
<PAGE>
                                                                    Exhibit 10.6

          Warrant to Purchase 1,082,200 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 III,
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"), 1,082,200 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 in such form. As soon as practicable after
                      each such exercise of the

                                      -1-
<PAGE>

                      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 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

                                      -2-
<PAGE>

                      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 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

                                      -3-
<PAGE>

                      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
                      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

                                      -4-
<PAGE>

                      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
                      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.

                                      -5-
<PAGE>

          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
                      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

                                      -6-
<PAGE>

                      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
          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.

                                      -7-
<PAGE>

     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.

                                      -8-
<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

                                      -9-
<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 ____________________________

                                      -10-
