EXHIBIT 3.1

                AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
                                       OF
                            STRUCTURAL GENOMIX, INC.

      Structural GenomiX, Inc., a corporation organized and existing under the
laws of the State of Delaware, hereby certifies as follows:

      A.    The corporation was originally incorporated under the name Protarch,
Inc., and the date of filing the original Certificate of Incorporation of this
corporation with the Secretary of State of the State of Delaware is July 16,
1998.

      B.    Pursuant to sections 242 and 245 of the General Corporation Law of
the State of Delaware, this Amended and Restated Certificate of Incorporation
amends and restates the provisions of the Amended and Restated Certificate of
Incorporation of this corporation.

      C.    The Amended and Restated Certificate of Incorporation of this
corporation is hereby amended and restated to read in its entirety as follows:

      ONE. The name of the corporation is Structural GenomiX, Inc. (the
"CORPORATION").

      TWO. The address of the registered office of the Corporation in the State
of Delaware is Corporation Trust Center, 1209 Orange Street, Wilmington, New
Castle County, Delaware 19801 and the name of the registered agent at that
address is The Corporation Trust Company.

      THREE. The purpose of the Corporation is to engage in any lawful act or
activity for which a corporation may be organized under the General Corporation
Law of the State of Delaware.

      FOUR.

      A.    AUTHORIZED CAPITAL; DESIGNATION OF PREFERRED STOCK INTO SERIES.

            1.    The Corporation is authorized to issue two classes of stock to
be designated, respectively, "Common Stock" and "Preferred Stock." The total
number of shares which the Corporation is authorized to issue is Fifty Million
(50,000,000) shares of Common Stock (the "COMMON STOCK") and Nineteen Million
(19,000,000) shares of Preferred Stock (the "PREFERRED STOCK"), of which Fifteen
Million (15,000,000) shares of Preferred Stock are designated Series A Preferred
Stock (the "SERIES A PREFERRED") and Four Million (4,000,000) shares of
Preferred Stock are designated Series B Preferred Stock (the "SERIES B
PREFERRED" and, together with the Series A Preferred, the "SERIES PREFERRED").
The Preferred Stock shall have a par value of one tenth of one cent ($0.001) per
share, and the Common Stock shall have a par value of one tenth of one cent
($0.001) per share.



      B.    RIGHTS, PREFERENCES AND PRIVILEGES OF PREFERRED STOCK.

      The rights, preferences, privileges and restrictions granted to or imposed
upon the Preferred Stock and the holders thereof are as follows in this Section
B and as stated elsewhere in this Amended and Restated Certificate of
Incorporation. Such rights, preferences and privileges, as well as those of the
Common Stock and the holders thereof, are expressly subject to the rights,
preferences and privileges of any other series of Preferred Stock that may be
authorized or designated and issued in the future which may have rights,
preferences and privileges that are senior to or on parity with those of
existing series of Preferred Stock.

            1.    DIVIDENDS. The holders of Series B Preferred shall be entitled
to receive dividends out of funds legally available therefor, at the annual rate
of $0.3768 per share of Series B Preferred held by them (as adjusted for stock
splits, stock combinations, stock dividends, recapitalizations, and similar
events), prior and in preference to the declaration or payment of any dividend
or other distribution (payable other than in Common Stock) with respect to the
Series A Preferred and Common Stock, when, as and if declared by the
Corporation's Board of Directors (the "BOARD OF DIRECTORS"). After payment to
the holders of the Series B Preferred of the full amount of any dividend
declared by the Board of Directors out of funds legally available therefor to
which such holders of Series B Preferred are entitled hereunder, the holders of
the Series A Preferred shall be entitled to receive dividends out of funds
legally available therefor, at the annual rate of $0.1971 per share of Series A
Preferred held by them (as adjusted for stock splits, stock combinations, stock
dividends, recapitalizations, and similar events), prior and in preference to
the declaration or payment of any dividend or other distribution (payable other
than in Common Stock) with respect to the Common Stock, when, as and if declared
by the Board of Directors. Such dividends shall not be cumulative and no right
to such dividends shall accrue to holders of Series Preferred unless declared by
the Board of Directors. No dividends or other distributions shall be made with
respect to the Series A Preferred, other than dividends payable solely in Common
Stock, unless dividends shall have been paid or declared and set apart for
payment, on account of all shares of Series B Preferred then issued and
outstanding, at the aforesaid rate for such calendar year. No dividends or other
distributions shall be made with respect to the Common Stock, other than
dividends payable solely in Common Stock, unless dividends shall have been paid
or declared and set apart for payment, on account of all shares of Series
Preferred then issued and outstanding, at the aforesaid rate for such calendar
year. After payment of dividends at the annual rate set forth above, any
additional dividends declared shall be distributed among all holders of Series
Preferred and Common Stock in proportion to the number of shares of Common Stock
which would be held by such holder if all shares of Series Preferred were
converted into Common Stock at the then effective and applicable Conversion
Price (as defined in Section B.3(a) below).

