<PAGE>

                                                                   EXHIBIT 10.31

     THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES
     ACT OF 1933. THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED, OR
     HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION
     STATEMENT RELATED THERETO OR AN OPINION OF COUNSEL (WHICH MAY BE
     COMPANY COUNSEL) REASONABLY SATISFACTORY TO THE COMPANY THAT SUCH
     REGISTRATION IS NOT REQUIRED UNDER THE SECURITIES ACT OF 1933.

                               WARRANT AGREEMENT

                 To Purchase Shares of the Preferred Stock of

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

         Originally Dated as of April 25, 1995 (the "Effective Date")

                         Reissued as of July 21, 1998

     WHEREAS, 3-Dimensional Pharmaceuticals, Inc., a Delaware corporation (the
"Company") - has entered into a Master Lease Agreement dated as of March 7, 1994
and Equipment Schedule No. VL-2 dated as of April 25, 1995, and related
Schedules (the "Leases") with Comdisco, Inc., a Delaware corporation (the
"Warrantholder") and

     WHEREAS, the Company desires to grant to Warrantholder, in consideration
for such Leases, the right to purchase shares of its Series A Preferred Stock;

     NOW, THEREFORE, in consideration of the Warrantholder executing and
delivering such Leases and in consideration of mutual covenants and agreements
contained herein, the Company and Warrantholder agree as follows:

1.   GRANT OF THE RIGHT TO PURCHASE PREFERRED STOCK.
     ----------------------------------------------

     The Company hereby grants to the Warrantholder, and the Warrantholder is
entitled, upon the terms and subject to the conditions hereinafter set forth, to
subscribe to and purchase, from the Company, 54,113 fully paid and non-
assessable shares of the Company's Series A Preferred Stock ("Preferred Stock")
at a purchase price of $1.00 per share (the "Exercise Price"). The number and
purchase price of such shares are subject to adjustment as provided in Section 8
hereof.

                                       1
<PAGE>

2.   TERM OF THE WARRANT AGREEMENT.
     -----------------------------

     Except as otherwise provided for herein, the term of this Warrant Agreement
and the right to purchase Preferred Stock as granted herein shall commence on
the Effective Date and shall be exercisable for a period of (i) ten (10) years
or (ii) five (5) years from the effective date of the Company's initial public
offering, whichever is longer.

3.   EXERCISE OF THE PURCHASE RIGHTS.
     -------------------------------

     The purchase rights set forth in this Warrant Agreement are exercisable by
the Warrantholder, in whole or in part, at any time, or from time to time, prior
to the expiration of the term set forth in Section 2 above, by tendering to the
Company at its principal office a notice of exercise in the form attached hereto
as Exhibit I (the "Notice of Exercise"), duly completed and executed. Promptly
upon receipt of the Notice of Exercise and the payment of the purchase price in
accordance with the terms set forth below, and in no event later than twenty-one
(21) days thereafter, the company shall issue to the Warrantholder a certificate
for the number of shares of Preferred Stock purchased and shall execute the
Notice of Exercise indicating the number of shares which remain subject to
future purchases, if any.

The Exercise Price may be paid at the Warrantholder's election either (i) by
cash or check, or (ii) by surrender of Warrants ("Net Issuance") as determined
below. If the Warrantholder elects the Net Issuance method, the Company will
issue Preferred Stock in accordance with the following formula:

          X   =    Y(A-B)
                   ------

                      A

Where:    X   =    the number of shares of Preferred Stock to be issued to the
                   warrantholder.

          Y   =    the number of shares of Preferred Stock requested to be
                   exercised under this Warrant Agreement.

          A   =    the fair market value of one (1) share of Common Stock.

          B   =    the Exercise Price.

