Document:

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                                                                    EXHIBIT 4.2

THIS WARRANT AND THE UNDERLYING SECURITIES HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED (THE "ACT"). THEY MAY NOT BE SOLD, OFFERED
FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION
STATEMENT AS TO SUCH SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL
SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED.

                            STRUCTURAL GENOMIX, INC.

                        WARRANT TO PURCHASE COMMON STOCK

NO. CW-[__]                                                     JULY [___], 2005

                           VOID AFTER JULY [__], 2010

      THIS CERTIFIES THAT, for value received, ________________, or ____ assigns
(the "HOLDER"), is entitled to subscribe for and purchase from STRUCTURAL
GENOMIX, INC., a Delaware corporation, with its principal office at 10505
Roselle Street, San Diego, CA 92121 (the "COMPANY") __________ Exercise Shares
at the Exercise Price (each subject to adjustment as provided herein).

      1. DEFINITIONS. As used herein, the following terms shall have the
following respective meanings:

            (a) "EXERCISE PERIOD" shall mean the period commencing on the date
hereof and ending five (5) years later, unless sooner terminated as provided
below.

            (b) "EXERCISE PRICE" shall mean $0.50 per Exercise Share subject to
adjustment pursuant to Sections 5 below.

            (c) "EXERCISE SHARES" shall mean shares of the Company's Common
Stock issuable upon exercise of this Warrant, subject to adjustment pursuant to
Section 5 below.

      2. EXERCISE OF WARRANT. The rights represented by this Warrant may be
exercised in whole or in part at any time during the Exercise Period, by
delivery of the following to the Company at its address set forth above (or at
such other address as it may designate by notice in writing to the Holder):

            (a)   An executed Notice of Exercise in the form attached hereto;

            (b)   If applicable, payment of the Exercise Price in cash or by
                  check; and

            (c)   This Warrant.

      Upon the exercise of the rights represented by this Warrant, a certificate
or certificates for the Exercise Shares so purchased, registered in the name of
the Holder or persons affiliated with the Holder, if the Holder so designates,
shall be issued and delivered to the Holder within a reasonable time after the
rights represented by this Warrant shall have been so exercised. In the event
that this Warrant is being exercised for less than all of the then-current
number of Exercise Shares purchasable hereunder, the Company shall, promptly
following the issuance by the

                                       1.
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Company of the number of Exercise Shares for which this Warrant is then being
exercised, issue a new Warrant exercisable for the remaining number of Exercise
Shares purchasable hereunder.

      The person in whose name any certificate or certificates for Exercise
Shares are to be issued upon exercise of this Warrant shall be deemed to have
become the holder of record of such shares on the date on which this Warrant was
surrendered and payment of the Exercise Price was made, irrespective of the date
of delivery of such certificate or certificates, except that, if the date of
such surrender and payment is a date when the stock transfer books of the
Company are closed, such person shall be deemed to have become the holder of
such shares at the close of business on the next succeeding date on which the
stock transfer books are open.

      2.1 NET EXERCISE. Notwithstanding any provisions herein to the contrary,
if the fair market value of one Exercise Share is greater than the Exercise
Price (at the date of calculation as set forth below), in lieu of exercising
this Warrant by payment of cash, the Holder may elect to receive shares equal to
the value (as determined below) of this Warrant (or the portion thereof being
canceled) by surrender of this Warrant at the principal office of the Company
together with the properly endorsed Notice of Exercise in which event the
Company shall issue to the Holder a number of Exercise Shares computed using the
following formula:

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

      Where  X   =      the number of Exercise Shares to be issued to the Holder

             Y   =      the number of Exercise Shares purchasable under the
                        Warrant or, if only a portion of the Warrant is being
                        exercised, that portion of the Warrant being canceled
                        (at the date of such calculation)

             A   =      the fair market value of one Exercise Share (at the date
                        of such calculation)

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

      For purposes of the above calculation, the fair market value of one
Exercise Share shall be determined by the Company's Board of Directors in good
faith; provided, however, that in the event that this Warrant is exercised
pursuant to this Section 2.1 in connection with the Company's initial public
offering of its Common Stock, the fair market value per share shall be the per
share offering price to the public of the Company's initial public offering.

      3. COVENANTS OF THE COMPANY.

            3.1 COVENANTS AS TO EXERCISE SHARES. The Company covenants and
agrees that all Exercise Shares that may be issued upon the exercise of the
rights represented by this Warrant will, upon issuance, be validly issued and
outstanding, fully paid and nonassessable, and free from all taxes, liens and
charges with respect to the issuance thereof. The Company further covenants and
agrees that the Company will at all times during the Exercise Period, have
authorized and reserved, free from preemptive rights, a sufficient number of
shares of the series of equity securities comprising the Exercise Shares to
provide for the exercise of the rights

                                       2.
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represented by this Warrant. If at any time during the Exercise Period the
number of authorized but unissued shares of such series of the Company's equity
securities shall not be sufficient to permit exercise of this Warrant, the
Company will take such corporate action as may, in the opinion of its counsel,
be necessary to increase its authorized but unissued shares of such series of
the Company's equity securities to such number of shares as shall be sufficient
for such purposes.

