qualified.  At each annual meeting of the stockholders
of the Corporation, the successors of the class of directors whose term expires
at that annual meeting of stockholders shall be elected to hold office for a
term expiring at the annual meeting of stockholders held in the third year
following the year of their election.  Notwithstanding the foregoing provisions
of this section, each director shall serve until his or her successor shall have
been duly elected and qualified or until such director's earlier death,
resignation or removal.

   (C)  Newly Created Directorships and Vacancies.  Subject to the rights of
          -----------------------------------------
any holders of any series of Preferred Stock to elect additional directors under
specified circumstances, and unless the Board of Directors otherwise determines,
newly created directorships resulting from any increase in the authorized number
of directors or any vacancies of the Board of Directors resulting from death,
resignation, retirement, disqualification, removal from office or other causes
shall be filled only by a majority vote of the directors then in office, though
less than a

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and directors so chosen shall hold office for a term for the remainder of the
full term of the class of directors in which the vacancy occurred or in which
the new directorship was created and until such director's successor shall have
been duly elected and qualified. No decrease in the numbers of authorized
directors constituting the entire Board of Directors shall shorten the term of
any incumbent director.

     (D)  Removal of Directors.  Subject to the rights of holders of any series
          --------------------
of Preferred Stock to elect additional directors under specified circumstances,
any director, or the entire Board of Directors, may be removed from office at
any time, but only for cause.

     (E)  Stockholder Nomination of Director Candidates and Introduction of
          -----------------------------------------------------------------
Business.  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.

     (F)  No Action Without Annual or Special Meeting.  Subject to the rights of
          -------------------------------------------
the holders of any series of Preferred Stock with respect to such series, (A)
any action required or permitted by the General Corporation Law of the State of
Delaware to be taken by the stockholders of the Corporation must be effected at
an annual or special meeting of the stockholders and may not be effected by any
consent in writing in lieu of a meeting by such stockholders; and (B) special
meetings of the stockholders may be called only by the Chairman of the Board or
by a majority of the Whole Board.

     (G)  Alteration, Amendment or Repeal.  Notwithstanding any other provisions
          -------------------------------
of this Certificate of Incorporation or any provision of law which might
otherwise permit a lesser vote or no vote, but in addition to any affirmative
vote of the holders of any particular class or series of the capital stock of
the Corporation required by law, this Certificate of Incorporation or any
Certificate of Designation for any series of Preferred Stock, the affirmative
vote of the holders of at least 80 percent of the voting power of all of the
then-outstanding shares of the Voting Stock of the Corporation, voting together
as a single class, shall be required in order for the stockholders to alter,
amend or repeal this Article FIFTH.

          SIXTH:  In furtherance and not in limitation of the powers conferred
by law, the Board of Directors of the Corporation is expressly authorized and
empowered to make, alter, amend and repeal the Bylaws of the Corporation,
subject to the power of the holders of the capital stock of the Corporation to
make, alter, amend or repeal the Bylaws; provided, however, that,
                                         -----------------
notwithstanding any other provisions of this Certificate of Incorporation, the
Bylaws or any provision of law which might otherwise permit a lesser vote or no
vote, but in addition to any affirmative vote of the holders of any particular
class or series of the capital stock of the Corporation required by law, this
Certificate of Incorporation, any Certificate of Designation for any series of
Preferred Stock, or the Bylaws, the affirmative vote of the holders of at least
80 percent of the voting power of all of the then-outstanding shares of the
Voting Stock of the Corporation, voting together as a single class, shall be
required to alter, amend or repeal this ARTICLE SIXTH or in order for the
stockholders to alter, amend or repeal any provision of the Bylaws of the
Corporation or to adopt any additional bylaws.

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          SEVENTH:  A director of the Corporation shall not be personally liable
to the Corporation or its stockholders for monetary damages for breach of
fiduciary duty as a director, except for liability (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 amended to authorize corporate action further eliminating
or limiting the liability of directors, then the liability of a director of the
Corporation shall be eliminated or limited to the fullest extent permitted by
the General Corporation Law of the State of Delaware, as so amended.  Any
amendment, alteration, change or repeal of this Article SEVENTH by the
stockholders of the Corporation shall not adversely affect any right or
protection of a director of the Corporation existing at the time of such repeal
or modification.

