Document:

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                                                                   Exhibit 10.13

             Warrant to Purchase 552,547 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, Biotech Growth SA or
assigns ("Holder") is entitled to purchase, subject to the provisions of this
Warrant, from 3-Dimensional Pharmaceuticals, Inc., a Delaware corporation (the
"Company"), 552,547 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
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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
<PAGE>

               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 ____________________________<PAGE>

                                                                   EXHIBIT 10.15

                              SETTLEMENT AGREEMENT

     This is a Settlement Agreement entered into March 7, 2000 (the "Effective
Date") by and between:

     Scriptgen Pharmaceuticals, Inc., a Delaware corporation having a principal
place of business at 610 Lincoln Street, Waltham, MA 02451 ("Scriptgen"); and

     3-Dimensional Pharmaceuticals, Inc., a Delaware corporation having a
principal place of business at 665 Stockton Drive, Exton, PA 19341 ("3DP").

     WHEREAS, Scriptgen is the owner of U.S. Patent 5,585,277 ("the `277
patent'"), and U.S. Patent No. 5,679,582 ("the `582 patent'");

     WHEREAS on October 13, 1998, Scriptgen filed an action in the United States
District Court for the District of Delaware, captioned Scriptgen
Pharmaceuticals, Inc. v. 3-Dimensional Pharmaceuticals, Inc., Civil Action No.
98-583-GMS, in which Scriptgen has asserted claims against 3DP for infringement
of the `277 patent and the `582 patent and 3DP has asserted defenses and
counterclaims against Scriptgen including the non-infringement, invalidity, and
unenforceability of the `277 patent and the `582 patent ("the Action"); and

     WHEREAS Scriptgen and 3DP desire to settle all claims that have been raised
in the Action and wish to avoid any further controversy between them as set
forth herein.

     NOW THEREFORE, in consideration of the mutual covenants and undertakings of
the parties, Scriptgen and 3DP agree as follows:

1.   DEFINITIONS

1.1  "Affiliate" shall mean an entity that directly, or indirectly through one
     or more intermediaries, controls, or is controlled by, or is under common
     control with, 3DP or Scriptgen, as applicable; provided further that
     "control(s)(led)" as used in this Section shall mean ownership by a third
     party, not including a venture capital fund or group of venture capital
     funds, of at least fifty percent (50%) of the equity capital of such
     entity.

1.2  "Atlas Technology" shall mean the methods and processes generally disclosed
     in the specifications and claims of the `277 patent, the `582 patent and/or
     Scriptgen International Application No. PCT/US96/19698.

1.3  "Calendar Quarter" shall mean each three month period, or any portion
     thereof, ending on March 31, June 30, September 30 and December 31.

1.4  "Development Compound" shall mean a compound that has entered pre-clinical
     regulatory drug safety studies conducted under good laboratory practice
     (GLP) guidelines.
<PAGE>

1.5  "Hepatitis C Virus Field" shall mean any program(s) whose intent is to
     discover or develope a drug that exerts a therapeutic effect in Hepatitis C
     Virus Infection.

1.6  "Infection" shall mean the field of treatment with, research on, and/or
     development of drugs whose principal aim is to treat or cure infectious
     disease in humans.
1.7  "Method Claims" shall mean any claim in a patent or application to a
     process or method and shall not include any claim to a product or
     apparatus.

1.8  "Net Revenues" shall mean the revenues actually received by a party from
     the offering or provision of drug screening services or from the sale of
     drug compounds, after allowing deductions for sales, use and other similar
     taxes (excluding taxes based on such party's income or revenues), the legal
     incidence of which is on such party, returns and other credits.

1.9  "Restriction Period" shall mean the period of time beginning from the
     Effective Date and ending on the third (3rd) anniversary of the Effective
     Date.

1.10 "Scriptgen" shall mean Scriptgen Pharmaceuticals, Inc., its present and
     future Affiliates, and any entity in which Scriptgen Pharmaceuticals, Inc.
     owns or controls a majority interest.

1.11 "ThermoFluor Deal" shall mean a business arrangement between 3DP and a
     third party collaborator, for any duration of time, involving the use of
     3DP's ThermoFluor(R) Screening Technology at one or more research sites
     anywhere in the world and operated by 3DP and/or such third party
     collaborating with 3DP.

1.12 "ThermoFluor Screening Technology" shall mean the methods, processes and
     apparatus generally disclosed in the specifications and claims of U.S.
     Patent No. 6,020,141 and/or allowed U.S. Patent Application Serial no.
     08/853,459.

