Document:

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                                                                    Exhibit 10.7

            Warrant to Purchase 317,800 Shares of Common Stock or
        such additional shares as this Warrant may entitle the holder
              to purchase pursuant to provisions of this Warrant.

                       WARRANT TO PURCHASE COMMON STOCK

                                      OF

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

          This is to Certify That, FOR VALUE RECEIVED, HealthCare Ventures IV,
L.P. or assigns ("Holder") is entitled to purchase, subject to the provisions of
this Warrant, from 3-Dimensional Pharmaceuticals, Inc., a Delaware corporation
(the "Company"), 317,800 fully paid, validly issued and nonassessable shares of
Common Stock, par value $.001 per share, of the Company ("Common Stock") at a
price of $1.25 per share during the Exercise Period (as defined below).  The
number of shares of Common Stock to be received upon the exercise of this
Warrant and the price to be paid for each share of Common Stock may be adjusted
from time to time as hereinafter set forth.  The shares of Common Stock
deliverable upon such exercise, and as adjusted from time to time, are
hereinafter sometimes referred to as "Warrant Shares" and the exercise price of
a share of Common Stock in effect at any time and as adjusted from time to time
is hereinafter sometimes referred to as the "Exercise Price."  This Warrant is
being issued in connection with the issuance by the Company of Warrants to
purchase shares of Common Stock and promissory notes in the aggregate principal
amount of up to $10,000,000 (the "Notes"), pursuant to a Note and Warrant
Purchase Agreement dated as of November 18, 1999 (the "Agreement").

     1.        EXERCISE OF WARRANT.

          a.        This Warrant may be exercised in whole or in part at any
               time or from time to time on or after November 18, 1999 until 5
               p.m. New York City Time on November 18, 2000 (the "Exercise
               Period"); provided, however, that if such day is a day on which
               banking institutions in the State of New York are authorized by
               law to close, then on the next succeeding day which shall not be
               such a day. This Warrant may be exercised by presentation and
               surrender hereof to the Company at its principal office, or at
               the office of its stock transfer agent, if any, with the Purchase
               Form annexed hereto duly executed and accompanied by payment of
               the Exercise Price for the number of Warrant Shares specified

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               in such form. As soon as practicable after each such exercise of
               the Warrants, but not later than seven (7) days from the date of
               such exercise, the Company shall issue and deliver to the Holder
               a certificate or certificates for the Warrant Shares issuable
               upon such exercise, registered in the name of the Holder or its
               designee. If this Warrant should be exercised in part only, the
               Company shall, upon surrender of this Warrant for cancellation,
               execute and deliver a new Warrant evidencing the rights of the
               Holder thereof to purchase the balance of the Warrant Shares
               purchasable thereunder. Upon receipt by the Company of this
               Warrant at its office, or by the stock transfer agent of the
               Company at its office, in proper form for exercise, the Holder
               shall be deemed to be the holder of record of the shares of
               Common Stock issuable upon such exercise, notwithstanding that
               the stock transfer books of the Company shall then be closed or
               that certificates representing such shares of Common Stock shall
               not then be physically delivered to the Holder.

          b.        At any time during the Exercise Period, the Holder may, at
               its option, exchange this Warrant, in whole or in part (a
               "Warrant Exchange") into the number of Warrant Shares determined
               in accordance with this Section (a)(ii), by surrendering this
               Warrant at the principal office of the Company or at the office
               of its stock transfer agent, accompanied by a notice stating such
               Holder's intent to effect such exchange, the number of Warrant
               Shares to be exchanged and the date on which the Holder requests
               that such Warrant Exchange occur (the "Notice of Exchange"). The
               Warrant Exchange shall take place on the date specified in the
               Notice of Exchange or, if later, the date the Notice of Exchange
               is received by the Company (the "Exchange Date"). Certificates
               for the shares issuable upon such Warrant Exchange and, if
               applicable, a new warrant of like tenor evidencing the balance of
               the shares remaining subject to this Warrant, shall be issued as
               of the Exchange Date and delivered to the Holder within seven (7)
               days following the Exchange Date. In connection with any Warrant
               Exchange, this Warrant shall represent the right to subscribe for
               and acquire the number of Warrant Shares (rounded to the next
               highest integer) equal to (i) the number of Warrant Shares
               specified by the Holder in its Notice of Exchange (the "Total
               Number") less (ii) the number of Warrant Shares equal to the
               quotient obtained by dividing (A) the product of the Total Number
               and the existing Exercise Price by (B) the Fair Market Value.
               "Fair Market Value" shall mean: (1) if the Common Stock is listed
               on a National Securities Exchange or admitted to unlisted trading
               privileges on such exchange or listed for trading on the NASDAQ
               system, the average of the last reported sale prices of the
               Common Stock on such exchange or system for the twenty (20)
               business days ending on the last business day prior to the date
               for which the determination is being made; or (2) if the

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               Common Stock is not so listed or admitted to unlisted trading
               privileges, the average of the means of the last reported bid and
               asked prices reported by the National Quotation Bureau, Inc. for
               the twenty (20) business days ending on the last business day
               prior to the date for which the determination is being made; or
               (3) if the Common Stock is not so listed or admitted to unlisted
               trading privileges and bid and asked prices are not so reported,
               an amount, not less than book value thereof as at the end of the
               most recent fiscal year of the Company ending prior to the
               Exchange Date, determined in such reasonable manner as may be
               prescribed by the Board of Directors of the Company.