            3.2 NOTICES OF RECORD DATE. In the event of any taking by the
Company of a record of the holders of any class of securities for the purpose of
determining the holders thereof who are entitled to receive any dividend (other
than a cash dividend which is the same as cash dividends paid in previous
quarters) or other distribution, the Company shall mail to the Holder, at least
ten (10) days prior to the date specified herein, a notice specifying the date
on which any such record is to be taken for the purpose of such dividend or
distribution.

      4. REPRESENTATIONS OF HOLDER.

            4.1 ACQUISITION OF WARRANT FOR PERSONAL ACCOUNT. The Holder
represents and warrants that it is acquiring the Warrant and the Exercise Shares
solely for its account for investment and not with a view to or for sale or
distribution of said Warrant or Exercise Shares or any part thereof. The Holder
also represents that the entire legal and beneficial interests of the Warrant
and Exercise Shares the Holder is acquiring is being acquired for, and will be
held for, its account only.

            4.2 SECURITIES ARE NOT REGISTERED.

                  (a) The Holder understands that the Warrant and the Exercise
Shares have not been registered under the Securities Act of 1933, as amended
(the "ACT") on the basis that no distribution or public offering of the stock of
the Company is to be effected. The Holder realizes that the basis for the
exemption may not be present if, notwithstanding its representations, the Holder
has a present intention of acquiring the securities for a fixed or determinable
period in the future, selling (in connection with a distribution or otherwise),
granting any participation in, or otherwise distributing the securities. The
Holder has no such present intention.

                  (b) The Holder recognizes that the Warrant and the Exercise
Shares must be held indefinitely unless they are subsequently registered under
the Act or an exemption from such registration is available. The Holder
recognizes that except as set forth in the Investor Rights Agreement, the
Company has no obligation to register the Warrant or the Exercise Shares of the
Company, or to comply with any exemption from such registration.

                  (c) The Holder is aware that neither the Warrant nor the
Exercise Shares may be sold pursuant to Rule 144 adopted under the Act unless
certain conditions are met, including, among other things, the existence of a
public market for the shares, the availability of certain current public
information about the Company, the resale following the required holding period
under Rule 144 and the number of shares being sold during any three month period
not exceeding specified limitations. Holder is aware that the conditions for
resale

                                       3.
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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.

            4.3 DISPOSITION OF WARRANT AND EXERCISE SHARES.

                  (a) The Holder further agrees not to make any disposition of
all or any part of the Warrant or Exercise Shares in any event unless and until:

                        (i) 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;

                        (ii) 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

                        (iii) 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
reasonably requested by the Company, the Holder shall have furnished the Company
with an opinion of counsel, reasonably satisfactory to the Company, for the
Holder to the effect that such disposition will not require registration of such
Warrant or Exercise Shares under the Act or any applicable state securities
laws. The Company agrees that it will not require an opinion of counsel with
respect to transactions under Rule 144 of the Securities Act of 1933, as
amended, except in unusual circumstances.

                  (b) Notwithstanding the provisions of subsection (a) above, no
such restriction shall apply to a transfer by the Holder to the Holder's family
member or trust for the benefit of the Holder; provided that in each case the
transferee will agree in writing to be subject to the terms of this Warrant to
the same extent as if ____ were an original Holder hereunder.

                  (c) The Holder understands and agrees that all certificates
evidencing the shares to be issued to the Holder may bear the following legend:

      THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF
      1933, AS AMENDED (THE "ACT"). THEY MAY NOT BE SOLD, OFFERED FOR SALE,
      PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION
      STATEMENT AS TO THE SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL
      SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED.

            4.4 ACCREDITED INVESTOR STATUS. The Holder is an "accredited
investor" as defined in Regulation D promulgated under the Act.

                                       4.
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      5. ADJUSTMENT OF EXERCISE PRICE AND NUMBER OF EXERCISE SHARES.