            2.    LIQUIDATION PREFERENCE.

                  (a)   SERIES PREFERRED PREFERENCES.

                        (i)   In the event of any liquidation, dissolution or
winding up of the corporation, either voluntary or involuntary (each a
"LIQUIDATION EVENT"), the holders of Series B Preferred shall be entitled to
receive, prior and in preference to any distribution of any of the assets or
surplus funds of the corporation to the holders of Series A Preferred and

                                       2.


Common Stock by reason of their ownership thereof, the amount of $4.71 per share
(as adjusted for any stock dividends, combinations or splits, recapitalizations
or other similar events with respect to such shares) for each share of Series B
Preferred then held and, in addition, an amount equal to all declared but unpaid
dividends on the Series B Preferred. If the assets and funds thus distributed
among the holders of the Series B Preferred are insufficient to permit the
payment to such holders of their full preferential amount, then the entire
assets and funds of the Corporation legally available for distribution shall be
distributed ratably among the holders of Series B Preferred in proportion to the
preferential amount each such holder is otherwise entitled to receive, prior and
in preference to any distribution of any of the assets or surplus funds of the
corporation to the holders of Series A Preferred and Common Stock by reason of
their ownership thereof.

                        (ii)  In the event of any Liquidation Event, after
payment to the holders of the Series B Preferred of the full amounts set forth
in Section B.2(a)(i) above, the holders of Series A Preferred shall be entitled
to receive, prior and in preference to any distribution of any of the assets or
surplus funds of the corporation to the holders of Common Stock by reason of
their ownership thereof, the amount of $2.4632352 per share (as adjusted for any
stock dividends, combinations or splits, recapitalizations or other similar
events with respect to such shares) for each share of Series A Preferred then
held and, in addition, an amount equal to all declared but unpaid dividends on
the Series A Preferred. If the assets and funds thus distributed among the
holders of the Series A Preferred are insufficient to permit the payment to such
holders of their full preferential amount, then the entire assets and funds of
the Corporation legally available for distribution shall be distributed ratably
among the holders of Series A Preferred in proportion to the preferential amount
each such holder is otherwise entitled to receive, prior and in preference to
any distribution of any of the assets or surplus funds of the corporation to the
holders of Common Stock by reason of their ownership thereof.

                  (b)   REMAINING ASSETS. After payment to the holders of the
Series Preferred of the amounts set forth in Sections B.2(a)(i) and B.2(a)(ii)
above, the remaining assets and funds of the Corporation legally available for
distribution, if any, shall be distributed ratably among the holders of Common
Stock and Series Preferred in proportion to the shares of Common Stock then held
by each such holder on an as-converted to Common Stock basis.

                  (c)   REORGANIZATION OR MERGER. A Liquidation Event within the
meaning of this Section B shall be deemed to be occasioned by, or to include,
(i) any consolidation or merger of the Corporation with or into any other
corporation or other entity or person, or any other corporate reorganization, in
which the stockholders of the Corporation immediately prior to such
consolidation, merger or reorganization, own less than fifty percent (50%) of
the Corporation's voting power (or of the surviving or resulting entity's voting
power or of the voting power of the parent entity of such Corporation or
surviving or resulting entity immediately after such consolidation, merger or
reorganization), or any transaction or series of related transactions to which
the Corporation is a party in which in excess of fifty percent (50%) of the
Corporation's voting power is transferred, excluding any equity financing in
which the Corporation is the surviving corporation and any consolidation or
merger effected exclusively to change the domicile of the Corporation; or (ii) a
sale or lease of all or substantially all of the assets of this Corporation.