     2.        RESERVATION OF SHARES. The Company shall at all times reserve for
          issuance and/or delivery upon exercise of this Warrant such number of
          shares of its Common Stock as shall be required for issuance and
          delivery upon exercise of the Warrants.

     3.        FRACTIONAL SHARES. No fractional shares or script representing
          fractional shares shall be issued upon the exercise of this Warrant.
          With respect to any fraction of a share called for upon any exercise
          hereof, the Company shall pay to the Holder an amount in cash equal to
          such fraction multiplied by the Fair Market Value of a share.

     4.        EXCHANGE, TRANSFER, ASSIGNMENT OR LOSS OF WARRANT.

               (i)  This Warrant is exchangeable, without expense, at the option
               of the Holder, upon presentation and surrender hereof to the
               Company or at the office of its stock transfer agent, if any, for
               other warrants of different denominations entitling the holder
               thereof to purchase in the aggregate the same number of shares of
               Common Stock purchasable hereunder. Subject to the restrictions
               set forth in subparagraph (ii) below, upon surrender of this
               Warrant to the Company at its principal office or at the office
               of its stock transfer agent, if any, with the Assignment Form
               annexed hereto duly executed and funds sufficient to pay any
               transfer tax, the Company shall, without charge, execute and
               deliver a new Warrant in the name of the assignee named in such
               instrument of assignment and this Warrant shall promptly be
               canceled. This Warrant may be divided or combined with other
               warrants which carry the same rights upon presentation hereof at
               the principal office of the Company or at the office of its stock
               transfer agent, if any, together with a written notice specifying
               the names and denominations in which new Warrants are to be
               issued and signed by the Holder hereof. The Term "Warrant" as
               used herein includes any Warrants into which this Warrant may be
               divided or exchanged. Upon receipt by the Company of evidence
               satisfactory to it of the loss, theft, destruction or mutilation
               of this Warrant, and (in the case of loss, theft or destruction)
               of

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               reasonably satisfactory indemnification, and upon surrender and
               cancellation of this Warrant, if mutilated, the Company will
               execute and deliver a new Warrant of like tenor and date. Any
               such new Warrant executed and delivered shall constitute an
               additional contractual obligation on the part of the Company,
               whether or not this Warrant so lost, stolen, destroyed, or
               mutilated shall be at any time enforceable by anyone.

               (ii) This Warrant and the shares of Common Stock issuable upon
               exercise hereof have not been registered under the Securities Act
               of 1933, as amended, or state securities laws by reason of an
               exemption therefrom. The shares of Common Stock issuable upon
               exercise of this Warrant are not transferable except as provided
               in the Agreement and the Stockholders' Agreement dated as of
               January 6, 1998, as amended from time to time ("Stockholders'
               Agreement"). Shares of Common Stock issuable upon exercise of
               this Warrant will bear an appropriate legend to this effect. The
               restrictions contained herein shall be binding on any transferee
               of the Common Stock issuable upon exercise of this Warrant and
               the Company may require any such transferee to execute an
               instrument agreeing in writing to be bound by these restrictions
               as a condition to transfer.

     5.        RIGHTS OF THE HOLDER. The Holder shall not, by virtue hereof, be
          entitled to any rights of a shareholder in the Company, either at law
          or equity, and the rights of the Holder are limited to those expressed
          in the Warrant and are not enforceable against the Company except to
          the extent set forth herein.

     6.        ANTI-DILUTION PROVISIONS. The Exercise Price in effect at any
          time and the number and kind of securities purchasable upon the
          exercise of the Warrants shall be subject to adjustment from time to
          time upon the happening of certain events as follows:

          a.        In case the Company shall (i) declare a dividend or make a
               distribution on its outstanding shares of Common Stock in shares
               of Common Stock, (ii) subdivide or reclassify its outstanding
               shares of Common Stock into a greater number of shares, or (iii)
               combine or reclassify its outstanding shares of Common Stock into
               a smaller number of shares, the Exercise Price in effect at the
               time of the record date for such dividend or distribution or of
               the effective date of such subdivision, combination or
               reclassification shall be adjusted so that it shall equal the
               price determined by multiplying the Exercise Price by a fraction,
               the denominator of which shall be the number of shares of Common
               Stock outstanding after giving effect to such action, and the
               numerator of which shall be the number of shares of Common Stock
               outstanding immediately

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               prior to such action. Such adjustment shall be made successively
               whenever any event listed above shall occur.