            5.1 CHANGES IN SECURITIES. In the event of changes in the
outstanding Common Stock of the Company by reason of stock dividends, splits,
recapitalizations, reclassifications, combinations or exchanges of shares,
separations, reorganizations, liquidations, or the like, the number and class of
Exercise Shares available under the Warrant in the aggregate and the Aggregate
Exercise Price (as defined below) shall be correspondingly adjusted to give the
Holder of the Warrant, on exercise for the same Aggregate Exercise Price, the
total number, class, and kind of shares as the Holder would have owned had the
Warrant been exercised prior to the event and had the Holder continued to hold
such shares until after the event requiring adjustment. For purposes of this
Section 5.1, the "AGGREGATE EXERCISE PRICE" shall mean the aggregate Exercise
Price payable in connection with the exercise in full of this Warrant. The form
of this Warrant need not be changed because of any adjustment in the number of
Exercise Shares subject to this Warrant.

      6. FRACTIONAL SHARES. No fractional shares shall be issued upon the
exercise of this Warrant as a consequence of any adjustment pursuant hereto. All
Exercise Shares (including fractions) to be issued upon exercise of this Warrant
shall be aggregated for purposes of determining whether the exercise would
result in the issuance of any fractional share. If, after aggregation, the
exercise would result in the issuance of a fractional share, the Company shall,
in lieu of issuance of any fractional share, pay the Holder otherwise entitled
to such fraction a sum in cash equal to the product resulting from multiplying
the then current fair market value of one Exercise Share by such fraction.

      7. EARLY TERMINATION. In the event of, at any time during the Exercise
Period, an Acquisition or Asset Transfer (each as defined in the Company's
Amended and Restated Certificate of Incorporation, as such may be amended from
time to time), the Company shall provide to the Holder ten (10) days advance
written notice of such Acquisition or Asset Transfer, and this Warrant shall be
deemed exercised pursuant to Section 2.1 immediately prior to the date of
closing of such Acquisition or Asset Transfer.

      8. MARKET STAND-OFF AGREEMENT. Each Holder hereby agrees that such Holder
shall 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, any Common Stock (or other securities) of the
Company held by such Holder (other than those included in the registration) for
a period specified by the representative of the underwriters of Common Stock (or
other securities) of the Company not to exceed one hundred eighty (180) days
following the effective date of a registration statement of the Company filed
under the Securities Act. 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 8 and
shall have the right, power and authority to enforce the provisions hereof as
though they were a party hereto.

                                       5.
<PAGE>

      9. NO STOCKHOLDER RIGHTS. This Warrant in and of itself shall not entitle
the Holder to any voting rights or other rights as a stockholder of the Company.

      10. TRANSFER OF WARRANT. Subject to applicable laws and the restriction on
transfer set forth on the first page of this Warrant and in Section 4.3 hereof,
this Warrant and all rights hereunder are transferable, by the Holder in person
or by duly authorized attorney, upon delivery of this Warrant and the form of
assignment attached hereto to any transferee designated by Holder. The
transferee shall sign an investment letter in form and substance satisfactory to
the Company.

      11. LOST, STOLEN, MUTILATED OR DESTROYED WARRANT. If this Warrant is lost,
stolen, mutilated or destroyed, the Company may, on such terms as to indemnity
or otherwise as it may reasonably impose (which shall, in the case of a
mutilated Warrant, include the surrender thereof), issue a new Warrant of like
denomination and tenor as the Warrant so lost, stolen, mutilated or destroyed.
Any such new Warrant shall constitute an original contractual obligation of the
Company, whether or not the allegedly lost, stolen, mutilated or destroyed
Warrant shall be at any time enforceable by anyone.

      12. AMENDMENT. Any term of this Warrant may be amended or waived with the
written consent of the Company and the Holder.

      13. NOTICES, ETC. All notices required or permitted hereunder shall be in
writing and shall be deemed effectively given: (a) upon personal delivery to the
party to be notified, (b) when sent by confirmed telex or facsimile if sent
during normal business hours of the recipient, if not, then on the next business
day, (c) five (5) days after having been sent by registered or certified mail,
return receipt requested, postage prepaid, or (d) one (1) day after deposit with
a nationally recognized overnight courier, specifying next day delivery, with
written verification of receipt. All communications shall be sent to the Company
at the address listed on the signature page and to Holder at
[___________________________] or at such other address as the Company or Holder
may designate by ten (10) days advance written notice to the other parties
hereto.

      14. ACCEPTANCE. Receipt of this Warrant by the Holder shall constitute
acceptance of and agreement to all of the terms and conditions contained herein.

      15. ADDITIONAL TERMS/ACKNOWLEDGEMENTS. The Holder acknowledges receipt of,
and understands and agrees to, this Warrant. The Holder further acknowledges
that as of the date hereof, this Warrant sets forth the entire understanding
between the Holder and the Company regarding the acquisition of stock or options
or warrants to acquire stock in the Company and supersedes all prior oral and
written agreements on that subject, including without limitation any equity
compensation or stock options described or referenced in that certain letter
agreement dated ___________________, and the undersigned Holder further
acknowledges and agrees that this Warrant is in lieu of and represents
satisfaction in full of any equity compensation or stock options set forth in
such letter agreement or other prior oral or written agreement, with the
exception of (i) vested options previously granted and delivered to the Holder
in the amount of _________________, and (ii) __________ outstanding shares of
the Company's Common Stock previously issued to Holder.