     As used herein, current fair market value of Common Stock shall mean with
respect to each share of Common Stock:

     (i)  if the exercise is in connection with an initial public offering, and
     if the Company's Registration Statement relating to such public offering
     has been declared effective by the SEC, then the initial "Price to Public"
     specified in the final prospectus with respect to the offering;

                                       2
<PAGE>

      (ii) if this Warrant is exercised after, and not in connection with the
      Company's initial public offering, and:

           (a)  if traded on a securities exchange, the fair market value shall
be deemed to be the average of the closing prices on the principal securities
exchange over a twenty-one (21) day period ending three days before the day the
current fair market value of the securities is being determined; or

           (b)  if actively traded over-the-counter, the fair market value shall
be deemed to be the average of the closing bid and asked prices quoted on the
NASDAQ system (or similar system) over the twenty-one (21) day period ending
three days before the day the current fair market value of the securities is
being determined;

(iii) if at any time the Common Stock is not listed on any securities exchange
      or quoted in the NASDAQ System or the over-the-counter market, the current
      fair market value of Common Stock shall be the highest price per share
      which the Company could obtain from a willing buyer (not a current
      employee or director) for shares of Common Stock sold by the Company, from
      authorized but unissued shares, as determined in good faith by its Board
      of Directors, unless the Company shall become subject to a merger,
      acquisition or other consolidation pursuant to which the company is not
      the surviving party, in which case the fair market value of Common Stock
      shall be deemed to be the value received by the holders of the Company's
      Preferred Stock on a common equivalent basis pursuant to such merger or
      acquisition.

      Upon partial exercise by either cash or Net Issuance, the Company shall
promptly issue an amended Warrant Agreement representing the remaining number of
shares purchasable hereunder. All other terms and conditions of such amended
Warrant Agreement shall be identical to those contained herein, including, but
not limited to the Effective Date hereof.

4.    RESERVATION OF SHARES.
      ---------------------

      (a) Authorization and Reservation of Shares. During the term of this
          ---------------------------------------
Warrant Agreement, the Company will at all times have authorized and reserved a
sufficient number of shares of its Preferred Stock to provide for the exercise
of the rights to purchase Preferred Stock as provided for herein.

      (b) Registration or List. If any shares of Preferred Stock required to
          --------------------
be reserved hereunder require registration with or approval of any governmental
authority under any Federal or State law (other than any registration under the
1933 Act, as then in effect, or any similar Federal statute then enforced, or
any state securities law, required by reason of any transfer involved in such
conversion), or listing on any domestic securities exchange, before such shares
may be issued upon conversion, the Company will, at its expense and as
expeditiously as possible, use its best efforts to cause such shares to be duly
registered, listed or approved for listing on such domestic securities exchange,
as the case may be.

                                       3
<PAGE>

5.   NO FRACTIONAL SHARES OR SCRIP.
     -----------------------------

     No fractional shares or scrip representing fractional shares shall be
issued upon the exercise of the Warrant, but in lieu of such fractional shares
the Company shall make a cash payment therefor upon the basis of the Exercise
Price then in effect.

6.   NO RIGHTS AS SHAREHOLDER.
     ------------------------

     This Warrant Agreement does not entitle the Warrantholder to any voting
rights, the right to receive cash dividends or other rights as a shareholder of
the Company prior to the exercise of the Warrant.

7.   WARRANTHOLDER REGISTRY.
     ----------------------

     The Company shall maintain a registry showing the name and address of the
registered holder of this Warrant Agreement.

8.   ADJUSTMENT RIGHTS.
     -----------------

     The purchase price per share and the number of shares of Preferred Stock
purchasable hereunder are subject to adjustment, as follows:

     (a)  Merger and Sale of Assets. If at any time there shall be a capital
reorganization of the shares of the Company's Preferred Stock (other than a
combination, reclassification, exchange or subdivision of shares otherwise
provided for herein), or a merger or consolidation of the Company with or into
another corporation when the Company is not the surviving corporation, or the
sale of all or substantially all of the Company's properties and assets to any
other person (hereinafter referred to as a "Merger Event"), then, as a part of
such Merger Event, lawful provision shall be made so that the Warrantholder
shall thereafter be entitled to receive, upon exercise of the Warrant, the
number of shares of Preferred Stock or other securities of the successor
corporation resulting from such Merger Event, equivalent in value to that which
would have been issuable if Warrantholder had exercised this Warrant immediately
prior to the Merger Event. In any such case, appropriate adjustment (as
determined in good faith by the Company's Board of Directors) shall be made in
the application of the provisions of this Warrant Agreement with respect to the
rights and interest of the Warrantholder after the Merger Event to the end that
the provisions of this Warrant Agreement (including adjustments of the Exercise
Price and number of shares of Preferred Stock purchasable) shall be applicable
to the greatest extent possible.

                                       4
<PAGE>

     (b)  Reclassification of Shares. If the Company at any time shall, by
          --------------------------
combination, reclassification, exchange or subdivision of securities or
otherwise, change any of the securities as to which purchase rights under this
Warrant Agreement exist into the same or a different number of securities of any
other class or classes, this Warrant Agreement shall thereafter represent the
right to acquire such number and kind of securities as would have been issuable
as the result of such change with respect to the securities which were subject
to the purchase rights under this Warrant Agreement immediately prior to such
combination, reclassification, exchange, subdivision or other change.

     (c)  Subdivision or Combination of Shares. If the Company at any time shall
          ------------------------------------
combine or subdivide its Preferred Stock, the Exercise Price shall be
proportionately decreased in the case of a subdivision, or proportionately
increased in the case of a combination.

     (d)  Stock Dividends. If the Company at any time shall pay a dividend
          ---------------
payable in, or make any other distribution (except any distribution specifically
provided for in the foregoing subsections (a) or (b)) of the Company's stock,
then the Exercise Price shall be adjusted, from and after the record date of
such dividend or distribution, to that price determined by multiplying the
Exercise Price in effect immediately prior to such record date by a fraction (i)
the numerator of which shall be the total number of all shares of the Company's
stock out-standing immediately prior to such dividend or distribution, and (ii)
the denominator of which shall be the total number of all shares of the
Company's stock outstanding immediately after such dividend or distribution. The
Warrantholder shall thereafter be entitled to purchase, at the Exercise Price
resulting from such adjustment, the number of shares of Preferred Stock
(calculated to the nearest whole share) obtained by multiplying the Exercise
Price in effect immediately prior to such adjustment by the number of shares of
Preferred Stock issuable upon the exercise hereof immediately prior to such
adjustment and dividing the product thereof by the Exercise Price resulting from
such adjustment. Notwithstanding the foregoing, no adjustment shall be made for
a dividend payable in the Company's Common Stock if adjustment hereunder would
compound an adjustment made upon conversion of the Preferred Stock issuable upon
exercise of this Warrant into Common Stock, which would result in double
adjustment for a single Common Stock dividend.

     (e)  Right to Purchase Additional Stock.If, the Warrantholder's total cost
          ----------------------------------
of equipment leased pursuant to the Leases exceeds $1,500,000.00, Warrantholder
shall have the right to purchase from the Company, at the Exercise Price
(adjusted as set forth herein), an additional number of shares, which number
shall be determined by (i) multiplying the amount by which the Warrantholder's
total equipment cost exceeds $1,500,000.00 by 9.25%, and (ii) dividing the
product thereof by the Exercise Price per share referenced above.

     (f)  Antidilution Rights; Notice of Stock Issuance. Additional antidilution
          ---------------------------------------------
rights applicable to the Preferred Stock purchasable hereunder are as set forth
in the Company's Restated certificate of Incorporation, as amended through the
Effective Date, a true and complete copy of which is attached hereto as Exhibit
III(the "Charter"). The Company shall promptly provide the Warrantholder with
any restatement, amendment, modification or waiver of the Charter. The Company
shall provide Warrantholder with prior written notice of any issuance of

                                       5
<PAGE>

its stock or other equity security to occur after the Effective Date of this
Warrant, other than Excluded Stock, as defined in the Charter, which notice
shall include (a) the price at which such stock or security is to be sold, (b)
the number of shares to be issued, and (c) such other information as necessary
for Warrantholder to determine if a dilutive event has occurred.

