<PAGE>


                                                                     EXHIBIT 4.4

NEITHER THIS AMENDED AND RESTATED WARRANT NOR THE SECURITIES UNDERLYING THIS
AMENDED AND RESTATED WARRANT HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF
1933, AS AMENDED. NO SALE OR DISPOSITION MAY BE EFFECTED EXCEPT IN COMPLIANCE
WITH RULE 144 UNDER SAID ACT OR WITHOUT AN EFFECTIVE REGISTRATION STATEMENT
RELATED THERETO OR AN OPINION OF COUNSEL FOR THE HOLDER, SATISFACTORY TO THE
COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A
NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION.

                            STRUCTURAL GENOMIX, INC.

                           VOID AFTER AUGUST 28, 2009

                          AMENDED AND RESTATED WARRANT
                      TO PURCHASE SHARES OF PREFERRED STOCK

                                                       Dated: September 30, 2004

THIS CERTIFIES THAT, for value received, Oxford Finance Corporation ("Holder"),
is entitled to subscribe for and purchase that number of the fully paid and
nonassessable shares of Series Preferred (as defined below and as adjusted
pursuant to Section 7 hereof, the "Shares") of Structural GenomiX, Inc., a
Delaware corporation (the "Company"), as is determined pursuant to the next
paragraph hereof at the price per share as is determined pursuant to the next
paragraph hereof (such price and such other price as shall result, from time to
time, from the adjustments specified in Section 7 hereof is herein referred to
as the Warrant Price), subject to the provisions and upon the terms and
conditions hereinafter set forth. As used herein, the term "Series Preferred"
shall mean: (a) the Company's presently authorized Series C-1 Preferred Stock,
or (b) in the event that immediately following a Financing (as defined below)
the initial Warrant Price is less than $8.45 (as equitably adjusted for any
stock split, recapitalization or the like affecting the Company's presently
authorized Series C-1 Preferred Stock), the same series of convertible preferred
stock as sold by the Company in its next Financing, and, in either case, any
stock into or for which such stock may hereafter be converted or exchanged, and
(c) after the automatic conversion of the Series Preferred issuable hereunder to
the Company's Common Stock (the "Common Stock"), the Common Stock.

1.    Warrant Price and Number of Shares. The Warrant Price shall be the lower
      of: (a) $8.45 (as equitably adjusted for any stock split, recapitalization
      or the like affecting the Company's presently authorized Series C-1
      Preferred Stock) per share; and (b) the lowest effective price per share
      (on a common stock equivalent basis and taking into account any securities
      issued together with the preferred stock) at which shares of the Company's
      convertible preferred stock are sold in a Financing; provided that if a
      Financing has not closed prior to the exercise or expiration of this
      warrant (the "Amended and Restated Warrant"), then the Warrant Price shall
      be determined pursuant to clause (a) above. A "Financing" shall mean the
      sale of the convertible preferred stock (anticipated to be Series E-1

                                       1.
<PAGE>

      Preferred Stock) of the Company to purchasers which include venture
      capital investors. The number of shares for which this Amended and
      Restated Warrant is exercisable shall be the nearest whole number equal to
      the sum of .02 multiplied by the amount actually loaned by the Holder to
      the Company pursuant to that certain Master Loan and Security Agreement
      dated as of August 28, 2002 by and between the Holder and the Company,
      divided by the Warrant Price determined pursuant to this paragraph.

2.    Conditions to Exercise. The purchase right represented by this Amended and
      Restated Warrant may be exercised at any time, or from time to time, in
      whole or in part during the term commencing on August 28, 2002 (the
      "Original Warrant Grant Date") and ending on the earlier of:

      (a)   5:00 P.M. Eastern Standard time on the seventh annual anniversary of
            the Original Warrant Grant Date; or

      (b)   the closing of the initial public offering of Common Stock pursuant
            to a registration statement under the Securities Act of 1933, as
            amended (the "Initial Public Offering"). The Company shall provide
            notice of the Initial Public Offering to the Holder at least 20 days
            prior to the closing thereof; or

      (c)   the effective date of the merger of the Company with or into, the
            consolidation of the Company with, or the sale by the Company of all
            or substantially all of its assets or all or substantially all of
            its shares to another corporation or other entity (other than such a
            transaction wherein the stockholders of the Company retain or obtain
            a majority of the voting capital stock of the surviving, resulting,
            or purchasing corporation); provided that the Company shall notify
            the registered Holder of this Amended and Restated Warrant of the
            proposed effective date of the merger, consolidation, or sale at
            least 20 days prior to the effectiveness thereof.