          b.        In case the Company shall fix a record date for the issuance
               of rights or warrants to all holders of its Common Stock
               entitling them to subscribe for or purchase shares of Common
               Stock (or securities convertible into Common Stock) at a price
               (the "Subscription Price") (or having a conversion price per
               share) less than the Exercise Price on the record date mentioned
               below, the Exercise Price shall be adjusted so that the same
               shall equal the price determined by multiplying the Exercise
               Price in effect immediately prior to the date of issuance by a
               fraction, the numerator of which shall be the sum of the number
               of shares outstanding on the record date mentioned below and the
               number of additional shares of Common Stock which the aggregate
               offering price of the total number of shares of Common Stock so
               offered (or the aggregate conversion price of the convertible
               securities so offered) would purchase at the Exercise Price in
               effect immediately prior to the date of such issuance, and the
               denominator of which shall be the sum of the number of shares of
               Common Stock outstanding on the record date mentioned below and
               the number of additional shares of Common Stock offered for
               subscription or purchase (or into which the convertible
               securities so offered are convertible). Such adjustment shall be
               made successively whenever such rights or warrants are issued and
               shall become effective immediately after the record date for the
               determination of shareholders entitled to receive such rights or
               warrants; and to the extent that shares of Common Stock are not
               delivered (or securities convertible into Common Stock are not
               delivered) after the expiration of such rights or warrants the
               Exercise Price shall be readjusted to the Exercise Price which
               would then be in effect had the adjustments made upon the
               issuance of such rights or warrants been made upon the basis of
               delivery of only the number of shares of Common Stock (or
               securities convertible into Common Stock) actually delivered.

          c.        In case the Company shall hereafter distribute to the
               holders of its Common Stock evidences of its indebtedness or
               assets (excluding cash dividends or distributions and dividends
               or distributions referred to in Subsection (i) above) or
               subscription rights or warrants (excluding those referred to in
               Subsection (ii) above), then in each such case the Exercise Price
               in effect thereafter shall be determined by multiplying the
               Exercise Price in effect immediately prior thereto by a fraction,
               the numerator of which shall be the total number of shares of
               Common Stock outstanding multiplied by the Fair Market Value per
               share of Common Stock, less the fair market value (as determined
               by the Company's Board of Directors) of said assets or evidences
               of indebtedness so distributed or of such rights or warrants, and
               the denominator of which shall be the total number of shares

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               of Common Stock outstanding multiplied by the Fair Market Value
               per share of Common Stock. Such adjustment shall be made
               successively whenever such a record date is fixed. Such
               adjustment shall be made whenever any such distribution is made
               and shall become effective immediately after the record date for
               the determination of shareholders entitled to receive such
               distribution.

          d.        Whenever the Exercise Price payable upon exercise of each
               Warrant is adjusted pursuant to Subsections (i), (ii) or (iii)
               above, the number of Shares purchasable upon exercise of this
               Warrant shall simultaneously be adjusted by multiplying the
               number of Shares initially issuable upon exercise of this Warrant
               by the Exercise Price in effect on the date hereof and dividing
               the product so obtained by the Exercise Price, as adjusted.

          e.        No adjustment in the Exercise Price shall be required unless
               such adjustment would require an increase or decrease of at least
               5% in such price; provided, however, that any adjustments which
               by reason of this Subsection (v) are not required to be made
               shall be carried forward and taken into account in any subsequent
               adjustment required to be made hereunder. All calculations under
               this Section (f) shall be made to the nearest cent or to the
               nearest one-hundredth of a share, as the case may be. Anything in
               this Section (f) to the contrary notwithstanding, the Company
               shall be entitled, but shall not be required, to make such
               changes in the Exercise Price, in addition to those required by
               this Section (f), as it shall determine, in its sole discretion,
               to be advisable in order that any dividend or distribution in
               shares of Common Stock, or any subdivision, reclassification or
               combination of Common Stock, hereafter made by the Company shall
               not result in any Federal Income tax liability to the holders of
               Common Stock or securities convertible into Common Stock
               (including Warrants).

          f.        Whenever the Exercise Price is adjusted, as herein provided,
               the Company shall promptly but no later than 10 days after any
               request for such an adjustment by the Holder, cause a notice
               setting forth the adjusted Exercise Price and adjusted number of
               Shares issuable upon exercise of each Warrant, and, if requested,
               information describing the transactions giving rise to such
               adjustments, to be mailed to the Holders at their last addresses
               appearing in the Warrant Register, and shall cause a certified
               copy thereof to be mailed to its transfer agent, if any. The
               Company may retain a firm of independent certified public
               accountants selected by the Board of Directors (who may be the
               regular accountants employed by the Company) to make any
               computation required by this Section (f), and a

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               certificate signed by such firm shall be conclusive evidence of
               the correctness of such adjustment.

          g.        In the event that at any time, as a result of an adjustment
               made pursuant to Subsection (i) above, the Holder of this Warrant
               thereafter shall become entitled to receive any shares of the
               Company, other than Common Stock, thereafter the number of such
               other shares so receivable upon exercise of this Warrant shall be
               subject to adjustment from time to time in a manner and on terms
               as nearly equivalent as practicable to the provisions with
               respect to the Common Stock contained in Subsections (i) to (vi),
               inclusive above.

          h.        Irrespective of any adjustments in the Exercise Price or the
               number or kind of shares purchasable upon exercise of this
               Warrant, Warrants theretofore or thereafter issued may continue
               to express the same price and number and kind of shares as are
               stated in the similar Warrants initially issuable pursuant to the
               Agreement.

