Warrant to Purchase Common Stock

WARRANT TO PURCHASE COMMON STOCK




                                                                   EXHIBIT 10.10

             Warrant to Purchase 10,500 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, Henry Rothman or assigns
("Holder") is entitled to purchase, subject to the provisions of this Warrant,
from 3-Dimensional Pharmaceuticals, Inc., a Delaware corporation (the
"Company"), 10,500 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 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 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 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 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.

        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 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.

    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.


                              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


                                 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 ____________________________