1.13 "3DP" shall mean 3-Dimensional Pharmaceuticals, Inc., its present and
     future Affiliates, and any entity in which 3-Dimensional Pharmaceuticals,
     Inc. owns or controls a majority interest.

1.14 "3DP Internal Program(s)" shall mean drug discovery and/or development
     program(s) in any therapeutic field conducted for and by 3DP on-site at a
     3DP facility.

2.   FINANCIAL PAYMENT AND RELEASE

2.1  [**]

2.2  Each payment shall be by wire transfer to [**]. A letter confirming the
     transfer shall be delivered to Scriptgen's counsel, DARBY & DARBY, PC, 805
     Third Avenue, New York, NY 10022, by overnight courier.

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.

                                      -2-
<PAGE>

2.3  Upon full execution of this Agreement by the parties and receipt by
     Scriptgen of the initial non-refundable payment specified in Section 2.1(a)
     above, Scriptgen for itself and for its shareholders, officers, directors,
     agents, representatives and all persons and entities claiming under or
     through it, releases 3DP, and its shareholders, employees, agents,
     officers, directors, representatives, customers, suppliers, manufacturers,
     partners and distributors, from any and all claims of infringement of the
     `277 patent and the `582 patent, and from all injuries and damages which
     may have resulted therefrom, whether now known, unforeseen, unanticipated
     or latent which Scriptgen ever had, now has, or hereafter can, shall or may
     have, by reason of any act, omission or occurrence prior to the Effective
     Date.

2.4  3DP, for itself and for its shareholders, officers, directors, agents,
     representatives and all persons and entities claiming under or through it,
     releases Scriptgen and its shareholders, employees, agents, officers,
     directors, representatives, customers, suppliers, manufacturers, partners
     and distributors, from any and all claims of any kind and from all injuries
     and damages which may have resulted therefrom, whether now known,
     unforeseen, unanticipated or latent which 3DP ever had, now has, or
     hereafter can, shall or may have, by reason of any act, omission or
     occurrence prior to the Effective Date with respect to the subject matter
     of the Action.

2.5  The parties will direct their attorneys to sign the Stipulated Order of
     Dismissal attached hereto as Exhibit A simultaneously with signing this
     Agreement and to cause their respective attorneys to file the signed
     Stipulated Order of Dismissal with the Court in the Action within five (5)
     days after the full execution of this Agreement and the receipt by
     Scriptgen of the initial non-refundable payment specified in Section 2.1(a)
     above.

2.6  The parties each agree that within sixty (60) days after entry of the
     Stipulated Order of Dismissal, they will each return to the other party, in
     accordance with paragraph sixteen (16) of the Stipulation and Order
     Governing the Protection and Exchange of Confidential Material in the
     Action, dated March 23, 1999, or certify the destruction of, all
     confidential documents that were produced by the other party during the
     course of the Action.

3.   LICENSE GRANT BY SCRIPTGEN TO 3DP

3.1  In settlement of the Action, Scriptgen hereby grants to 3DP beginning on
     the Effective Date, and subject to Sections 3.2 through 3.11, a perpetual,
     non-exclusive, worldwide, fully-paid license, with the right to sub-
     license, under the `277 patent, the `582 patent, and any patents issuing
     from Scriptgen International Application No. PCT/US96/19698, any and all
     continuing applications, divisional applications, continuation-in-part
     applications, reissues, extensions, renewals and reexaminations thereof,
     and any U.S. and foreign counterparts thereof. In addition, Scriptgen
     agrees not to file any future patent infringement actions against 3DP for
     3DP's use of ThermoFluor Screening Technology that is consistent with the
     terms of this Agreement.

                                      -3-
<PAGE>

3.2  3DP shall not have the right to assign the license granted herein
     except as part of the sale of its ThermoFluor Screening Technology or
     business, the sale of substantially all the capital stock or assets of the
     corporation, or the merger or consolidation of the corporation.

3.3  During the Restriction Period, 3DP shall be permitted to enter into only
     one (1) ThermoFluor Deal, including the right to sub-license, and including
     unrestricted sales of ThermoFluor Screening Technology instruments, where
     the principal focus of such business arrangement is Infection, provided
     however that such ThermoFluor Deal may not involve the Hepatitis C Virus
     Field, nor involve more than three (3) other anti-viral targets.