      In the event that, although the Company shall have given notice of a
transaction pursuant to subparagraph (b) or subparagraph (c) hereof, the
transaction does not close within 90 days of the day specified by the Company,
unless otherwise elected by the Holder any exercise of the Amended and Restated
Warrant subsequent to the giving of such notice shall be rescinded and the
Amended and Restated Warrant shall again be exercisable until terminated in
accordance with this Section 2.

3.    Method of Exercise; Payment; Issuance of Shares; Issuance of New Amended
      and Restated Warrant.

      (a)   Cash Exercise. Subject to Section 2 hereof, the purchase right
            represented by this Amended and Restated Warrant may be exercised by
            the Holder hereof, in whole or in part, by the surrender of this
            Amended and Restated Warrant (with a duly executed Notice of
            Exercise in the form attached

                                       2.
<PAGE>

            hereto) at the principal office of the Company as set forth in
            Section 18 below (or at such other address as the Company may
            designate by notice in writing to the Holder) and by payment to the
            Company, by check, of an amount equal to the then applicable Warrant
            Price per share multiplied by the number of shares then being
            purchased. In the event of any exercise of the rights represented by
            this Amended and Restated Warrant, certificates for the shares of
            stock so purchased shall be in the name of, and delivered to, the
            Holder, or as such Holder may direct (subject to the terms of
            transfer contained herein and upon payment by such Holder hereof of
            any applicable transfer taxes). Such delivery shall be made within
            20 days after exercise of the Amended and Restated Warrant and at
            the Company's expense and, unless this Amended and Restated Warrant
            has been fully exercised or expired, a new Amended and Restated
            Warrant having terms and conditions substantially identical to this
            Amended and Restated Warrant and representing the portion of the
            Shares, if any, with respect to which this Amended and Restated
            Warrant shall not have been exercised, shall also be issued to the
            Holder within 20 days after exercise of the Amended and Restated
            Warrant.

      (b)   Net Issue Exercise. If the Fair Market Value (defined below) of one
            share of Series Preferred is greater than the Warrant Price (at the
            date of such calculation), in lieu of exercising this Amended and
            Restated Warrant pursuant to Section 3(a), Holder may elect to
            receive shares equal to the value of this Amended and Restated
            Warrant (or of any portion thereof remaining unexercised) by
            surrender of this Amended and Restated Warrant at the principal
            office of the Company together with notice of such election, in
            which event the Company shall issue to Holder the number of shares
            of Series Preferred computed using the following formula:

            X = Y (A-B)
            ----------
                  A

            Where X = the number of shares of Series Preferred to be issued to
            Holder.

            Y = the number of shares of Series Preferred purchasable under this
            Amended and Restated Warrant or, if only a portion of the Amended
            and Restated Warrant is being exercised, the portion of the Amended
            and Restated Warrant being canceled (at the date of such
            calculation).

            A = the Fair Market Value of one share of the Company's Series
            Preferred (at the date of such calculation).

            B = Warrant Price (as adjusted to the date of such calculation).