                                       3.


                  (d)   NON-CASH CONSIDERATION. If the consideration received by
this Corporation is other than cash, its value will be deemed its fair market
value as determined in good faith by the Board of Directors. Any securities
shall be valued as follows:

                        (i)   Securities not subject to investment letter or
other similar restrictions on free marketability covered by (ii) below:

                              (A)   if traded on a securities exchange or
through the Nasdaq National Market, the value shall be deemed to be the average
of the closing prices of the securities on such quotation system over the thirty
(30) day period ending three (3) days prior to the closing;

                              (B)   if actively traded over-the-counter, the
value shall be deemed to be the average of the closing bid or sale prices
(whichever is applicable) over the thirty (30) day period ending three (3) days
prior to the closing; and

                              (C)   if there is no active public market, the
value shall be the fair market value thereof, as mutually determined by the
Board of Directors and the holders of at least a majority of the voting power of
all then outstanding shares of Series Preferred.

                        (ii)  The method of valuation of securities subject to
investment letter or other restrictions on free marketability (other than
restrictions arising solely by virtue of a shareholder's status as an affiliate
or former affiliate) shall be to make an appropriate discount from the market
value determined as above in (i)(A), (B) or (C) to reflect the approximate fair
market value thereof, as mutually determined by the Board of Directors and the
holders of at least a majority of the voting power of all then outstanding
shares of such Series Preferred.

            3.    CONVERSION. The holders of Series Preferred shall have
conversion rights as follows (the "CONVERSION RIGHTS"):

                  (a)   RIGHT TO CONVERT. Each share of Series Preferred shall
be convertible, at the option of and without the payment of any additional
consideration by the holder thereof, at any time into such number of fully paid
and nonassessable shares of Common Stock as is determined by dividing the
applicable Issuance Price (as defined below) by the applicable Conversion Price
(as defined below) in effect at the time of conversion. The "ISSUANCE PRICE" for
the Series A Preferred shall be $2.46 and for the Series B Preferred shall be
$4.71. The "CONVERSION PRICE" for the Series A Preferred shall initially be
$2.46 and for the Series B Preferred shall initially be $4.71, each subject to
adjustment as provided below. The number of shares of Common Stock into which a
share of Series A Preferred is convertible is hereinafter referred to as the
"SERIES A CONVERSION RATE" and the number of shares of Common Stock into which a
share of Series B Preferred is convertible is hereinafter referred to as the
"SERIES B CONVERSION RATE." The Series A Conversion Rate and the Series B
Conversion Rate are each referred to herein as a "CONVERSION RATE."

                  (b)   AUTOMATIC CONVERSION. Each share of Series Preferred
shall automatically be converted into shares of Common Stock at the then
effective applicable Conversion Rate: (i) immediately prior to the closing of a
firm commitment underwritten public offering pursuant to an effective
registration statement under the Securities Act of 1933, as

                                       4.


amended (the "ACT") covering the offer and sale of Common Stock for the account
of the Corporation to the public at a minimum per share purchase price of $5.00
(as adjusted for stock splits, dividends, combinations and the like) with net
proceeds to the Corporation (after deduction of underwriters commissions and
expenses) of not less than $25,000,000 (a "QUALIFIED INITIAL PUBLIC OFFERING"),
or (ii) the date specified by the written consent or vote of the holders of more
than fifty percent (50%) of the Series Preferred then outstanding.