3.4  3DP shall be able to freely secure any partnerships or other business
     arrangements involving ThermoFluor Screening Technology, except that during
     the Restriction Period the principal focus may not be Infection and 3DP
     shall not grant any sublicenses for Infection during the Restriction
     Period, except as permitted under Sections 3.3 and 3.10 of this Agreement.
     In the event that a partner or other third party requests that 3DP screen,
     during the Restriction Period, multiple targets which include Intended
     Infection targets, 3DP shall inform such party that it cannot screen such
     Infection targets, but shall disclose that such screening can be conducted
     by Scriptgen. Scriptgen shall pay to 3DP [**] of all Net Revenues received
     during the first year of an agreement which demonstrably resulted from such
     an introduction by 3DP.

3.5  During the Restriction Period, Scriptgen may refer to 3DP any third parties
     that have requested that Scriptgen screen multiple targets to identify
     leads or drugs that are effective in any field other than Infection. In
     such event, 3DP shall pay to Scriptgen [**] of all Net Revenues received
     during the first year of an agreement which demonstrably resulted from such
     an introduction by Scriptgen, if such third party or its Affiliates were
     not previously contacted by 3DP.

3.6  3DP shall be free to use ThermoFluor Screening Technology without
     restriction in any 3DP Internal Program, except in the Hepatitis C Virus
     Field during the Restriction Period, and to license or transfer, in any
     manner, any compounds discovered or optimized through such use of
     ThermoFluor Screening Technology. 3DP shall not use ThermoFluor Screening
     Technology in the Hepatitis C Virus Field during the Restriction Period.

3.7  In the event that 3DP uses ThermoFluor Screening Technology in a 3DP
     Internal Program that leads to the designation, during the Restriction
     Period, of a Development Compound that leads to a drug in Infection, 3DP
     shall pay to Scriptgen a sliding-scale royalty based on 3DP's Net Revenues
     from the sale of such drug by 3DP, as follows:

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.

                                      -4-
<PAGE>

                            Category                                Royalty
                            --------                                -------

All anti-infectives, except anti-virals:

[**]                                                                  [**]

[**]                                                                  [**]

All anti-virals                                                       [**]

Nothing in this Section 3.7 shall be construed as giving 3DP the right to use
ThermoFluor Screening Technology in the Hepatitis C Virus field during the
Restriction Period.

3.8  The maximum aggregate amount of all royalty payments made under Section
     3.7, on a cumulative basis including all such 3DP Internal Programs, shall
     not exceed five million United States dollars ($5,000,000).

3.9  In the event that 3DP uses ThermoFluor Screening Technology, in a 3DP
     Internal Program that leads to the designation, during the Restriction
     Period, of a Development Compound that leads to a drug in Infection, and
     3DP subsequently licenses or sells the rights to such drug to a third
     party, 3DP shall pay to Scriptgen [**] in the case of anti-infectives
     (excluding anti-virals), or [**] in the case of anti-virals, of the up-
     front cash payments or sales price received by 3DP from such transaction.
     The maximum amount of all such payments in aggregate shall not exceed two
     million United States dollars ($2,000,000). Notwithstanding the foregoing,
     if any such up-front payments are in the form of an investment in equity
     securities of 3DP, the amount of such investment, calculated on a per share
     basis, that is in excess of [**] of the amount per share paid in the last
     3DP equity financing (or, if 3DP is public, [**] of the closing price
     immediately prior to the transaction) shall be deemed to be an "up-front
     payment" for purposes of this calculation.

3.10 There shall be no limitations on sales, licenses (including the right to
     grant sublicenses limited to use of the ThermoFluor Screening Technology
     instruments), or leases of ThermoFluor Screening Technology instruments,
     except that during the Restriction Period, in the therapeutic field of
     Infection, 3DP may only sell, license (including the right to grant
     sublicenses limited to use of ThermoFluor Screening Technology
     instruments), or lease ThermoFluor Screening Technology instruments as part
     of the permitted ThermoFluor Deal in Infection specified in Section 3.3
     above.

3.11 The license of Section 3.1 shall not be deemed to grant a license,
     directly, or by implication or otherwise, under any know-how, copyright,
     trademark, or other intellectual property right.

**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission.  The omitted
portions have been filed separately with the Commission.

                                      -5-
<PAGE>

4.   THE RESTRICTION PERIOD

4.1  The restrictions of Sections 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9 and 3.10 on
     the perpetual, nonexclusive, worldwide, fully-paid license granted by
     Scriptgen in Section 3.1 above, shall terminate on the earlier of:

     (a)  The end of the Restriction Period; or

     (b)  Any finding of invalidity or unenforceability of claims 1 and 17 of
          the 277 patent and claims 1, 3, 5, 20, 23 and 26 of the 582 patent by
          the USPTO or by a court of competent jurisdiction from either of which
          an appeal can no longer be taken.