     7.        OFFICER'S CERTIFICATE. Whenever the Exercise Price shall be
          adjusted as required by the provisions of the foregoing Section, the
          Company shall forthwith file in the custody of its Secretary or an
          Assistant Secretary at its principal office and with its stock
          transfer agent, if any, an officer's certificate showing the adjusted
          Exercise Price determined as herein provided, setting forth in
          reasonable detail the facts requiring such adjustment, including a
          statement of the number of additional shares of Common Stock, if any,
          and such other facts as shall be necessary to show the reason for and
          the manner of computing such adjustment. Each such officer's
          certificate shall be made available at all reasonable times for
          inspection by the holder or any holder of a Warrant executed and
          delivered pursuant to Section (a) and the Company shall, forthwith
          after each such adjustment, mail a copy by certified mail of such
          certificate to the Holder or any such holder.

     8.        NOTICES TO WARRANT HOLDERS. So long as this Warrant shall be
          outstanding, (i) if the Company shall pay any dividend or make any
          distribution upon the Common Stock or (ii) if the Company shall offer
          to the Holders of Common Stock for subscription or purchase by them
          any share of any class or any other rights or (iii) if any capital
          reorganization of the Company, reclassification of the capital stock
          of the Company, consolidation or merger of the Company with or into
          another corporation, sale, lease or transfer of all or substantially
          all of the property and assets of the Company to another corporation,
          or voluntary or involuntary dissolution, liquidation or winding up of
          the Company shall be effected, then in any such case, the Company
          shall cause to be mailed by certified mail to the Holder, at least
          fifteen days prior to the date specified in (x) or (y) below, as the
          case may be, a notice containing a brief description of the proposed

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          action and stating the date on which (x) a record is to be taken for
          the purpose of such dividend, distribution or rights, or (y) such
          reclassification, reorganization, consolidation, merger, conveyance,
          lease, dissolution, liquidation or winding up is to take place and the
          date, if any is to be fixed, as of which the Holders of Common Stock
          or other securities shall receive cash or other property deliverable
          upon such reclassification, reorganization, consolidation, merger,
          conveyance, dissolution, liquidation or winding up.

     9.        RECLASSIFICATION, REORGANIZATION OR MERGER. In case of any
          reclassification, capital reorganization or other change of
          outstanding shares of Common Stock of the Company, or in case of any
          consolidation or merger of the Company with or into another
          corporation (other than a merger with a subsidiary in which merger the
          Company is the continuing corporation and which does not result in any
          reclassification, capital reorganization or other change of
          outstanding shares of Common Stock of the class issuable upon exercise
          of this Warrant) or in case of any sale, lease or conveyance to
          another corporation of the property of the Company as an entirety, the
          Company shall, as a condition precedent to such transaction, cause
          effective provisions to be made so that the Holder shall have the
          right thereafter by exercising this Warrant at any time prior to the
          expiration of the Warrant, to purchase the kind and amount of shares
          of stock and other securities and property receivable upon such
          reclassification, capital reorganization and other change,
          consolidation, merger, sale or conveyance by a holder of the number of
          shares of Common Stock which might have been purchased upon exercise
          of this Warrant immediately prior to such reclassification, change,
          consolidation, merger, sale or conveyance. Any such provision shall
          include provision for adjustments which shall be as nearly equivalent
          as may be practicable to the adjustments provided for in this Warrant.
          The foregoing provisions of this Section (i) shall similarly apply to
          successive reclassifications, capital reorganizations and changes of
          shares of Common Stock and to successive consolidations, mergers,
          sales or conveyances. In the event that in connection with any such
          capital reorganization or reclassification, consolidation, merger,
          sale or conveyance, additional shares of Common Stock shall be issued
          in exchange, conversion, substitution or payment, in whole or in part,
          for a security of the Company other than Common Stock, any such issue
          shall be treated as an issue of Common Stock covered by the provisions
          of Subsection (i) of Section (f)hereof.

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                                             3-DIMENSIONAL PHARMACEUTICALS, INC.

                                             By   /s/ David C. U'Prichard
                                                ________________________________
                                             Name: David C. U'Prichard
                                             Title: Chief Executive Officer

[SEAL]

Dated: November 18, 1999

Attest:

  /s/ Scott M. Horvitz
_____________________________
Secretary

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                                 PURCHASE FORM
                                 -------------

                                                         Dated __________, ____

     The undersigned hereby irrevocably elects to exercise the within Warrant to
the extent of purchasing _________ shares of Common Stock and hereby makes
payment of in payment of the actual exercise price thereof

                                   ---------

                    INSTRUCTIONS FOR REGISTRATION OF STOCK
                    --------------------------------------

Name __________________________________
     (Please typewrite or print in block letters)

Address __________________________________________________

Signature ________________________________________________

                                   ---------

                                ASSIGNMENT FORM
                                ---------------

     FOR VALUE RECEIVED, __________________________ hereby sells, assigns and
transfers unto

Name _____________________________________________________
     (Please typewrite or print in block letters)

Address __________________________________________________
the right to purchase Common Stock represented by this Warrant to the extent of
_____ shares as to which such right is exercisable and does hereby irrevocably
constitute and appoint ____________________ Attorney, to transfer the same on
the books of the Company with full power of substitution in the premises.

Date _____________, _____

Signature _________________________

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                                                                    Exhibit 10.8

           Warrant to Purchase 1,050,000 Shares of Common Stock or
        such additional shares as this Warrant may entitle the holder
              to purchase pursuant to provisions of this Warrant.