                  (c)   MECHANICS OF CONVERSION. Before any holder of Series
Preferred shall be entitled to convert the same into full shares of Common Stock
and to receive certificates therefor, the holder shall surrender the certificate
or certificates therefor, duly endorsed, at the office of the Corporation or of
any transfer agent for the Series Preferred, and shall give written notice to
the Corporation at such office that such holder elects to convert the same;
provided, however, that in the event of any automatic conversion pursuant to
Section B.3(b) above, the outstanding shares of Series Preferred shall be
converted automatically without any further action by the holders of such shares
and whether or not the certificates representing such shares are surrendered to
the Corporation or its transfer agent; provided further, that the Corporation
shall not be obligated to issue certificates evidencing the shares of Common
Stock issuable upon any automatic conversion pursuant to Section B.3(b) above
unless the certificates evidencing such shares of Series Preferred are either
delivered to the Corporation or its transfer agent as provided above, or the
holder notifies the Corporation or its transfer agent that such certificates
have been lost, stolen or destroyed and executes an agreement reasonably
satisfactory to the Corporation to indemnify the Corporation from any loss
incurred by it in connection with the loss of such certificates. The Corporation
shall, as soon as practicable after such delivery, or such agreement and
indemnification in the case of a lost certificate, issue and deliver at such
office to such holder of Series Preferred, a certificate or certificates for the
number of shares of Common Stock to which the holder shall be entitled and a
check payable to the holder in the amount of any cash amounts payable as the
result of a conversion into fractional shares of Common Stock. Such conversion
shall be deemed to have been made immediately prior to the close of business on
the date of such surrender of the shares of Series Preferred to be converted, or
in the case of automatic conversion pursuant to Section B.3(b) above,
immediately prior to the closing of the offering or on the date specified by the
written consent or vote of the holders of more than fifty percent (50%) of the
Series Preferred then outstanding, as applicable, and the person or persons
entitled to receive the shares of Common Stock issuable upon such conversion
shall be treated for all purposes as the record holder or holders of such shares
of Common Stock on such date.

                  (d)   ADJUSTMENTS TO CONVERSION PRICE OF SERIES PREFERRED FOR
DILUTIVE ISSUES.

                        (i)   SPECIAL DEFINITIONS. For purposes of this Section
B.3(d), the following definitions shall apply:

                              (A)   "ADDITIONAL SHARES OF COMMON STOCK" shall
mean all shares of Common Stock issued (or, pursuant to Section B.3(d)(ii),
deemed to be issued) by the Corporation, other than:

                                       5.


                                    (1)   shares of Common Stock issued upon
conversion of the Series Preferred;

                                    (2)   up to 3,510,000 shares (or such
greater number of shares as may be approved in writing by the holders of a
majority of the then outstanding shares of Series Preferred, voting together as
a single class) of Common Stock, or the grant of options therefor, including
shares issued after the Original Issue Date upon exercise of options outstanding
on the date of filing of this Amended and Restated Certificate of Incorporation
(such number to be proportionately adjusted in the event of any stock splits,
stock dividends, recapitalizations or similar events occurring after the
Original Issue Date) to officers, directors, consultants and employees of the
Corporation or any subsidiary pursuant to any stock option plan or restricted
stock plan approved by a vote of not less than a majority of the Board of
Directors, and shares of Common Stock issued or issuable upon exercise of the
warrant issued to Russell Reynolds Associates, Inc. dated November 13, 2001 in
connection with services provided to the Corporation;

                                    (3)   shares of Common Stock issued in
connection with any stock split or stock dividend by the Corporation;

                                    (4)   up to 200,000 shares (or such greater
number of shares as may be approved in writing by the holders of a majority of
the then outstanding shares of Series Preferred, voting together as a single
class) of Common Stock issued (or, pursuant to Section B.3(d)(ii), deemed to be
issued) after the Original Issue Date in connection with strategic transactions
involving the Corporation and other entities, including (i) joint ventures,
manufacturing, marketing or distribution arrangements or (ii) technology
transfer, licensing, development or similar arrangements; provided that such
strategic transactions and the issuance of shares therein, has been approved by
the Board of Directors;