5.  LICENSE GRANT BY 3DP TO SCRIPTGEN

5.1  (a)  In settlement of the Action, 3DP hereby grants to Scriptgen beginning
          on the Effective Date a perpetual, non-exclusive, worldwide, fully
          paid license, under any Method Claims found in: (a) U.S. Patent No.
          6,020,141; (b) any U.S. patents issuing from allowed U.S. Patent
          Application Serial No. 08/853,459; (c) any patents issuing from any
          and all continuing applications, divisional applications,
          continuation-in-part applications of said `141 patent, said `459
          application and/or the application on which said `141 patent was
          granted, and any reissues, extensions, renewals and reexaminations of
          such patents or patent applications; and/or (d) any foreign
          counterparts of the patents in (a), (b) and (c). The license granted
          to Scriptgen herein shall include the right to sublicense solely in
                                                                    ------
          the field of Infection. In addition, 3DP agrees not to file any future
          patent infringement actions against Scriptgen for Scriptgen's use of
          Atlas Technology that is consistent with the terms of this Agreement.

     (b)  During the first three years after the Effective Date, screening
          collaborations conducted by Scriptgen on behalf of third parties
          outside the field of Infection shall be conducted on-site at a
          Scriptgen facility only and shall not exceed ten (10) such screening
          collaborations; provided however that this limitation shall expire at
          the end of the three-year period.

5.2  The license of Section 5.1 shall not be deemed to grant a license, directly
     or by implication or otherwise, under any know-how, copyright, trademark,
     or any other intellectual property right.

5.3  Scriptgen shall not have the right to assign the license granted herein
     except as part of the sale of its Atlas Technology or business, the sale of
     substantially all the capital stock or assets of the corporation, or the
     merger or consolidation of the corporation.

6.  ROYALTY PAYMENTS, RECORDS AND INSPECTION

6.1  All payments based upon Net Revenues payable hereunder ("Royalty" or
     "Royalties") which have accrued in any Calendar Quarter shall be made
     within forty-five (45) days after the end of such Calendar Quarter.

                                       6
<PAGE>

6.2  Each party shall keep accurate records and books of account in sufficient
     detail to enable all Royalty payments to be determined. A written report
     shall accompany each Royalty payment setting forth in reasonable detail,
     for the applicable Calendar Quarter, the total Royalties that are to be
     paid to a party hereunder and the other party's calculation thereof.

6.3  Upon ten (10) days' prior written notice to a party and during normal
     business hours, but not more frequently than annually, an independent
     auditor of nationally recognized standing agreed to by both parties and
     paid for by the other party may inspect such books and records of such
     party for the one-year period immediately preceding the date of inspection
     to verify the correctness of the reports given to the other party under
     this Section 6. If a material discrepancy is found in such books and
     records, the right of inspection shall extend to books and records for
     periods prior to such one-year period. Each party shall pay any deficiency,
     plus interest thereon from the date each payment was due, calculated at the
     prime rate of Citibank of New York, within thirty (30) days of the date of
     any notice of such discrepancy. If the deficiency for any year is greater
     than ten percent (10%), the reasonable costs of the audit shall be paid by
     such party. All information learned in the course of any examination of
     each party's books and records hereunder, except when it is necessary to
     reveal such information in order to enforce any rights under this Agreement
     in court, or similar dispute resolution or enforcement proceeding or
     action, shall be treated as confidential information.

7.   PRESS RELEASES AND CONFIDENTIALITY

7.1  Upon executing this Agreement, the parties shall issue a joint press
     release as appearing in Exhibit B.

7.2  Upon entering the permitted ThermoFluor Deal in Infection specified in
     Section 3.3 above, 3DP shall issue a press release which identifies
     Scriptgen as part (i.e., a contributing licensor) of the collaboration
     agreement and states that Scriptgen maintains exclusivity under its
     intellectual property rights regarding future Infection collaborations.

7.3  The parties agree that except as provided in Sections 7.1 and 7.2 above,
     the terms and provisions contained herein shall be confidential. It shall
     not be a breach of this Agreement, however, for any party to: (a) disclose
     this Agreement to its outside counsel, or the financial effect hereof to
     its own accountants, auditors, creditors, investors, potential investors,
     merger partners or potential merger partners, provided that such recipients
     are directed to keep the terms confidential; or (b) make any disclosure
     necessary to comply with the financial, public disclosure or other
     reporting requirements under any applicable laws.