                                       3.
<PAGE>

      (c)   Fair Market Value. For purposes of this Section 3, the Fair Market
            Value of one share of the Company's Series Preferred shall mean:

            (i)   the event of an exercise in connection with an Initial Public
                  Offering, the per share Fair Market Value for the Series
                  Preferred shall be the offering price at which the
                  underwriters initially sell Common Stock to the public
                  multiplied by the number of shares of Common Stock into which
                  each share of Series Preferred is then convertible; or

            (ii)  In the event of an exercise in connection with a merger,
                  acquisition or other consolidation in which the Company is not
                  the surviving entity, as described in Section 2(c), the per
                  share Fair Market Value for the Series Preferred shall be the
                  value to be received per share of Series Preferred by all
                  holders of the Series Preferred in such transaction as
                  determined by the Company's Board of Directors; or

            (iii) In any other instance, the per share Fair Market Value for the
                  Series Preferred shall be as determined in good faith by the
                  Company's Board of Directors unless Holder elects to have such
                  fair market value determined by an independent appraiser,
                  which election must be made by Holder within ten (10) business
                  days of the date the Company notifies Holder of the fair
                  market value as determined by the Company's Board of
                  Directors. In the event of such an appraisal, the cost thereof
                  shall be borne by the Holder unless such appraisal results in
                  a fair market value in excess of 115% of that determined by
                  the Company's Board of Directors, in which event the Company
                  shall bear the cost of such appraisal.

      (d)   Automatic Exercise. To the extent this Amended and Restated Warrant
            is not previously exercised, and if the Fair Market Value of one
            share of Series Preferred is greater than the Warrant Price then in
            effect, it shall be automatically exercised in accordance with
            Sections 3(b) and 3(c) hereof (even if not surrendered) immediately
            before: (i) its expiration, (ii) the closing of the Initial Public
            Offering, or (iii) the consummation of any consolidation or merger
            of the Company, or any sale or transfer of a majority of the
            Company's assets or shares pursuant to Section 2(c).

4.    Representations and Warranties of Holder and Restrictions on Transfer
      Imposed by the Securities Act of 1933.

      (a)   Representations and Warranties by Holder. The Holder represents and
            warrants to the Company with respect to the Securities (defined
            below) as follows:

                                       4.
<PAGE>

            (i)   The Holder has substantial experience in evaluating and
                  investing in private placement transactions of securities of
                  companies similar to the Company so that the Holder is capable
                  of evaluating the merits and risks of its investment in the
                  Company and has the capacity to protect its interests. The
                  Holder is an "accredited investor" as that term is defined in
                  Rule 501 promulgated under the Securities Act of 1933, as
                  amended (the "Act").

            (ii)  The Holder is acquiring the Amended and Restated Warrant, the
                  shares of Series Preferred issuable upon exercise of the
                  Amended and Restated Warrant and the shares of Common Stock
                  issuable upon conversion thereof (collectively the
                  "Securities") solely for its own account and not with a view
                  to, or for resale in connection with, any distribution of the
                  Securities or any part thereof. The Holder also represents
                  that the entire legal and beneficial interests of the
                  Securities the Holder is acquiring is being acquired for, and
                  will be held for, its account only. The Holder understands
                  that the Securities have not been registered under the Act by
                  reason of a specific exemption from the registration
                  provisions of the Act which depends upon, among other things,
                  the bona fide nature of the investment intent as expressed
                  herein. In this connection, the Holder understands that, in
                  the view of the Securities and Exchange Commission (the
                  "SEC"), the statutory basis for such exemption may be
                  unavailable if this representation was predicated solely upon
                  a present intention to hold the Securities for the minimum
                  capital gains period specified under tax statutes, for a
                  deferred sale, for or until an increase or decrease in the
                  market price of the Securities or for a period of one year or
                  any other fixed period in the future.

            (iii) The Holder acknowledges that the Securities must be held
                  indefinitely unless subsequently registered under the Act or
                  an exemption from such registration is available. The Holder
                  recognizes that the Company has no obligation to register the
                  Securities or any part thereof, or to comply with any
                  exemption from such registration. The Holder is aware of the
                  provisions of Rule 144 promulgated under the Act ("Rule 144")
                  which permits limited resale of securities purchased in a
                  private placement subject to the satisfaction of certain
                  conditions, including, in case the securities have been held
                  for more than one but less than two years, the existence of a
                  public market for the shares, the availability of certain
                  public information about the Company, the resale occurring not
                  less than one year after a party has purchased and paid for
                  the security to be sold, the sale being through a "broker's
                  transaction" or in a transaction directly with a "market
                  maker" (as provided by Rule 144(f)) and the number of shares
                  or other securities being sold during any three-month period
                  not

                                       5.
<PAGE>

                  exceeding specified limitations. Holder is aware that the
                  conditions for resale set forth in Rule 144 have not been
                  satisfied and that the Company presently has no plans to
                  satisfy these conditions in the foreseeable future.