                       WARRANT TO PURCHASE COMMON STOCK

                                      OF

                      3-DIMENSIONAL PHARMACEUTICALS, INC.

          This is to Certify That, FOR VALUE RECEIVED, Rho Management Trust II
or assigns ("Holder") is entitled to purchase, subject to the provisions of this
Warrant, from 3-Dimensional Pharmaceuticals, Inc., a Delaware corporation (the
"Company"), 1,050,000 fully paid, validly issued and nonassessable shares of
Common Stock, par value $.001 per share, of the Company ("Common Stock") at a
price of $1.25 per share during the Exercise Period (as defined below). The
number of shares of Common Stock to be received upon the exercise of this
Warrant and the price to be paid for each share of Common Stock may be adjusted
from time to time as hereinafter set forth. The shares of Common Stock
deliverable upon such exercise, and as adjusted from time to time, are
hereinafter sometimes referred to as "Warrant Shares" and the exercise price of
a share of Common Stock in effect at any time and as adjusted from time to time
is hereinafter sometimes referred to as the "Exercise Price." This Warrant is
being issued in connection with the issuance by the Company of Warrants to
purchase shares of Common Stock and promissory notes in the aggregate principal
amount of up to $10,000,000 (the "Notes"), pursuant to a Note and Warrant
Purchase Agreement dated as of November 18, 1999 (the "Agreement").

     1.        EXERCISE OF WARRANT.

          a.        This Warrant may be exercised in whole or in part at any
               time or from time to time on or after November 18, 1999 until 5
               p.m. New York City Time on November 18, 2000 (the "Exercise
               Period"); provided, however, that if such day is a day on which
               banking institutions in the State of New York are authorized by
               law to close, then on the next succeeding day which shall not be
               such a day. This Warrant may be exercised by presentation and
               surrender hereof to the Company at its principal office, or at
               the office of its stock transfer agent, if any, with the Purchase
               Form annexed hereto duly executed and accompanied by payment of
               the Exercise Price for the number of Warrant Shares specified
<PAGE>

               in such form. As soon as practicable after each such exercise of
               the Warrants, but not later than seven (7) days from the date of
               such exercise, the Company shall issue and deliver to the Holder
               a certificate or certificates for the Warrant Shares issuable
               upon such exercise, registered in the name of the Holder or its
               designee. If this Warrant should be exercised in part only, the
               Company shall, upon surrender of this Warrant for cancellation,
               execute and deliver a new Warrant evidencing the rights of the
               Holder thereof to purchase the balance of the Warrant Shares
               purchasable thereunder. Upon receipt by the Company of this
               Warrant at its office, or by the stock transfer agent of the
               Company at its office, in proper form for exercise, the Holder
               shall be deemed to be the holder of record of the shares of
               Common Stock issuable upon such exercise, notwithstanding that
               the stock transfer books of the Company shall then be closed or
               that certificates representing such shares of Common Stock shall
               not then be physically delivered to the Holder.

     b.        At any time during the Exercise Period, the Holder may, at its
               option, exchange this Warrant, in whole or in part (a "Warrant
               Exchange") into the number of Warrant Shares determined in
               accordance with this Section (a)(ii), by surrendering this
               Warrant at the principal office of the Company or at the office
               of its stock transfer agent, accompanied by a notice stating such
               Holder's intent to effect such exchange, the number of Warrant
               Shares to be exchanged and the date on which the Holder requests
               that such Warrant Exchange occur (the "Notice of Exchange"). The
               Warrant Exchange shall take place on the date specified in the
               Notice of Exchange or, if later, the date the Notice of Exchange
               is received by the Company (the "Exchange Date"). Certificates
               for the shares issuable upon such Warrant Exchange and, if
               applicable, a new warrant of like tenor evidencing the balance of
               the shares remaining subject to this Warrant, shall be issued as
               of the Exchange Date and delivered to the Holder within seven (7)
               days following the Exchange Date. In connection with any Warrant
               Exchange, this Warrant shall represent the right to subscribe for
               and acquire the number of Warrant Shares (rounded to the next
               highest integer) equal to (i) the number of Warrant Shares
               specified by the Holder in its Notice of Exchange (the "Total
               Number") less (ii) the number of Warrant Shares equal to the
               quotient obtained by dividing (A) the product of the Total Number
               and the existing Exercise Price by (B) the Fair Market Value.
               "Fair Market Value" shall mean: (1) if the Common Stock is listed
               on a National Securities Exchange or admitted to unlisted trading
               privileges on such exchange or listed for trading on the NASDAQ
               system, the average of the last reported sale prices of the
               Common Stock on such exchange or system for the twenty (20)
               business days ending on the last business day prior to the date
               for which the determination is being made; or (2) if the
<PAGE>

               Common Stock is not so listed or admitted to unlisted trading
               privileges, the average of the means of the last reported bid and
               asked prices reported by the National Quotation Bureau, Inc. for
               the twenty (20) business days ending on the last business day
               prior to the date for which the determination is being made; or
               (3) if the Common Stock is not so listed or admitted to unlisted
               trading privileges and bid and asked prices are not so reported,
               an amount, not less than book value thereof as at the end of the
               most recent fiscal year of the Company ending prior to the
               Exchange Date, determined in such reasonable manner as may be
               prescribed by the Board of Directors of the Company.