8.  NOTICES

8.1  Under this Agreement, all required notices or communications shall be in
     writing and deemed effective upon receipt if sent by first class mail
     (postage prepaid), courier, or facsimile, and addressed as follows:

                                       7
<PAGE>

     For Scriptgen:      Mark T. Weedon
                         President & CEO
                         Scriptgen Pharmaceuticals, Inc.
                         610 Lincoln Street
                         Waltham, MA 02451
                         Telephone: (781) 768-3400
                         Facsimile: (781) 768-5628

     For 3DP:            David C. U'Prichard, Ph.D.
                         Chief Executive Officer
                         3-Dimensional Pharmaceuticals, Inc.
                         Eagleview Corporate Center
                         665 Stockton Drive, Suite 104
                         Exton, Pa 19341
                         Telephone: (610) 458-8959
                         Facsimile: (610) 458-8258

8.2  The address of either party may be changed by notice duly given to the
     other party.

9.   GENERAL PROVISIONS

9.1  This Agreement is executed voluntarily and without any duress or undue
     influence on the parties or their officers, employees, agents, or
     attorneys. Neither party is relying on any inducements, promises, or
     representations not contained herein made by the other party or any of its
     officers, employees, agents, or attorneys.

9.2  If any legal action or other proceeding is brought to enforce the terms of
     this Agreement, the prevailing party shall be entitled to recover its
     reasonable attorneys' fees and other costs incurred in bringing such action
     or proceeding, in addition to any other relief to which such party may be
     entitled.

9.3  Any provision of this Agreement which is invalid, illegal, or unenforceable
     in any jurisdiction shall, as to that jurisdiction, be ineffective only to
     the extent of such invalidity, illegality, or unenforceability, and shall
     not in any manner affect the remaining provisions hereof in such
     jurisdiction or render any other provision of this Agreement invalid,
     illegal, or unenforceable in any other jurisdiction.

9.4  This Agreement shall be governed by and interpreted in accordance with the
     laws of the State of Delaware, United States of America, without regard to
     the conflict of laws principles thereof.

9.5  The headings used herein are for reference and convenience only, and shall
     not enter into the interpretation of this Agreement. This Agreement
     contains the entire agreement between the parties as to the subject matter
     hereof. This Agreement may not be modified or amended except by a written
     amendment signed by an officer of each party.

                                       8
<PAGE>

9.6  Subject to Sections 3.2 and 5.3, this Agreement shall inure to the benefit
     of and be binding on any and all successors in interest to the parties
     hereto.

9.7  It shall not be a breach of this Agreement for either party to fail to
     perform its obligations under this Agreement on account of any act of God
     or other cause beyond the control of the affected party, subject to such
     party performing such obligation as soon as possible thereafter.

9.8  A breach of any provision of this Agreement may only be waived in writing
     and the waiver of such breach shall not operate or be construed as a waiver
     of any subsequent breach.

9.9  Each party represents and warrants that it has the full and unencumbered
     right, power and authority to enter into this Agreement, to grant the
     license rights granted hereunder, and otherwise to carry out its
     obligations thereunder.

9.10 In making and performing this Agreement, the parties hereto are acting and
     shall act as independent contractors. Neither party is, nor will be deemed
     to be, an agent, legal representative, joint venturer or partner of the
     other party for any purpose. Neither party will be entitled to bind the
     other party without prior written approval, and each party shall bear its
     own expenses and costs in connection with performing its obligations under
     this Agreement.

9.11 This Agreement may be executed originally or by facsimile signature in
     multiple counterparts, each of which shall be deemed an original and all of
     which together shall constitute one instrument, provided however, that this
     Agreement shall not be binding upon either of the parties until such time
     it is actually executed by duly authorized officers of both parties.

IN WITNESS WHEREOF, the parties hereto have caused duplicate originals of this
Settlement Agreement to be executed by their duly authorized officers on the
date(s) set forth below:

Scriptgen Pharmaceuticals, Inc.              3-Dimensional Pharmaceuticals, Inc.