            (iv)  The Holder further understands that at the time the Holder
                  wishes to sell the Securities there may be no public market
                  upon which such a sale may be effected, and that even if such
                  a public market exists, the Company may not be satisfying the
                  current public information requirements of Rule 144, and that
                  in such event, the Holder may be precluded from selling the
                  Securities under Rule 144 unless (a) a one-year minimum
                  holding period has been satisfied and (b) the Holder was not
                  at the time of the sale nor at any time during the three-month
                  period prior to such sale an affiliate of the Company.

            (v)   The Holder has had an opportunity to discuss the Company's
                  business, management and financial affairs with its management
                  and an opportunity to review the Company's facilities. The
                  Holder understands that such discussions, as well as the
                  written information issued by the Company, were intended to
                  describe the aspects of the Company's business and prospects
                  which it believes to be material but were not necessarily a
                  thorough or exhaustive description.

            (vi)  The Holder further agrees not to make any disposition of all
                  or any part of the Securities in any event unless and until:

                  (a)   The Company shall have received a letter secured by the
                        Holder from the Securities and Exchange Commission
                        stating that no action will be recommended to the
                        Commission with respect to the proposed disposition;

                  (b)   There is then in effect a registration statement under
                        the Act covering such proposed disposition and such
                        disposition is made in accordance with said registration
                        statement; or

                  (c)   The Holder shall have notified the Company of the
                        proposed disposition and shall have furnished the
                        Company with a detailed statement of the circumstances
                        surrounding the proposed disposition, and if requested
                        by the Company, the Holder shall have furnished the
                        Company with an opinion of counsel, satisfactory to the
                        Company, for the Holder to the effect that such
                        disposition will not require registration of such
                        Securities under the Act or any applicable state
                        securities laws.

                                       6.
<PAGE>

      (b)   Legends. Each certificate representing the Securities shall be
            endorsed with the following legend:

            THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT
            OF 1933 AND MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR
            HYPOTHECATED UNLESS COVERED BY AN EFFECTIVE REGISTRATION STATEMENT
            UNDER SAID ACT, A "NO ACTION" LETTER FROM THE SECURITIES AND
            EXCHANGE COMMISSION WITH RESPECT TO SUCH TRANSFER, A TRANSFER
            MEETING THE REQUIREMENTS OF RULE 144 OF THE SECURITIES AND EXCHANGE
            COMMISSION, OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY TO
            THE EFFECT THAT ANY SUCH TRANSFER IS EXEMPT FROM SUCH REGISTRATION.

            The Company need not enter into its stock register a transfer of
            Securities unless the conditions specified in the foregoing legend
            are satisfied. The Company may also instruct its transfer agent not
            to register the transfer of any of the Shares unless the conditions
            specified in the foregoing legend are satisfied.

      (c)   Removal of Legend and Transfer Restrictions. The legend relating to
            the Act endorsed on a certificate pursuant to paragraph 4(b) of this
            Amended and Restated Warrant and the stop transfer instructions with
            respect to the Securities represented by such certificate shall be
            removed and the Company shall issue a certificate without such
            legend to the Holder of the Securities if (i) the Securities are
            registered under the Act and a prospectus meeting the requirements
            of Section 10 of the Act is available or (ii) the Holder provides to
            the Company an opinion of counsel for the Holder satisfactory to the
            Company, or a no-action letter or interpretive opinion of the staff
            of the SEC reasonably satisfactory to the Company, to the effect
            that public sale, transfer or assignment of the Securities may be
            made without registration and without compliance with any
            restriction such as Rule 144.