     (g)  Notice of Adjustments. If: (i) the Company shall declare any dividend
          ---------------------
or distribution upon its stock, whether in cash (except for regular cash
dividends as set forth in the terms of the Preferred Stock Section 4 A(l) (d) of
the Charter), property, stock or other securities; (ii) the Company shall offer
for subscription prorata to the holders of any class of its Preferred or other
convertible stock any additional shares of stock of any class or other rights;
(iii) there shall be any Merger Event; or (iv) there shall be any voluntary or
involuntary dissolution, liquidation or winding up of the Company; then, in
connection with each such event, the Company shall send to the Warrantholder:
(A) at least twenty (20) days" prior written notice of the date on which the
books of the Company shall close or a record shall be taken for such dividend,
distribution, subscription rights (specifying the date on which the holders of
Preferred Stock shall be entitled thereto) or for determining rights to vote in
respect of such Merger Event, dissolution, liquidation or winding up, and (B) in
the case of any such Merger Event, dissolution, liquidation or winding up, at
least twenty (20) days" prior written notice of the date when the same shall
take place (and specifying the date on which the holders of Preferred Stock
shall be entitled to exchange their Preferred Stock for securities or other
property deliverable upon such Merger Event, dissolution, liquidation or winding
up). In the case of a public offering, the Company shall give Warrantholder at
least twenty (20) days written notice prior to the effective date thereof.

     Each such written notice shall set forth, in reasonable detail, (i) the
event requiring the adjustment, (ii) the amount of the adjustment, (iii) the
method by which such adjustment was calculated, (iv) the Exercise Price, and (v)
the number of shares subject to purchase hereunder after giving effect to such
adjustment, and shall be given by first class mail, postage prepaid, addressed
to the Warrantholder, at the address as shown on the books of the Company.

     (h)  Timely Notice. Failure to timely provide such notice required by
          -------------
subsection (g) above shall entitle Warrantholder to retain the benefit of the
applicable notice period notwithstanding anything to the contrary contained in
any insufficient notice received by Warrantholder. The notice period shall begin
on the date Warrantholder actually receives a written notice containing all the
information specified above.

9.   REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE COMPANY.
     --------------------------------------------------------

     (a)  Reservation of Preferred Stock. The Preferred Stock issuable upon
          ------------------------------
exercise of the Warrantholder's rights, except with respect to Section e(e)
hereof, has been duly and validly reserved and, when issued in accordance with
the provisions of this Warrant Agreement, will be validly issued, fully paid and
non-assessable, and will be free of any taxes, liens, charges or encumbrances of
any nature whatsoever; provided, however, that the Preferred Stock issuable
pursuant to this Warrant Agreement may be subject to restrictions on transfer
under state and/or Federal securities laws. The Company has made available to
the Warrantholder true, correct

                                       6
<PAGE>

and complete copies of its Charter and Bylaws, as amended, and minutes of all
Board of Directors (including all committees of the Board of Directors, if any)
and Shareholder meetings from March 11, 1993 through February 15, 1995. The
issuance of certificates for shares of Preferred Stock upon exercise of the
Warrant Agreement shall be made without charge to the Warrantholder for any
issuance tax in respect thereof, or other cost incurred by the Company in
connection with such exercise and the related issuance of shares of Preferred
Stock. The Company shall not be required to pay any tax which may be payable in
respect of any transfer involved and the issuance and delivery of any
certificate in a name other than that of the Warrantholder.