By: /s/ Mark T. Weedon                       By: /s/ David C. U'Prichard
    --------------------------------             -------------------------------
Printed Name: Mark T. Weedon
Title: President & Chief Executive Officer   Printed Name:  David C. U'Prichard
Date: March 7, 2000                          Title:  Chief Executive Officer

                                       9

<PAGE>

                                      10
<PAGE>

                                                                       Exhibit A
                                                                       ---------

                      IN THE UNITED STATES DISTRICT COURT

                          FOR THE DISTRICT OF DELAWARE

SCRIPTGEN PHARMACEUTICALS, INC.,              :

               Plaintiff,                     :

     v.                                       :       C.A. No. 98-583 (GMS)

3-DIMENSIONAL PHARMACEUTICALS, INC.,          :

                                              :

               Defendant.                     :

                         STIPULATED ORDER OF DISMISSAL
                         -----------------------------

     Pursuant to Fed. R.Civ.P. 41(a)(1), it is hereby stipulated by the parties,
subject to the approval of the Court, that this action, including all claims and
counterclaims, is dismissed, with each party to bear its own costs.

                                    POTTER ANDERSON & CORROON LLP

                                    -------------------------------
                                    Richard L. Horwitz (#2246)
                                    Joanne Ceballos (#2854)
                                    Hercules Plaza
                                    P.O. Box 951
                                    Wilmington, Delaware 19899-0951
                                    (302) 984-6000

                                    Attorneys for Plaintiff
                                    Scriptgen Pharmaceuticals, Inc.
<PAGE>

                                    MORRIS, NICHOLS, ARSHT &
                                    TUNNELL

                                    -------------------------------
                                    Jack B. Blumenfeld (#1014)
                                    Julia Heaney (#3052)
                                    1201 N. Market Street
                                    P.O. Box 1347
                                    Wilmington, DE 19899-1347
                                    (302) 658-9200

                                    Attorneys for Defendant
                                    3-Dimensional Pharmaceuticals, Inc.

SO ORDERED this _ day of

__________________, 2000

_____________________________
United States District Judge
<PAGE>

                                                         Exhibit B
                                                         ---------
Contacts:

For Scriptgen:
  Mark T. Weedon                                  Gretchen L.P. Schwaltzer
  Chief Executive Officer                         Feinstein Kean Healthcare
  (781) 768-3400                                  (617) 577-8110

For 3-Dimensional Pharmaceuticals, Inc.
  Michael J. Wassil                               Jerry Parrott
  Chief Financial Officer                         Jerry Parrott & Associates
   (610) 458-6073                                 (212) 472-1244

For Immediate Release
---------------------

                    Scriptgen and 3DP Settle Patent Dispute

        Companies Cross-License High Throughout Screening - Technologies
                           To Advance Drug Discovery

Waltham, Massachusetts, and Exton, Pennsylvania, January XX, 2000 - Scriptgen
Pharmaceuticals, Inc. and 3-Dimensional Pharmaceuticals, Inc. (3DP) announced
today a mutually beneficial settlement of their dispute over Intellectual
property.  3DP has agreed to purchase a limited, non-exclusive worldwide license
to current and pending patents relating to Scriptgen's ATLAS(R) (Any Target
Ligand Affinity Screen) assay technology - a system for identifying compounds
that are drug candidates.  3DP will grant Scriptgen a limited, non-exclusive
worldwide license to pending patents relating to 3DP's ThermoFluor(R) assay
technology.  Under the agreement, both companies can utilize their respective
assay technologies for the identification of novel drugs in a broad range of
therapeutic areas, however, Scriptgen does maintain a preferential position in
the area of anti-infectives.  Financial terms were not disclosed.

Scriptgen Pharmaceuticals, Inc. (http://www.scriptgen.com) is a leader in the
discovery of drugs to control the expression of genes.  Current programs in the
anti-infective area have identified multiple new drug targets and lead compounds
effective against drug-resistant bacterial, fungal and viral pathogens.
Scriptgen's products include GATH, a family of high-throughput target.
Identification and validation technologies and ATLAS and SCAN, high-throughput
screening technologies for proteins and RNA targets, respectively.

3-Dimensional Pharmaceuticals, Inc. is a drug discovery company using
DiscoverWorks(TM), a proprietary technology platform, to reduce the costs and
improve the quality of drugs entering clinical trials.  DiscoverWorks(TM)
uniquely integrates high-throughput screening, combinatorial chemistry and
structure-based drug design for efficient drug discovery using targets from
genome sequencing.  3DP uses DiscoverWorks(TM) in its own drug discovery
programs and to provide discovery services to pharmaceutical and agrochemical
partners.  The company's
<PAGE>

internal research programs are focused on the discovery of orally active small-
molecule pharmaceuticals for the treatment of cardiovascular disease and cancer.
(http://www.3dp.com).

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