     2.        RESERVATION OF SHARES. The Company shall at all times reserve for
          issuance and/or delivery upon exercise of this Warrant such number of
          shares of its Common Stock as shall be required for issuance and
          delivery upon exercise of the Warrants.

     3.        FRACTIONAL SHARES. No fractional shares or script representing
          fractional shares shall be issued upon the exercise of this Warrant.
          With respect to any fraction of a share called for upon any exercise
          hereof, the Company shall pay to the Holder an amount in cash equal to
          such fraction multiplied by the Fair Market Value of a share.

     4.        EXCHANGE, TRANSFER, ASSIGNMENT OR LOSS OF WARRANT.

               (i)  This Warrant is exchangeable, without expense, at the option
               of the Holder, upon presentation and surrender hereof to the
               Company or at the office of its stock transfer agent, if any, for
               other warrants of different denominations entitling the holder
               thereof to purchase in the aggregate the same number of shares of
               Common Stock purchasable hereunder. Subject to the restrictions
               set forth in subparagraph (ii) below, upon surrender of this
               Warrant to the Company at its principal office or at the office
               of its stock transfer agent, if any, with the Assignment Form
               annexed hereto duly executed and funds sufficient to pay any
               transfer tax, the Company shall, without charge, execute and
               deliver a new Warrant in the name of the assignee named in such
               instrument of assignment and this Warrant shall promptly be
               canceled. This Warrant may be divided or combined with other
               warrants which carry the same rights upon presentation hereof at
               the principal office of the Company or at the office of its stock
               transfer agent, if any, together with a written notice specifying
               the names and denominations in which new Warrants are to be
               issued and signed by the Holder hereof. The term "Warrant" as
               used herein includes any Warrants into which this Warrant may be
               divided or exchanged. Upon receipt by the Company of evidence
               satisfactory to it of the loss, theft, destruction or mutilation
               of this Warrant, and (in the case of loss, theft or destruction)
               of
<PAGE>

               reasonably satisfactory indemnification, and upon surrender and
               cancellation of this Warrant, if mutilated, the Company will
               execute and deliver a new Warrant of like tenor and date. Any
               such new Warrant executed and delivered shall constitute an
               additional contractual obligation on the part of the Company,
               whether or not this Warrant so lost, stolen, destroyed, or
               mutilated shall be at any time enforceable by anyone.

               (ii) This Warrant and the shares of Common Stock issuable upon
               exercise hereof have not been registered under the Securities Act
               of 1933, as amended, or state securities laws by reason of an
               exemption therefrom. The shares of Common Stock issuable upon
               exercise of this Warrant are not transferable except as provided
               in the Agreement and the Stockholders' Agreement dated as of
               January 6, 1998, as amended from time to time ("Stockholders"
               Agreement"). Shares of Common Stock issuable upon exercise of
               this Warrant will bear an appropriate legend to this effect. The
               restrictions contained herein shall be binding on any transferee
               of the Common Stock issuable upon exercise of this Warrant and
               the Company may require any such transferee to execute an
               instrument agreeing in writing to be bound by these restrictions
               as a condition to transfer.

     5.        RIGHTS OF THE HOLDER. The Holder shall not, by virtue hereof, be
          entitled to any rights of a shareholder in the Company, either at law
          or equity, and the rights of the Holder are limited to those expressed
          in the Warrant and are not enforceable against the Company except to
          the extent set forth herein.

     6.        ANTI-DILUTION PROVISIONS. The Exercise Price in effect at any
          time and the number and kind of securities purchasable upon the
          exercise of the Warrants shall be subject to adjustment from time to
          time upon the happening of certain events as follows:

          a.        In case the Company shall (i) declare a dividend or make a
               distribution on its outstanding shares of Common Stock in shares
               of Common Stock, (ii) subdivide or reclassify its outstanding
               shares of Common Stock into a greater number of shares, or (iii)
               combine or reclassify its outstanding shares of Common Stock into
               a smaller number of shares, the Exercise Price in effect at the
               time of the record date for such dividend or distribution or of
               the effective date of such subdivision, combination or
               reclassification shall be adjusted so that it shall equal the
               price determined by multiplying the Exercise Price by a fraction,
               the denominator of which shall be the number of shares of Common
               Stock outstanding after giving effect to such action, and the
               numerator of which shall be the number of shares of Common Stock
               outstanding immediately
<PAGE>

               prior to such action. Such adjustment shall be made successively
               whenever any event listed above shall occur.