                                       6.
<PAGE>

      16. GOVERNING LAW. This Warrant and all rights, obligations and
liabilities hereunder shall be governed by and construed under the laws of the
State of California as applied to agreements among California residents, made
and to be performed entirely within the State of California without giving
effect to conflicts of laws principles.

                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

                                       7.
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      IN WITNESS WHEREOF, the Company has caused this Warrant to be executed by
its duly authorized officer as of July ___, 2005.

                                      STRUCTURAL GENOMIX, INC.

                                      By:_______________________________________

                                      Name:_____________________________________

                                      Title:____________________________________

ACKNOWLEDGED AND ACCEPTED:

__________________________________

                                [SIGNATURE PAGE]

<PAGE>

                               NOTICE OF EXERCISE

TO: STRUCTURAL GENOMIX, INC.

      (1)   [ ] The undersigned hereby elects to purchase ________ shares of
Common Stock (the "EXERCISE SHARES") of STRUCTURAL GENOMIX, INC. (the "COMPANY")
pursuant to the terms of the attached Warrant, and tenders herewith payment of
the exercise price in full, together with all applicable transfer taxes, if any.

            [ ] The undersigned hereby elects to purchase ________ shares of
Common Stock (the "EXERCISE SHARES") of STRUCTURAL GENOMIX, INC. (the "COMPANY")
pursuant to the terms of the net exercise provisions set forth in Section 2.1 of
the attached Warrant, and tenders herewith payment of all applicable transfer
taxes, if any.

      (2) Please issue a certificate or certificates representing said Exercise
Shares in the name of the undersigned or in such other name as is specified
below:

                          _____________________________
                                     (Name)

                          _____________________________

                          _____________________________
                                    (Address)

      (3) The undersigned represents that (i) the aforesaid Exercise Shares are
being acquired for the account of the undersigned for investment and not with a
view to, or for resale in connection with, the distribution thereof and that the
undersigned has no present intention of distributing or reselling such shares;
(ii) the undersigned is aware of the Company's business affairs and financial
condition and has acquired sufficient information about the Company to reach an
informed and knowledgeable decision regarding its investment in the Company;
(iii) the undersigned is experienced in making investments of this type and has
such knowledge and background in financial and business matters that the
undersigned is capable of evaluating the merits and risks of this investment and
protecting the undersigned's own interests; (iv) the undersigned understands
that Exercise Shares issuable upon exercise of this Warrant have not been
registered under the Securities Act of 1933, as amended (the "SECURITIES ACT"),
by reason of a specific exemption from the registration provisions of the
Securities Act, which exemption depends upon, among other things, the bona fide
nature of the investment intent as expressed herein, and, because such
securities have not been registered under the Securities Act, they must be held
indefinitely unless subsequently registered under the Securities Act or an
exemption from such registration is available; (v) the undersigned is aware that
the aforesaid Exercise Shares may not be sold pursuant to Rule 144 adopted under
the Securities Act unless certain conditions are met and until the undersigned
has held the shares for the number of years prescribed by Rule 144, that among
the conditions for use of the Rule is the availability of current information to
the public about the Company and the Company has not made such information
available and has no present plans to do so; and (vi) the undersigned agrees not
to make any disposition of all or any part of the aforesaid shares of Exercise
Shares unless and until there is then in effect a registration statement under
the Securities Act covering such proposed disposition and such disposition is
made in accordance with said registration statement, or, if

                                       1.
<PAGE>

reasonably requested by the Company, the undersigned has provided the Company
with an opinion of counsel satisfactory to the Company, stating that such
registration is not required, or as otherwise permitted by Section 4.3 of the
Warrant

______________________________________    ______________________________________
(Date)                                    (Signature)

                                          ______________________________________
                                          (Print name)

                                       2.
<PAGE>

                                 ASSIGNMENT FORM

                 (To assign the foregoing Warrant, execute this form
                 and supply required information. Do not use this form
                 to purchase shares.)

      FOR VALUE RECEIVED, the foregoing Warrant and all rights evidenced thereby
are hereby assigned to

Name: __________________________________________________________________________
                                 (Please Print)

Address: _______________________________________________________________________
                                 (Please Print)

Dated: __________, 20__

Holder's
Signature: _______________________________________

Holder's
Address: _________________________________________

NOTE: The signature to this Assignment Form must correspond with the name as it
appears on the face of the Warrant, without alteration or enlargement or any
change whatever. Officers of corporations and those acting in a fiduciary or
other representative capacity should file proper evidence of authority to assign
the foregoing Warrant.