     (b)  Due Authority. The execution and delivery by the Company of this
          -------------
Warrant Agreement and the performance of all obligations of the Company
hereunder, including the issuance to Warrantholder of the right to acquire the
shares of Preferred Stock, have been duly authorized by all necessary corporate
action on the part of the Company, and the Leases and this Warrant Agreement are
not inconsistent with the Company's Charter or Bylaws, do not contravene any law
or governmental rule, regulation or order applicable to it, do not and will not
contravene any provision of, or constitute a default under, any indenture,
mortgage, contract or other instrument to which it is a party or by which it is
bound, and the Leases and this Warrant Agreement constitute legal, valid and
binding agreements of the Company, enforceable in accordance with their
respective terms.

     (c)  Consents and Approvals. No consent or approval of, giving of notice
          ----------------------
to, registration with, or taking of any other action in respect of any state,
Federal or other governmental authority or agency is required with respect to
the execution, delivery and performance by the Company of its obligations under
this Warrant Agreement.

     (d)  Issued Securities. All issued and outstanding shares of Common Stock,
          -----------------
Preferred Stock or any other securities of the Company have been duly authorized
and validly issued and are fully paid and nonassessable. All outstanding shares
of Common Stock, Preferred Stock and any other securities were issued in full
compliance with all Federal and state securities laws. In addition:

          (i)  The authorized capital of the Company consists of (A) 5,038,100
shares of Common Stock, of which 405,000 shares are issued and outstanding, and
(B) 3,928,100 shares of preferred stock, of which 3,610,000 shares are issued
and outstanding and are convertible into 3,610,000 shares of Common Stock at
$1.00 per share.

          (ii) The Company has reserved 810,000 shares of Common Stock for
issuance under its Equity Compensation Plan, under which 280,950 options are
outstanding, and 405,000 shares of restricted stock are outstanding. With the
exception of: (A) the Warrant Agreement dated March 7, 1994, issued to Comdisco,
Inc. for 179,350 shares of the Company's Series A Preferred Stock and (B) a
Warrant Agreement to be issued pursuant to a Loan Agreement dated as of December
15, 1994 between the Company and their Venture Capital investors for a maximum
of 300,000 shares of the Company's Common Stock; there are no other options,

                                       7
<PAGE>

warrants, conversion privileges or other rights presently outstanding to
purchase or otherwise acquire any authorized but unissued shares of the
Company's capital stock or other securities of the Company.

          (iii)  Except as set forth in Section 4 of the Company's Stockholders'
Agreement dated October 15, 1993, as amended (the 'Stockholders' Agreement"), no
shareholder of the Company has preemptive rights to purchase new issuances of
the Company's capital stock.

     (e)  Insurance. The Company has in full force and effect insurance
          ---------
policies, with extended coverage, insuring the Company and its property and
business against such losses and risks, and in such amounts, as are customary
for corporations engaged in a similar business and similarly situated and as
otherwise may be required pursuant to the terms of any other contract or
agreement.

     (f)  Other Commitments to Register Securities. Except as set forth in this
          ----------------------------------------
Stockholders" Agreement, the Company is not, pursuant to the terms of any other
agreement currently in existence, under any obligation to register under the
1933 Act any of its presently outstanding securities or any of its securities
which may hereafter be issued.

     (g)  Exempt Transaction. Subject to the accuracy of the Warrantholder's
          ------------------
representations in Section 10 hereof, the issuance of the Preferred Stock upon
exercise of this Warrant will constitute a transaction exempt from (i) the
registration requirements of Section 5 of the 1933 Act, in reliance upon Section
4(2) thereof, and (ii) the qualification requirements of the Illinois Securities
Law of 1953, in reliance upon Section 4(c) thereof.

     (h)  Compliance with Rule 144. At the written request of the Warrantholder,
          ------------------------
who proposes to sell Preferred Stock issuable upon the exercise of the Warrant
in compliance with Rule 144 promulgated by the Securities and Exchange
Commission, the Company shall furnish to the Warrantholder, within ten days
after receipt of such request, a written statement confirming the Company's
compliance with the filing requirements of the Securities and Exchange
Commission as set forth in such Rule, as such Rule may be amended from time to
time.