          b.        In case the Company shall fix a record date for the issuance
               of rights or warrants to all holders of its Common Stock
               entitling them to subscribe for or purchase shares of Common
               Stock (or securities convertible into Common Stock) at a price
               (the "Subscription Price") (or having a conversion price per
               share) less than the Exercise Price on the record date mentioned
               below, the Exercise Price shall be adjusted so that the same
               shall equal the price determined by multiplying the Exercise
               Price in effect immediately prior to the date of issuance by a
               fraction, the numerator of which shall be the sum of the number
               of shares outstanding on the record date mentioned below and the
               number of additional shares of Common Stock which the aggregate
               offering price of the total number of shares of Common Stock so
               offered (or the aggregate conversion price of the convertible
               securities so offered) would purchase at the Exercise Price in
               effect immediately prior to the date of such issuance, and the
               denominator of which shall be the sum of the number of shares of
               Common Stock outstanding on the record date mentioned below and
               the number of additional shares of Common Stock offered for
               subscription or purchase (or into which the convertible
               securities so offered are convertible). Such adjustment shall be
               made successively whenever such rights or warrants are issued and
               shall become effective immediately after the record date for the
               determination of shareholders entitled to receive such rights or
               warrants; and to the extent that shares of Common Stock are not
               delivered (or securities convertible into Common Stock are not
               delivered) after the expiration of such rights or warrants the
               Exercise Price shall be readjusted to the Exercise Price which
               would then be in effect had the adjustments made upon the
               issuance of such rights or warrants been made upon the basis of
               delivery of only the number of shares of Common Stock (or
               securities convertible into Common Stock) actually delivered.

          c.        In case the Company shall hereafter distribute to the
               holders of its Common Stock evidences of its indebtedness or
               assets (excluding cash dividends or distributions and dividends
               or distributions referred to in Subsection (i) above) or
               subscription rights or warrants (excluding those referred to in
               Subsection (ii) above), then in each such case the Exercise Price
               in effect thereafter shall be determined by multiplying the
               Exercise Price in effect immediately prior thereto by a fraction,
               the numerator of which shall be the total number of shares
<PAGE>

               of Common Stock outstanding multiplied by the Fair Market Value
               per share of Common Stock, less the fair market value (as
               determined by the Company's Board of Directors) of said assets or
               evidences of indebtedness so distributed or of such rights or
               warrants, and the denominator of which shall be the total number
               of shares of Common Stock outstanding multiplied by the Fair
               Market Value per share of Common Stock. Such adjustment shall be
               made successively whenever such a record date is fixed. Such
               adjustment shall be made whenever any such distribution is made
               and shall become effective immediately after the record date for
               the determination of shareholders entitled to receive such
               distribution.

          d.        Whenever the Exercise Price payable upon exercise of
               each Warrant is adjusted pursuant to Subsections (i), (ii) or
               (iii) above, the number of Shares purchasable upon exercise of
               this Warrant shall simultaneously be adjusted by multiplying the
               number of Shares initially issuable upon exercise of this Warrant
               by the Exercise Price in effect on the date hereof and dividing
               the product so obtained by the Exercise Price, as adjusted.

          e.        No adjustment in the Exercise Price shall be required
               unless such adjustment would require an increase or decrease of
               at least 5% in such price; provided, however, that any
               adjustments which by reason of this Subsection (v) are not
               required to be made shall be carried forward and taken into
               account in any subsequent adjustment required to be made
               hereunder. All calculations under this Section (f) shall be made
               to the nearest cent or to the nearest one-hundredth of a share,
               as the case may be. Anything in this Section (f) to the contrary
               notwithstanding, the Company shall be entitled, but shall not be
               required, to make such changes in the Exercise Price, in addition
               to those required by this Section (f), as it shall determine, in
               its sole discretion, to be advisable in order that any dividend
               or distribution in shares of Common Stock, or any subdivision,
               reclassification or combination of Common Stock, hereafter made
               by the Company shall not result in any Federal Income tax
               liability to the holders of Common Stock or securities
               convertible into Common Stock (including Warrants).

          f.        Whenever the Exercise Price is adjusted, as herein
               provided, the Company shall promptly but no later than 10 days
               after any request for such an adjustment by the Holder, cause a
               notice setting forth the adjusted Exercise Price and adjusted
               number of Shares issuable upon exercise of each Warrant, and, if
               requested, information describing the transactions giving rise to
               such adjustments, to be mailed to the Holders at their last
               addresses appearing in the Warrant Register, and shall cause a
               certified copy thereof to be mailed to its transfer agent, if
               any. The Company may retain a firm of independent certified
               public accountants selected by the Board of Directors (who may be
               the regular accountants employed by the Company) to make any
               computation required by this Section (f), and a
<PAGE>

               certificate signed by such firm shall be conclusive evidence of
               the correctness of such adjustment.

          g.        In the event that at any time, as a result of an
               adjustment made pursuant to Subsection (i) above, the Holder of
               this Warrant thereafter shall become entitled to receive any
               shares of the Company, other than Common Stock, thereafter the
               number of such other shares so receivable upon exercise of this
               Warrant shall be subject to adjustment from time to time in a
               manner and on terms as nearly equivalent as practicable to the
               provisions with respect to the Common Stock contained in
               Subsections (i) to (vi), inclusive above.

          h.        Irrespective of any adjustments in the Exercise Price or the
               number or kind of shares purchasable upon exercise of this
               Warrant, Warrants theretofore or thereafter issued may continue
               to express the same price and number and kind of shares as are
               stated in the similar Warrants initially issuable pursuant to the
               Agreement.