                                       3.<PAGE>
                                                                     EXHIBIT 4.6

    THIS NOTE IS A RESTRICTED SECURITY WITHIN THE MEANING OF THE SECURITIES ACT
OF 1933, AS AMENDED (THE "ACT"), AND ANY APPLICABLE STATE SECURITIES LAWS, AND
MAY NOT BE OFFERED, SOLD, PLEDGED, OR OTHERWISE TRANSFERRED WITHOUT REGISTRATION
UNDER THE ACT OR THE OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT AN
EXEMPTION FROM REGISTRATION IS AVAILABLE OR THAT SUCH TRANSFER MAY OTHERWISE
LAWFULLY BE MADE.

                            STRUCTURAL GENOMIX, INC.
                AMENDED AND RESTATED CONVERTIBLE PROMISSORY NOTE

$6,000,000.00                                          Dated:  December 16, 2004

San Diego, California

      This Amended and Restated Convertible Promissory Note is made as of the
16th day of December, 2004, ("Restatement Date") by and between Structural
GenomiX, Inc., a corporation duly organized and existing under the laws of
Delaware (the "Company") and Millennium Pharmaceuticals, Inc. (as successor in
interest to mHOLDINGS TRUST) or registered assigns (the "Holder").

Preliminary Statements:

      1. Holder received from Company a Convertible Promissory Note dated
December 21, 2001 in the principal sum of USD $6,000,000, as previously amended
by Amendment No. 1 dated March 14, 2003, Amendment No. 2 dated August 29, 2003
and Amendment No. 3 dated February 5, 2004; (the "Note").

      2. Company and Holder now wish to amend and restate the Note to set out
fully their respective rights and obligations as set forth below.

      NOW, THEREFORE, for good and valuable consideration, the receipt and
sufficiency of which hereby are acknowledged, each of the undersigned hereby
agrees as follows:

      Structural GenomiX, Inc., a corporation duly organized and existing under
the laws of Delaware (the "Company"), for value received, hereby promises to pay
to mHOLDINGS TRUST or registered assigns (the "Holder"), the principal sum of
$6,000,000.00. This Note is executed and delivered in connection with that
certain Convertible Promissory Note Purchase Agreement dated December 21, 2001
by and among the Company, the Holder and Millennium Pharmaceuticals, Inc.
("Millennium") (as the same may be amended, modified or supplemented or
restated, the "Purchase Agreement"). All capitalized terms used herein and not
otherwise defined herein shall have the respective meanings given to them in the
Purchase Agreement.

                                       1.
<PAGE>
      1. Principal;. As of the Restatement Date, the full principal amount of
this Note has converted to the Convertible Amount pursuant to Section 5.

      2. Interest. No interest shall accrue on the unpaid principal balance of
this Note. Interest shall accrue on overdue payments of principal, unless such
payments have been extended by the Holder, at the annual rate of fifteen percent
(15%).

      3. Registration and Transfer of the Note. The Company will keep the
registration and transfer books for the Note. The Note may be transferred only
on the books of the Company. The Note may not be transferred without the prior
written consent of the Company, except to affiliates of mHoldings Trust (the
"Permitted Transferees"). The Note may be transferred to a Permitted Transferee
only if (a) prior to any such transfer, the Permitted Transferee enters into a
written agreement in form and substance acceptable to the Company pursuant to
which the Permitted Transferee agrees to be bound by all of the provisions of
the Note and the Purchase Agreement and (b) such transfer complies with all
applicable federal and state securities laws and prior to any such transfer, and
if requested by the Company, the Holder provides to the Company an opinion of
counsel satisfactory to the Company regarding compliance with applicable federal
and state securities laws. Upon surrender or transfer of the Note at the
principal office of the Company, duly endorsed for transfer or accompanied by a
proper assignment duly executed by the registered owner or such owner's attorney
duly authorized in writing, and accompanied by the documents described in the
preceding sentence, the Company will issue and deliver to the transferee a new,
fully registered Note in like principal amount. Any attempted transfer of the
Note, any portion thereof or any interest therein that is not in compliance with
the provisions of this Section 4 shall be null and void.

      4. No Prepayment. This Note may not be prepaid without the prior written
consent of the Holder, except as expressly provided herein.