10.  REPRESENTATIONS AND COVENANTS OF THE WARRANTHOLDER.
     --------------------------------------------------

     This Warrant Agreement has been entered into by the Company in reliance
upon the following representations and covenants of the Warrantholder:

     (a)  Investment Purpose. The right to acquire Preferred Stock or the
          ------------------
Preferred Stock issuable upon exercise of the Warrantholder's rights contained
herein and the Common Stock issuable upon conversion of the Preferred Stock will
be acquired for investment and not with a view to the sale or distribution of
any part thereof, and the Warrantholder has no present

                                       8
<PAGE>

intention of selling or engaging in any public distribution of the same except
pursuant to a registration or exemption.

     (b)  Private Issue. The Warrantholder understands (i) that the Preferred
          -------------
Stock issuable upon exercise of this Warrant and the Common Stock issuable upon
conversion of the Preferred Stock are not registered under the 1933 Act or
qualified under applicable state securities laws on the ground that the issuance
contemplated by this Warrant Agreement will be exempt from the registration and
qualifications requirements thereof, and (ii) that the Company's reliance on
such exemption is predicated on the representations set forth in this Section
10.

     (c)  Disposition of Warrantholder's Rights. In no event will the
          -------------------------------------
Warrantholder make a disposition of any of its rights to acquire Preferred Stock
or Preferred Stock issuable upon exercise of such rights unless and until (i) it
shall have notified the Company of the proposed disposition, and (ii) if
requested by the Company, it shall have furnished the Company with an opinion of
counsel (which counsel may either be inside or outside counsel to the
Warrantholder) satisfactory to the Company and its counsel to the effect that
(A) appropriate action necessary for compliance with the 1933 Act has been
taken, or (B) an exemption from the registration requirements of the 1933 Act is
available. Notwithstanding the foregoing, the restrictions imposed upon the
transferability of any of its rights to acquire Preferred Stock or Preferred
Stock issuable on the exercise of such rights of or the Common Stock issuable
upon conversion of the Preferred Stock do not apply to transfers from the
beneficial owner of any of the aforementioned securities to its nominee or from
such nominee to its beneficial owner, and shall terminate as to any particular
share of Preferred Stock or Common Stock when (1) such security shall have been
effectively registered under the 1933 Act and sold by the holder thereof in
accordance with such registration or (2) such security shall have been sold
without registration in compliance with Rule 144 under the 1933 Act, or (3) a
letter shall have been issued to the Warrantholder at its request by the staff
of the Securities and Exchange Commission or a ruling shall have been issued to
the Warrantholder at its request by such Commission stating that no action shall
be recommended by such staff or taken by such Commission, as the case may be, if
such security is transferred without registration under the 1933 Act in
accordance with the conditions set forth in such letter or ruling and such
letter or ruling specifies that no subsequent restrictions on transfer are
required. Whenever the restrictions imposed hereunder shall terminate, as
hereinabove provided, the Warrantholder or holder of a share of Preferred Stock
or Common Stock then outstanding as to which such restrictions have terminated
shall be entitled to receive from the Company, without expense to such holder,
one or more new certificates for the Warrant or for such shares of Preferred
Stock or Common Stock not bearing any restrictive legend.

     (d)  Financial Risk. The Warrantholder has such knowledge and experience
          --------------
in financial and business matters as to be capable of evaluating the merits and
risks of its investment, and has the ability to bear the economic risks of its
investment.

     (e)  Risk of No Registration. The Warrantholder understands that if the
          -----------------------
Company does not register with the Securities and Exchange Commission pursuant
to Section 12 of the 1934 Act, or file reports pursuant to Section 15(d), of the
Securities Exchange Act of 1934 (the

                                       9
<PAGE>

"1934 Act"), or if a registration statement covering the securities under the
1933 Act is not in effect when it desires to sell (i) the rights to purchase
Preferred Stock pursuant to this Warrant Agreement, or (ii) the Preferred Stock
issuable upon exercise of the right to purchase, it may be required to hold such
securities for an indefinite period. The Warrantholder also understands that any
sale of its rights of the Warrantholder to purchase Preferred Stock or Preferred
Stock which might be made by it in reliance upon Rule 144 under the 1933 Act may
be made only in accordance with the terms and conditions of that Rule.