     7.        OFFICER'S CERTIFICATE. Whenever the Exercise Price shall be
          adjusted as required by the provisions of the foregoing Section, the
          Company shall forthwith file in the custody of its Secretary or an
          Assistant Secretary at its principal office and with its stock
          transfer agent, if any, an officer's certificate showing the adjusted
          Exercise Price determined as herein provided, setting forth in
          reasonable detail the facts requiring such adjustment, including a
          statement of the number of additional shares of Common Stock, if any,
          and such other facts as shall be necessary to show the reason for and
          the manner of computing such adjustment. Each such officer's
          certificate shall be made available at all reasonable times for
          inspection by the holder or any holder of a Warrant executed and
          delivered pursuant to Section (a) and the Company shall, forthwith
          after each such adjustment, mail a copy by certified mail of such
          certificate to the Holder or any such holder.

     8.        NOTICES TO WARRANT HOLDERS. So long as this Warrant shall be
          outstanding, (i) if the Company shall pay any dividend or make any
          distribution upon the Common Stock or (ii) if the Company shall offer
          to the Holders of Common Stock for subscription or purchase by them
          any share of any class or any other rights or (iii) if any capital
          reorganization of the Company, reclassification of the capital stock
          of the Company, consolidation or merger of the Company with or into
          another corporation, sale, lease or transfer of all or substantially
          all of the property and assets of the Company to another corporation,
          or voluntary or involuntary dissolution, liquidation or winding up of
          the Company shall be effected, then in any such case, the Company
          shall cause to be mailed by certified mail to the Holder, at least
          fifteen days prior to the date specified in (x) or (y) below, as the
          case may be, a notice containing a brief description of the proposed
<PAGE>

          action and stating the date on which (x) a record is to be taken for
          the purpose of such dividend, distribution or rights, or (y) such
          reclassification, reorganization, consolidation, merger, conveyance,
          lease, dissolution, liquidation or winding up is to take place and the
          date, if any is to be fixed, as of which the Holders of Common Stock
          or other securities shall receive cash or other property deliverable
          upon such reclassification, reorganization, consolidation, merger,
          conveyance, dissolution, liquidation or winding up.

     9.        RECLASSIFICATION, REORGANIZATION OR MERGER. In case of any
          reclassification, capital reorganization or other change of
          outstanding shares of Common Stock of the Company, or in case of any
          consolidation or merger of the Company with or into another
          corporation (other than a merger with a subsidiary in which merger the
          Company is the continuing corporation and which does not result in any
          reclassification, capital reorganization or other change of
          outstanding shares of Common Stock of the class issuable upon exercise
          of this Warrant) or in case of any sale, lease or conveyance to
          another corporation of the property of the Company as an entirety, the
          Company shall, as a condition precedent to such transaction, cause
          effective provisions to be made so that the Holder shall have the
          right thereafter by exercising this Warrant at any time prior to the
          expiration of the Warrant, to purchase the kind and amount of shares
          of stock and other securities and property receivable upon such
          reclassification, capital reorganization and other change,
          consolidation, merger, sale or conveyance by a holder of the number of
          shares of Common Stock which might have been purchased upon exercise
          of this Warrant immediately prior to such reclassification, change,
          consolidation, merger, sale or conveyance. Any such provision shall
          include provision for adjustments which shall be as nearly equivalent
          as may be practicable to the adjustments provided for in this Warrant.
          The foregoing provisions of this Section (i) shall similarly apply to
          successive reclassifications, capital reorganizations and changes of
          shares of Common Stock and to successive consolidations, mergers,
          sales or conveyances. In the event that in connection with any such
          capital reorganization or reclassification, consolidation, merger,
          sale or conveyance, additional shares of Common Stock shall be issued
          in exchange, conversion, substitution or payment, in whole or in part,
          for a security of the Company other than Common Stock, any such issue
          shall be treated as an issue of Common Stock covered by the provisions
          of Subsection (i) of Section (f)hereof.
<PAGE>

                                   3-DIMENSIONAL PHARMACEUTICALS, INC.

                                   By   /s/ David C. U'Prichard
                                      _____________________________________
                                   Name:  David C. U'Prichard
                                   Title:  Chief Executive Officer

[SEAL]

Dated:  November 18, 1999

Attest:

  /s/ Scott M. Horvitz
_____________________________
Secretary
<PAGE>

                                 PURCHASE FORM
                                 -------------

                                                       Dated _____________,____

     The undersigned hereby irrevocably elects to exercise the within Warrant to
the extent of purchasing _________ shares of Common Stock and hereby makes
payment of in payment of the actual exercise price thereof

                                   ---------

                    INSTRUCTIONS FOR REGISTRATION OF STOCK
                    --------------------------------------

Name _____________________________________________
     (Please typewrite or print in block letters)

Address __________________________________________

Signature_________________________________________

                                   ---------

                                ASSIGNMENT FORM
                                ---------------

     FOR VALUE RECEIVED, __________________________ hereby sells, assigns and
transfers unto

Name _____________________________________________________
     (Please typewrite or print in block letters)

Address  __________________________________________________
the right to purchase Common Stock represented by this Warrant to the extent of
_____ shares as to which such right is exercisable and does hereby irrevocably
constitute and appoint ____________________ Attorney, to transfer the same on
the books of the Company with full power of substitution in the premises.

Date _____________, _____

Signature ____________________________

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