5.    Condition of Transfer or Exercise of Amended and Restated Warrant. It
      shall be a condition to any transfer or exercise of this Amended and
      Restated Warrant that at the time of such transfer or exercise, the Holder
      or transferee, as applicable, shall provide the Company with a
      representation in writing that the Holder or transferee, as applicable, is
      acquiring this Amended and Restated Warrant and the shares of Series
      Preferred to be issued upon exercise, for investment purposes only and not
      with a view to any sale or distribution, or will provide the Company with
      a statement of pertinent facts covering any proposed distribution. As a
      further condition to any transfer of this Amended and Restated Warrant or
      any or all of the shares of Series Preferred issuable upon exercise of
      this Amended and Restated Warrant, other than a transfer registered under
      the Act, the Company must have received a legal opinion, in form and
      substance satisfactory to the

                                       7.
<PAGE>

      Company and its counsel, reciting the pertinent circumstances surrounding
      the proposed transfer and stating that such transfer is exempt from the
      registration and prospectus delivery requirements of the Act. Each
      certificate evidencing the shares issued upon exercise of the Amended and
      Restated Warrant or upon any transfer of the shares (other than a transfer
      registered under the Act or any subsequent transfer of shares so
      registered) shall, at the Company's option, contain a legend in form and
      substance satisfactory to the Company and its counsel, restricting the
      transfer of the shares to sales or other dispositions exempt from the
      requirements of the Act.

      As further condition to each transfer, the Holder shall surrender this
      Amended and Restated Warrant to the Company and the transferee shall
      receive and accept an Amended and Restated Warrant, of like tenor and
      date, executed by the Company.

6.    Stock Fully Paid; Reservation of Shares. All Shares which may be issued
      upon the exercise of the rights represented by this Amended and Restated
      Warrant will, upon issuance, be fully paid and nonassessable, and free
      from all taxes, liens, and charges with respect to the issue thereof.
      During the period within which the rights represented by this Amended and
      Restated Warrant may be exercised, the Company will at all times have
      authorized, and reserved for issuance upon exercise of the purchase rights
      evidenced by this Amended and Restated Warrant, a sufficient number of
      shares of its Series Preferred to provide for the exercise of the rights
      represented by this Amended and Restated Warrant.

7.    Adjustment for Certain Events. In the event of changes in the outstanding
      Common Stock by reason of stock dividends, split-ups, recapitalizations,
      reclassifications, mergers, consolidations, combinations or exchanges of
      shares, separations, reorganizations, liquidations, or the like, the
      number and class of shares available under the Amended and Restated
      Warrant in the aggregate and the Warrant Price shall be correspondingly
      adjusted, as appropriate, by the Board of Directors of the Company. The
      adjustment shall be such as will give the Holder of this Amended and
      Restated Warrant upon exercise for the same aggregate Warrant Price the
      total number, class and kind of shares as it would have owned had the
      Amended and Restated Warrant been exercised prior to the event and had it
      continued to hold such shares until after the event requiring adjustment.

8.    Notice of Adjustments. Whenever any Warrant Price shall be adjusted
      pursuant to Section 7 hereof, the Company shall prepare a certificate
      signed by its chief financial officer setting forth, in reasonable detail,
      the event requiring the adjustment, the amount of the adjustment, the
      method by which such adjustment was calculated, and the Warrant Price and
      number of shares issuable upon exercise of the Amended and Restated
      Warrant after giving effect to such adjustment, and shall cause copies of
      such certificate to be mailed (by certified or registered mail, return
      receipt required, postage prepaid) within thirty (30) days of such
      adjustment to the Holder of this Amended and Restated Warrant as set forth
      in Section 18 hereof.