      5.    Conversion.

      (a)   Subject to Sections 5(b) - (e) below, portions of the principal
on the Note will convert into the right of the Holder to receive shares of the
Company's equity securities as set forth below in this Section 5 (the
"Conversion Securities"). The amount so converted into the obligation to issue
shares of the Conversion Securities shall at any time be referred to as the
"Convertible Amount": As of the Restatement Date, the full principal amount of
this Note ($6,000,000) has converted to the Convertible Amount;

      (b) Actual conversion of the Convertible Amount into the Conversion
Securities shall occur immediately upon the closing of a firmly underwritten
public offering pursuant to an effective registration statement under the
Securities Act of 1933, as amended, covering the offer and sale of the Company's
Common Stock, (the "Common Stock") or other class of stock for the account of
the Company and listing on a U.S. national securities exchange or admitted for
quotation on the Nasdaq National Market (the " IPO") or immediately prior to the
closing of any

                                       2.
<PAGE>
Sale of the Company (as defined below) upon the following terms:

            (i) if the Convertible Amount converts pursuant to an IPO, then upon
the closing of the IPO, the Convertible Amount shall convert automatically,
without further action by the Company or the Holder, into Common Stock or such
other class or type of securities registered pursuant to the IPO (the "IPO
Stock") at the same price per share that the IPO Stock is first sold to the
public in the IPO and the Company shall promptly notify its transfer agent to
issue a certificate to the Holder for such IPO stock; and

            (ii) if the Convertible Amount converts pursuant to a Sale of the
Company, then immediately prior to the closing of the Sale of the Company, the
Convertible Amount shall convert automatically, without further action by the
Company or the Holder, into the same type(s) and class(es) of securities issued
at the Company's most recently completed round of financing which yielded at
least $5,000,000 in gross proceeds to the Company (a "Qualified Financing"). The
price at which the Convertible Amount converts into such Conversion Securities
shall be the Sale Value per share of such securities. The "Sale Value" per share
of the Conversion Securities shall be (i) if the Conversion Securities will be
sold for cash in the Sale of the Company, the amount of cash received per share
for the Conversion Securities; (ii) if the Conversion Securities will be
exchanged for property other than cash, the fair market value of the
consideration received per share in exchange for the Conversion Securities;
(iii) if all or substantially all of the assets of the Company will be sold,
leased or otherwise disposed (the "Asset Sale"), the net book value per share of
the Conversion Securities as measured by taking the total amount received in the
Asset Sale, subtracting any liabilities of the Company and the Convertible
Amount existing immediately prior to the Asset Sale, and dividing the result by
the Company's total issued and outstanding shares of Common Stock on an as
converted basis immediately prior to the Asset Sale; or (iv) any combination of
the foregoing, as applicable.

"Sale of the Company" shall mean (A) any consolidation or merger of the Company
with or into any other corporation or other entity or person, or any other
corporate reorganization, in which the stockholders of the Company immediately
prior to such consolidation, merger or reorganization, own less than fifty
percent (50%) of the voting power of the surviving entity immediately after such
consolidation, merger or reorganization; or (B) any transaction or series of
related transactions to which the Company is a party in which in excess of fifty
percent (50%) of the Company's voting power is transferred; or (C) any Asset
Sale; provided that, notwithstanding the foregoing, "Sale of the Company" shall
not include (x) any consolidation or merger effected exclusively to change the
domicile of the Company, or (y) any transaction or series of transactions
principally for bona fide equity financing purposes in which cash is receive by
the Company or indebtedness of the Company is cancelled or converted or a
combination thereof.

      (c) In no event shall the Convertible Amount convert into a total number
of Conversion Securities which on an as converted to Common Stock basis would
exceed 9.9% of the Company's total issued and outstanding shares of Common Stock
as of the date of such conversion (the "Applicable Conversion Date"); if
conversion of the Convertible Amount would exceed this 9.9% threshold, then only
that portion of the Convertible Amount that would convert into a total number of
Conversion Securities which on an as converted to Common Stock basis

                                       3.
<PAGE>
would equal 9.9% of the Company's total issued and outstanding shares of Common
Stock as of the Applicable Conversion Date (including, for purposes of such
calculation, any Conversion Securities issued previously upon conversion of any
Convertible Amount and currently held by the Holder as of the Applicable
Conversion Date) shall be so converted. Once such maximum conversion limitation
has been met, no further portion of the principal under the Note shall convert
into the Convertible Amount, and the remainder of such unconverted Convertible
Amount under the Note shall be repaid in a security to be negotiated at that
time.