     EIGHTH:  (A)  Right to Indemnification.  The Corporation shall indemnify
                   ------------------------
and hold harmless, to the fullest extent permitted by applicable law as it
presently exists or may hereafter be amended, any person (an "Indemnitee") who
was or is made or is threatened to be made a party or is otherwise involved in
any action, suit or proceeding, whether civil, criminal, administrative or
investigative (a "proceeding"), by reason of the fact that he, or a person for
whom he is the legal representative, is or was a director or officer of the
Corporation or, while a director or officer of the Corporation, is or was
serving at the request of the Corporation as a director, officer, employee or
agent of another corporation or of a partnership, joint venture, trust,
enterprise or nonprofit entity, including service with respect to employee
benefit plans, against all liability and loss suffered and expenses (including
attorneys' fees) reasonably incurred by such Indemnitee.  Notwithstanding the
preceding sentence, except as otherwise provided in Section (C) of this Article
EIGHTH, the Corporation shall be required to indemnify an Indemnitee in
connection with a proceeding (or part thereof) commenced by such Indemnitee only
if the commencement of such proceeding (or part thereof) by the Indemnitee was
authorized by the Board of Directors of the Corporation.

     (B)  Prepayment of Expenses.  The Corporation shall pay the expenses
          ----------------------
(including attorneys' fees) incurred by an Indemnitee in defending any
proceeding in advance of its final disposition, provided, however, that, to the
                                                --------  -------
extent required by law, such payment of expenses in advance of the final
disposition of the proceeding shall be made only upon receipt of an undertaking
by the Indemnitee to repay all amounts advanced if it should be ultimately
determined that the Indemnitee is not entitled to be indemnified under this
Article EIGHTH or otherwise.

     (C)  Claims.  If a claim for indemnification or payment of expenses under
          ------
this Article EIGHTH is not paid in full within sixty days after a written claim
therefor by the Indemnitee has been received by the Corporation, the Indemnitee
may file suit to recover the unpaid amount of such claim and, if successful in
whole or in part, shall be entitled to be paid the expense of prosecuting such
claim.  In any such action the Corporation shall have the burden of proving that
the Indemnitee is not entitled to the requested indemnification or payment of
expenses under applicable law.

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     (D)  Nonexclusivity of Rights.  The rights conferred on any Indemnitee by
          ------------------------
this Article EIGHTH shall not be exclusive of any other rights which such
Indemnitee may have or hereafter acquire under any statute, provision of this
Certificate of Incorporation, Bylaws, agreement, vote of stockholders or
disinterested directors or otherwise.

     (E)  Other Sources.  The Corporation's obligation, if any, to indemnify or
          -------------
to advance expenses to any Indemnitee who was or is serving at its request as a
director, officer, employee or agent of another corporation, partnership, joint
venture, trust, enterprise or nonprofit entity shall be reduced by any amount
such Indemnitee may collect as indemnification or advancement of expenses from
such other corporation, partnership, joint venture, trust, enterprise or
nonprofit enterprise.

     (F)  Amendment or Repeal.  Any repeal or modification of the foregoing
          -------------------
provisions of this Article EIGHTH shall not adversely affect any right or
protection hereunder of any Indemnitee in respect of any act or omission
occurring prior to the time of such repeal or modification.

     (G)  Other Indemnification and Prepayment of Expenses.  This Article EIGHTH
          ------------------------------------------------
shall not limit the right of the Corporation, to the extent and in the manner
permitted by law, to indemnify and to advance expenses to persons other than
Indemnitees when and as authorized by appropriate corporate action.

          NINTH:  The Corporation reserves the right to amend, alter, change or
repeal any provision contained in this Certificate of Incorporation, and any
other provisions authorized by the laws of the State of Delaware at the time in
force may be added or inserted, in the manner now or hereafter provided herein
or by statute, and all rights, preferences and privileges of whatsoever nature
conferred upon stockholders, directors or any other persons whomsoever by and
pursuant to this Certificate of Incorporation in its present form or as amended
are granted subject to the rights reserved in this Article NINTH.

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     IN WITNESS WHEREOF, the Corporation has caused this Ninth Restated
Certificate of Incorporation to be signed by its Chief Executive Officer this
_____ day of _____________, 2000.


                                        3-DIMENSIONAL PHARMACEUTICALS, INC.



                                        By:___________________________________
                                             David C. U'Prichard
                                             Chief Executive Officer

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