                                       8.
<PAGE>

9.    "Market Stand-Off" Agreement. Holder hereby agrees that for a period of up
      to 180 days following the effective date of the first registration
      statement of the Company covering common stock (or other securities) to be
      sold on its behalf of the Company in an underwritten public offering, it
      will not sell, dispose of, transfer, make any short sale of, grant any
      option for the purchase of, or enter into any hedging or similar
      transaction with the same economic effect as a sale (other than to
      designees or transferees who agree to be similarly bound), any of the
      Shares (or other securities of the Company) at any time during such period
      except Common Stock included in such registration; provided, however, that
      all officers and directors of the Company who hold securities of the
      Company or options to acquire securities of the Company and all other
      persons with registration rights enter into similar agreements. Holder
      agrees to execute and deliver such other agreements as may be reasonably
      requested by the Company and/or the managing underwriter(s) which are
      consistent with the foregoing or which are necessary to give further
      effect thereto. In order to enforce the foregoing covenant, the Company
      may impose stop-transfer instructions with respect to such Common Stock
      (or other securities) until the end of such period. The underwriters of
      the Company's stock are intended third party beneficiaries of this Section
      9 and shall have the right, power and authority to enforce the provisions
      hereof as though they were a party hereto.

10.   Transferability of Amended and Restated Warrant. This Amended and Restated
      Warrant is transferable on the books of the Company at its principal
      office by the registered Holder hereof upon surrender of this Amended and
      Restated Warrant properly endorsed, subject to compliance with Section 5
      and applicable federal and state securities laws. The Company shall issue
      and deliver to the transferee a new Amended and Restated Warrant
      representing the Amended and Restated Warrant so transferred. Upon any
      partial transfer, the Company will issue and deliver to Holder a new
      Amended and Restated Warrant with respect to the Amended and Restated
      Warrant not so transferred. Holder shall not have any right to transfer
      any portion of this Amended and Restated Warrant to any direct competitor
      of the Company. The transferee shall sign an investment letter
      satisfactory to the Company.

11.   No Fractional Shares. No fractional share of Series Preferred will be
      issued in connection with any exercise hereunder, but in lieu of such
      fractional share the Company shall make a cash payment therefor upon the
      basis of the Warrant Price then in effect.

12.   Charges, Taxes and Expenses. Issuance of certificates for shares of Series
      Preferred upon the exercise of this Amended and Restated Warrant shall be
      made without charge to the Holder for any United States or state of the
      United States documentary stamp tax or other incidental expense with
      respect to the issuance of such certificate, all of which taxes and
      expenses shall be paid by the Company, and such certificates shall be
      issued in the name of the Holder.

                                       9.
<PAGE>

13.   No Stockholder Rights Until Exercise. This Amended and Restated Warrant
      does not entitle the Holder hereof to any voting rights or other rights as
      a stockholder of the Company prior to the exercise hereof.

14.   Registry of Amended and Restated Warrant. The Company shall maintain a
      registry showing the name and address of the registered Holder of this
      Amended and Restated Warrant. This Amended and Restated Warrant may be
      surrendered for exchange or exercise, in accordance with its terms, at
      such office or agency of the Company, and the Company and Holder shall be
      entitled to rely in all respects, prior to written notice to the contrary,
      upon such registry.

15.   Loss, Theft, Destruction or Mutilation of Amended and Restated Warrant.
      Upon receipt by the Company of evidence reasonably satisfactory to it of
      the loss, theft, destruction or mutilation of this Amended and Restated
      Warrant, and, in the case of loss, theft, or destruction, of indemnity
      reasonably satisfactory to it, and, if mutilated, upon surrender and
      cancellation of this Amended and Restated Warrant, the Company will
      execute and deliver a new Amended and Restated Warrant, having terms and
      conditions substantially identical to this Amended and Restated Warrant,
      in lieu hereof.

16.   Miscellaneous.

      (a)   Amended and Restated Warrant Issue Date. The provisions of this
            Amended and Restated Warrant shall be construed and shall be given
            effect in all respect as if it had been issued and delivered by the
            Company on the date hereof.

      (b)   Successors. This Amended and Restated Warrant shall be binding upon
            any successors or assigns of the Company.

      (c)   Governing Law. This Amended and Restated Warrant shall be governed
            by and construed in accordance with the laws of the State of
            California.

      (d)   Headings. The headings used in this Amended and Restated Warrant are
            used for convenience only and are not to be considered in construing
            or interpreting this Amended and Restated Warrant.