      (d) Once the principal under the Note, or any portion thereof, has
converted into the Convertible Amount, such portion of the Note that has so
converted and the Convertible Amount shall represent solely the right to receive
Convertible Securities pursuant to this Section 5. After the Convertible Amount
has been converted pursuant to the terms of this Section 5, the Holder shall
surrender the Note at the office of the Company. If converted, the Company
shall, as soon as practicable thereafter, cause to be issued and delivered to
the Holder of this Note a certificate or certificates in the name of the Holder
(unless otherwise designated in writing by the Holder or Millennium) for the
number and type of shares to which the Holder of this Note shall be entitled.
The person or persons entitled to receive the shares issued upon conversion
shall be treated for all purposes as the record holder or holders of such shares
as of such date. No fractional shares shall be issued upon conversion of this
Note. In lieu thereof, the Company shall pay to the Holder the amount of
outstanding principal that is not so converted by wire transfer to a bank and an
account designated by the Holder.

      (e) If the Company shall by reclassification of securities or otherwise
change any of the Conversion Securities into the same or a different number of
securities of any other class or classes, this Note shall thereafter represent
the right to acquire such number and kind of securities as would have been
issuable as the result of such change with respect to the Conversion Securities
immediately prior to such reclassification.

      (f) At the time(s) of any conversion of the Convertible Amount into
Conversion Securities, the Company shall deliver to the Holder on the date(s) of
any such conversion an opinion of counsel from the Company's outside counsel
(such counsel being reasonably satisfactory to the Holder) stating that such
Convertible Securities are duly authorized, validly issued, fully paid and
non-assessable.

      6. Persons Deemed Owners. The person in whose name the Note is registered
on the books and records of the Company shall be deemed to be the absolute owner
thereof for all purposes, and payment of any principal or interest on such Note
shall be made only to the registered owner thereof or such owner's legal
representative. All payments made to the registered owner or such owner's legal
representative shall be valid and effectual to discharge the liability of the
Company upon this Note to the extent of the sum or sums so paid.

      7. Subordination. The indebtedness evidenced by this Note is hereby
expressly subordinated, to the extent and in the manner hereinafter set forth,
in right of payment to the prior payment in full of the Senior Indebtedness.
"Senior Indebtedness" shall mean, unless expressly subordinated to or made on a
parity with the amounts due under this Note, the principal of, unpaid interest
on and amounts for reasonable fees, expenses, costs of enforcement and other

                                       4.
<PAGE>
amounts due in connection with (a) indebtedness of the Company for borrowed
money to banks or commercial finance or other lending institutions regularly
engaged in the business of lending money (excluding venture capital, investment
banking or similar institutions and their affiliates which sometimes engage in
lending activities but which are primarily engaged in investments in equity
securities), and (b) any such indebtedness for borrowed money or any debentures
for borrowed money, notes or other evidence of indebtedness issued in exchange
for such Senior Indebtedness, or any indebtedness arising from the satisfaction
of such Senior Indebtedness by a guarantor.

      8. Insolvency Proceedings. If there shall occur any receivership,
insolvency, assignment for the benefit of creditors, bankruptcy, reorganization,
or arrangements with creditors (whether or not pursuant to bankruptcy or other
insolvency laws), sale of all or substantially all of the assets, dissolution,
liquidation, or any other marshaling of the assets and liabilities of the
Company, no amount shall be paid by the Company in respect of the principal of,
interest on or other amounts due with respect to this Note at the time
outstanding, unless and until the principal of and interest on the Senior
Indebtedness then outstanding shall be paid in full.

      9. Default on Senior Indebtedness. If there shall occur an event of
default which has been declared in writing with respect to any Senior
Indebtedness, as defined therein, or in the instrument under which it is
outstanding, permitting the holder to accelerate the maturity thereof and the
Holder shall have received written notice thereof from the holder of such Senior
Indebtedness, then, unless and until such event of default shall have been cured
or waived or shall have ceased to exist, or all such Senior Indebtedness shall
have been paid in full, no payment shall be made in respect of the principal of
or interest on this Note unless within one hundred eighty (1 80) days after the
happening of such event of default the maturity of such Senior Indebtedness
shall not have been accelerated and such payment blockage shall only continue so
long as collection of Senior Indebtedness is being diligently pursued. Not more
than one notice (in the aggregate) may be given to the Holder pursuant to the
terms of this Section 11 during any three hundred sixty day (360) day period.
Upon the cure, waiver or ceasing to exist of any such event of default, or upon
the payment in full of all such Senior Indebtedness, the Company shall
immediately pay to the Holder interest, at the rate set forth in Section 2 above
with respect to overdue amounts, on the outstanding amount hereunder from the
date of the happening of such event of default.

      10. Further Assurances. By acceptance of this Note, the Holder agrees to
execute and deliver customary forms of subordination agreement requested from
time to time by the holders of Senior Indebtedness and, as a condition to the
Holder's rights hereunder, the Company may require that the Holder execute such
forms of subordination agreement, provided that such forms shall not impose on
the Holder terms less favorable than those provided herein.