11.  TRANSFERS. Subject to the terms and conditions contained in Section 10
     ---------
hereof, this Warrant Agreement and all rights hereunder are transferable in
whole or in part by the Warrantholder and any successor transferee, provided,
however, in no event shall the number of transfers of the rights and interests
in all of the Warrants exceed three (3) transfers. The transfer shall be
recorded on the books of the Company upon receipt by the Company of a notice of
transfer in the form attached hereto as Exhibit II (the "Transfer Notice"), at
its principal offices and the payment to the Company of all transfer taxes and
other governmental charges imposed on such transfer.

12.  MISCELLANEOUS.
     -------------

     (a)  Effective Date. The provisions of this Warrant Agreement shall be
          --------------
construed and shall be given effect in all respects as if it had been executed
and delivered by the Company on the date hereof. This Warrant Agreement shall be
binding upon any successors or assigns of the Company.

     (b)  Attorney's Fees. In any litigation, arbitration or court proceeding
          ---------------
between the Company and the Warrantholder relating hereto, the prevailing party
shall be entitled to attorneys" fees and expenses and all costs of proceedings
incurred in enforcing this Warrant Agreement.

     (c)  Governing Law. This Warrant Agreement shall be governed by and
          -------------
construed for all purposes under and in accordance with the laws of the State of
Illinois.

     (d)  Counterparts. This Warrant Agreement may be executed in two or more
          ------------
counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument.

     (e)  Notices. Any notice required or permitted hereunder shall be given in
          -------
writing and shall be deemed effectively given upon personal delivery, facsimile
transmission (provided that the original is sent by personal delivery or mail as
hereinafter set forth) or seven (7) days after deposit in the United States
mail, by registered or certified mail, addressed (i) to the Warrantholder at
6111 North River Road, Rosemont, Illinois 60018, attention: James Labe, Venture
Leasing Director, cc: Legal Department, (and/or, if by facsimile, (847) 518-
5465) and (ii) to the Company at Eagleview Corporate Center, 665 Stockton Drive,
Suite 104 Exton,

                                       10
<PAGE>

Pennsylvania 19341, (and/or, if by facsimile, (610) 458-8249) or at such other
address as any such party may subsequently designate by written notice to the
other party.

     (f)  Remedies. In the event of any default hereunder, the non-defaulting
          --------
party may proceed to protect and enforce its rights either by suit in equity
and/or by action at law, including but not limited to an action for damages as a
result of any such default, and/or an action for specific performance for any
default where Warrantholder will not have an adequate remedy at law and where
damages will not be readily ascertainable. The Company expressly agrees that it
shall not oppose an application by the Warrantholder or any other person
entitled to the benefit of this Agreement requiring specific performance of any
or all provisions hereof or enjoining the Company from continuing to commit any
such breach of this Agreement.

     (g)  No Impairment of Rights. The Company will not, by amendment of its
          -----------------------
Charter or through any other means, avoid or seek to avoid the observance or
performance of any of the terms of this Warrant, but will at all times in good
faith assist in the carrying out of all such terms and in the taking of all such
actions as may be necessary or appropriate in order to protect the rights of the
Warrantholder against impairment.

     (h)  Survival. The representations, warranties, covenants and conditions of
          --------
the respective parties contained herein or made pursuant to this Warrant
Agreement shall survive the execution and delivery of this Warrant Agreement.

     (i)  Severability. In the event any one or more of the provisions of this
          ------------
Warrant Agreement shall for any reason be held invalid, illegal or
unenforceable, the remaining provisions of this Warrant Agreement shall be
unimpaired, and the invalid, illegal or unenforceable provision shall be
replaced by a mutually acceptable valid, legal and enforceable provision, which
comes closest to the intention of the parties underlying the invalid, illegal or
unenforceable provision.

