<PAGE>

                                                                   EXHIBIT 10.29
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 March 7, 1994 (the "Effective Date")
                         Re-Issued 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,
Equipment Schedule No. VL-1, and related Schedules (the "Leases") and a Loan
Agreement and associated Promissory Note dated as of March 7, 1994 (the "Loan")
with CDC Realty Inc., an Illinois corporation (the "Warrantholder"); and

     WHEREAS, the Company desires to grant to Warrantholder, in consideration
for such Leases and the Loan, 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, 161,415 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;

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.
<PAGE>

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;

     (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

                                       2
<PAGE>

               (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. AU 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 Listing. 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.

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.

                                       3
<PAGE>

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 50 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.

     (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 outstanding 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

                                       4
<PAGE>

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 $2,110,000.00,
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 $2,110,000.00 by 8.5%, 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 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(1) (ci)
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

                                       5
<PAGE>

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 8(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 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 April __, 1994. 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

                                       6
<PAGE>

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)
4,599,350 shares of Common Stock, of which 450,000 shares are issued and
outstanding, and (B) 3,789,350 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 112,200 options are
outstanding, and 450,000 shares of restricted stock are outstanding. There are
no other options, 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

                                       7
<PAGE>

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 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

                                       8
<PAGE>

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 "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

                                       9
<PAGE>

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,
Resonant, 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, 655 Stockton Drive, Suite 104, Exton,
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.

                                       10
<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:      Vice President Finance and Administration
                                      ------------------------------------------

                          Warrantholder:   CDC REALTY, INC.

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

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

                                       11
<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 dated the 7th day of March, 1994 (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 under-signed or in such other name
as is specified below.


--------------------------------------
(Name)

--------------------------------------
(Address)


Warrantholder:    CDC REALTY, INC.

By:    _______________________________

Title: _______________________________

Date:  _______________________________

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<PAGE>

                          ACKNOWLEDGEMENT OF EXERCISE

     The undersigned 3-Dimensional Pharmaceuticals, Inc., hereby acknowledge
receipt of the "Notice of Exercise" from CDC Realty, 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:  ____________________________

                                       13
<PAGE>

                                  EXHIBIT II

                                TRANSFER 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

_______________________________________________________________________________
(Please Print)

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 corporations and those acting in a fiduciary or
                  other representative capacity should file proper evidence of
                  authority to assign the foregoing Warrant Agreement.

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