      11. No Impairment. Subject to the rights, if any, of the holders of Senior
Indebtedness under this Note to receive cash, securities or other properties
otherwise payable or deliverable to the Holder, nothing contained in this Note
shall impair, as between the Company and the Holder, the obligation of the
Company, subject to the terms and conditions hereof, to pay to the Holder the
principal hereof and interest hereon as and when the same become due and

                                       5.
<PAGE>
payable, or shall prevent the Holder, upon default hereunder, from exercising
all rights, powers and remedies otherwise provided herein or by applicable law;
and notwithstanding such rights, if any, of the holders of Senior Indebtedness
under this Note, nothing contained in this Note shall impair the conversion of
the principal of this Note into the Convertible Amount or the conversion of the
Convertible Amount into the Conversion Securities, or the right of the Holder
(or its designee) to receive and retain, and not turn over to the holder of any
Senior Indebtedness, any Conversion Securities issued to the Holder or its
designee.

      12. Reliance of Holders of Senior Indebtedness. The Holder, by its
acceptance hereof, shall be deemed to acknowledge and agree that the foregoing
subordination provisions are, and are intended to be, an inducement to and a
consideration of each holder of Senior Indebtedness, whether such Senior
Indebtedness was created or acquired before or after the creation of the
indebtedness evidenced by this Note, and each such holder of Senior Indebtedness
shall be deemed conclusively to have relied on such subordination provisions in
acquiring and holding, or in continuing to hold, such Senior Indebtedness.

      13. Amendment. The terms of this Note may only be modified by the Holder
and the Company in writing.

      14. Additional Terms and Conditions. The Company (i) waives presentment,
demand, notice of demand, protest, notice of protest, and notice of nonpayment
and any other notice required to be given under the law to the Company, in
connection with the delivery, acceptance, performance, default or enforcement of
the Note, except for notice of proposed transfer of the Note in accordance with
the terms hereof and notices of default as provided herein or except as
otherwise expressly provided herein; (ii) agrees that any failure to act or
failure to exercise any right or remedy, on the part of the Holder shall not in
any way affect or impair the obligations of the Company or be construed as a
waiver by the Holder of, or otherwise affect, any of its rights under the Note;
and (iii) agrees to pay, on demand, all reasonable costs and expenses of
collection of the Note and for the enforcement of the Holder's right hereunder,
including reasonable attorney's fees and disbursements.

      15. Invalidity. In the event any one or more of the provisions of the Note
shall for any reason be held to be invalid, illegal or unenforceable, in whole
or in part or in any respect, or in the event that any one or more of the
provisions of the Note operate or would prospectively operate to invalidate the
Note, then and in either of those events, such provision or provisions only
shall be deemed null and void and shall not affect any other provision of the
Note and the remaining provisions of the Note shall remain operative and in full
force and effect and shall in no way be affected, prejudiced and disturbed
thereby.

      16. Governing Law. The General Corporation Law of the State of Delaware
shall govern all issues concerning the relative rights of the Company and its
stockholders. All other questions concerning the construction, validity and
interpretation of this Note shall be governed by, and construed and enforced in
accordance with, the laws of the State of California applicable to contracts
between California residents entered into and to be performed entirely within
the State of California.

                                       6.
<PAGE>
      17. Notices. All notices, requests, consents, and other communications
under this Note shall be in writing and shall be delivered by hand or mailed by
first class certified or registered mail, return receipt requested, postage
prepaid:

Notices to the Company shall be addressed to:

      Structural GenomiX, Inc.
      10505 Roselle Street
      San Diego, California  92121
      Attn: Vice President, Finance
      Telephone: (858) 558-4850
      Facsimile:  (858) 558-3402

Notices to Holder shall be addressed to:

      Millennium Pharmaceuticals, Inc.
      40 Landsdowne Street
      Cambridge, Massachusetts 02139-4815
      Attn:  General Counsel
      Telephone:  (617) 679-7000
      Facsimile:  (617-374-0074

      Notices provided in accordance with this Section 17 shall be deemed
delivered upon personal delivery or three (3) business days after deposit in the
mail or one (1) business day after deposit with a nationally recognized
overnight courier.

                                       7.
<PAGE>
    IN WITNESS WHEREOF, this Note has been duly executed and delivered by the
Company as of the date first written above.

COMPANY:

STRUCTURAL GENOMIX, INC.

By:  /s/ Herbert G. Mutter
     -----------------------------

Print Name:  Herbert G. Mutter
             ---------------------

Title:  Vice President, Finance

HOLDER:

MILLENNIUM PHARMACEUTICALS, INC.

By:  /s/ Neil Exler
     -----------------------------

Print Name:  Neil Exler
             ---------------------

Title:  VP
        --------------------------

                                       8.

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