     (j)  Amendments. Any provision of this Warrant Agreement may be amended by
          ----------
a  written instrument signed by the Company and by the Warrantholder.

     (k)  Additional Documents. The Company, upon execution of this Warrant
          --------------------
Agreement, shall provide the Warrantholder with certified resolutions with
           -----
respect to the representations, warranties and covenants set forth in
subparagraphs (a) through (d), (f) and (g) of Section 9 above. If the purchase
price for the Leases referenced in the preamble of this Warrant Agreement
exceeds $1,000,000, the Company will also provide Warrantholder with an opinion
from the Company's counsel with respect to those same representations,
warranties and covenants. The Company shall also supply such other documents as
the Warrantholder may from time to time reasonably request.

                                       11
<PAGE>

IN WITNESS WHEREOF, the parties hereto have caused this Warrant Agreement to be
executed by its officers thereunto duly authorized as of the Effective Date.



                                    Company: 3-DIMENSIONAL PHARMACEUTICALS, INC.




                                    By:/s/ Scott Horvitz
                                       -----------------------------

                                    Title: V.P. Finance and Adminstration
                                          -------------------------------

                                    Warrantholder: COMDISCO, INC.

                                    By:/s/ John J. Vosichy
                                       -----------------------------

                                    Title: Executive Vice President and CFO
                                           --------------------------------

DRS; 4/26/95

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<PAGE>

                                   EXHIBIT I

                              NOTICE OF EXERCISE

To:

(1)  The undersigned Warrantholder hereby elects to purchase shares of the
     Series A Preferred Stock of 3-Dimensional Pharmaceuticals, Inc., pursuant
     to the terms of the Warrant Agreement originally dated the 25th day of
     April, 1995 (the "Warrant Agreement") between 3-Dimensional
     Pharmaceuticals, Inc. and the Warrantholder, and tenders herewith payment
     of the purchase price for such shares in full, together with all applicable
     transfer taxes, if any.

(2)  In exercising its rights to purchase the Series A Preferred Stock of 3-
     Dimensional Pharmaceuticals, Inc., the undersigned hereby confirms and
     acknowledges the investment representations and warranties made in Section
     10 of the Warrant Agreement.

(3)  Please issue a certificate or certificates representing said shares of
     Series A Preferred Stock in the name of the undersigned or in such other
     name as is specified below.



_________________________________
(Name)

_________________________________
(Address)

Warrantholder: COMDISCO, INC.


By:______________________________

Title:___________________________

Date:____________________________

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<PAGE>

                          ACKNOWLEDGMENT OF EXERCISE

     The undersigned 3-Dimensional Pharmaceuticals, Inc., hereby acknowledge
receipt of the "Notice of Exercise" from Comdisco, Inc., to purchase ______
shares of the Series A Preferred Stock of 3-Dimensional Pharmaceuticals, Inc.,
pursuant to the terms of the Warrant Agreement, and further acknowledges that
________ shares remain subject to purchase under the terms of the Warrant
Agreement.



                                    Company: 3-Dimensional Pharmaceuticals, Inc.

                                             By:_______________________________

                                             Title:____________________________

                                             Date:_____________________________

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<PAGE>

                                  EXHIBIT II

                               TRANSFERS NOTICE

          (To transfer or assign the foregoing Warrant Agreement
          execute this form and supply required information. Do not
          use this form to purchase shares.)

     FOR VALUE RECEIVED, the foregoing Warrant Agreement and all rights
evidenced thereby are hereby transferred and assigned to _______________________

________________________________________________________________________________

whose address is _______________________________________________________________

________________________________________________________________________________

                    Dated ______________________________________________________

                    Holder's Signature _________________________________________

                    Holder's Address ___________________________________________

                    ____________________________________________________________

Signature Guaranteed: __________________________________________________________

NOTE: The signature to this Transfer Notice must correspond with the name as it
appears on the face of the Warrant Agreement, without alteration or enlargement
or any change whatever. officers of c

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