      (e)   Saturdays, Sundays, Holidays. If the last or appointed day for the
            taking of any action or the expiration of any right required or
            granted herein shall be a Saturday or a Sunday or shall be a legal
            holiday in the State of California, then such action may be taken or
            such right may be exercised on the next succeeding day not a legal
            holiday.

      (f)   Acceptance. Receipt of this Amended and Restated Warrant by the
            Holder shall constitute acceptance of and agreement to all of the
            terms and conditions contained herein.

                                      10.
<PAGE>

17.   No Impairment. The Company will not, by amendment of its Certificate of
      Incorporation or any other voluntary action, avoid or seek to avoid the
      observance or performance of any of the terms of this Amended and Restated
      Warrant, but will at all times in good faith assist in the carrying out of
      all such terms and in the taking of all such action as may be necessary or
      appropriate in order to protect the rights of the Holder hereof against
      impairment.

18.   Addresses. Any notice required or permitted hereunder shall be in writing
      and shall be mailed by overnight courier, registered or certified mail,
      return receipt required, and postage pre-paid, or otherwise delivered by
      hand or by messenger, addressed as set forth below, or at such other
      address as the Company or the Holder hereof shall have furnished to the
      other party.

      If to the Company:         Structural GenomiX, Inc.
                                 10505 Roselle Street
                                 San Diego, CA 92121
                                 Attention: Chief Financial Officer

      If to the Holder:          Oxford Finance Corporation
                                 133 N. Fairfax Street
                                 Alexandria, VA 22314
                                 Attention: Chief Financial Officer

19.   Amendment and Restatement of Prior Warrant. This Amended and Restated
      Warrant to Purchase Series C-1 Preferred Stock supersedes and restates in
      its entirety the Warrant to Purchase Shares of Preferred Stock dated
      August 28, 2002 (the "Prior Warrant"). Upon execution of this Amended and
      Restated Warrant, all provisions of, rights granted and covenants made in
      the Prior Warrant are hereby waived, released and terminated in their
      entirety and shall have no further force and effect.

                            [signature page follows]

                                      11.
<PAGE>

IN WITNESS WHEREOF, Structural GenomiX, Inc. has caused this Amended and
Restated Warrant to be executed by its officers thereunto duly authorized.

Dated as of September 30, 2004.

STRUCTURAL GENOMIX, INC.

By: /s/ Herbert G. Mutter
    ----------------------
Name:  Herbert G. Mutter
Title:  Vice President, Finance

                                      12.
<PAGE>

                                                                     EXHIBIT 4.4

NOTICE OF EXERCISE

TO:   Structural GenomiX, Inc.
      10505 Roselle Street
      San Diego, CA 92121

1.    The undersigned Warrantholder ("Holder") elects to acquire shares of the
      Series Preferred of STRUCTURAL GENOMIX, INC., (the "Company"), pursuant to
      the terms of the Amended and Restated Warrant to Purchase Shares of
      Preferred Stock dated September ___, 2004 (the "Amended and Restated
      Warrant").

2.    The Holder exercises its rights under the Amended and Restated Warrant as
      set forth below:

      (  )        The Holder elects to purchase ___________ shares of Series
                  Preferred as provided in Sections 3(a) and (c) and tenders
                  herewith a check in the amount of $_____________ as payment of
                  the purchase price.

      (  )        The Holder elects to convert the purchase rights into shares
                  of Series Preferred as provided in Sections 3(b) and (c) of
                  the Amended and Restated Warrant.

3.    The Holder surrenders the Amended and Restated Warrant with this Notice of
      Exercise.

4.    The Holder represents that it is acquiring the aforesaid shares of Series
      Preferred for investment and not with a view to, or for resale in
      connection with, distribution and that the Holder has no present intention
      of distributing or reselling the shares.

5.    Please issue a certificate representing the shares of the Series Preferred
      in the name of the Holder or in such other name as is specified below:

      Name:         Structural Genomix, Inc.
      Address:      10505 Roselle Street
                    San Diego, CA 92121

      Taxpayer I.D.:

      By:      Oxford Finance Corporation

      Name:  ________________________

      Title: ________________________

      Date:  ________________________