                                    (5)   shares of Common Stock issued (or,
pursuant to Section B.3(d)(ii), deemed to be issued) in connection with any
equipment leasing or loan arrangement, or debt financing from a bank or similar
financial or lending institution, including but not limited to the warrant
issued to General Electric Capital Corporation in 2000, warrants issued to GATX
Ventures, Inc. and Silicon Valley Bank each dated July 15, 2002, the warrant
issued to Oxford Finance Corporation dated August 28, 2002 (and in each case any
amendments thereof or warrants issued in exchange therefor) and in each case the
shares issuable upon exercise and conversion thereof; provided that such
transactions and amendments (and any warrants issued in exchange therefor) and
the issuance of shares therein, have been approved by the Board of Directors;

                                    (6)   up to 7,256 shares of Common Stock
issued in August 2003 to a former employee and up to 230,000 shares of Common
Stock issued (or, pursuant to Section B.3(d)(ii), deemed to be issued) upon
exercise of the warrants issued to Tim Harris and Linda Grais in July 2005; or

                                    (7)   shares of Common Stock issued (or,
pursuant to Section B.3(d)(ii), deemed to be issued) upon conversion of shares
of Series A Preferred, Series

                                       6.


B Preferred or other securities issued pursuant to the Series B Preferred Stock
Purchase Agreement (as defined below).

                              (B)   "CONVERTIBLE SECURITIES" shall mean any
evidences of indebtedness, shares (other than the Common Stock) or other
securities convertible into or exchangeable for Common Stock.

                              (C)   "OPTIONS" shall mean rights, options or
warrants to subscribe for, purchase or otherwise acquire either Common Stock or
Convertible Securities.

                              (D)   "ORIGINAL ISSUE DATE" shall mean the date
shares of Series B Preferred are first issued pursuant to the Series B Preferred
Stock Purchase Agreement.

                        (ii)  DEEMED ISSUE OF ADDITIONAL SHARES OF COMMON STOCK.
In the event the Corporation at any time or from time to time after the Original
Issue Date shall issue any Options or Convertible Securities or shall fix a
record date for the determination of holders of any class of securities entitled
to receive any such Options or Convertible Securities, then the maximum number
of shares (as set forth in the instrument relating thereto assuming the
satisfaction of any conditions to exercisability, including, without limitation,
the passage of time and without regard to any provisions contained therein for a
subsequent adjustment of such number) of Common Stock issuable upon the exercise
of such Options or, in the case of Convertible Securities and Options therefor,
the conversion or exchange of such Convertible Securities, shall be deemed to be
Additional Shares of Common Stock issued as of the time of such issue or, in
case such a record date shall have been fixed, as of the close of business on
such record date, provided that Additional Shares of Common Stock shall not be
deemed to have been issued, with respect to the Series Preferred, as applicable,
unless the consideration per share (determined pursuant to Section B.3(d)(iv)
hereof) of such Additional Shares of Common Stock would be less than the
Conversion Price for the Series Preferred, as applicable, in effect on the date
of and immediately prior to such issue, or such record date, as the case may be,
and provided further that in any such case in which Additional Shares of Common
Stock are deemed to be issued:

                              (A)   no further adjustment in the applicable
Conversion Price shall be made upon the subsequent issue of Convertible
Securities or shares of Common Stock upon the exercise of such Options or
conversion or exchange of such Convertible Securities;

                              (B)   if such Options or Convertible Securities by
their terms provide, with the passage of time or otherwise, for any increase or
decrease in the consideration payable to the Corporation, or in the number of
shares of Common Stock issuable, upon the exercise, conversion or exchange
thereof, the applicable Conversion Price computed upon the original issue
thereof (or upon the occurrence of a record date with respect thereto), and any
subsequent adjustments based thereon, shall, upon any such increase or decrease
becoming effective, be recomputed to reflect such increase or decrease insofar
as it affects such Options or the rights of conversion or exchange under such
Convertible Securities;

                                       7.


                              (C)   upon the expiration of any such Options or
any rights of conversion or exchange under such Convertible Securities which
shall not have been exercised, the applicable Conversion Price computed upon the
original issue thereof (or upon the occurrence of a record date with respect
thereto), and any subsequent adjustments based thereon, shall, upon such
expiration, be recomputed as if:

                                    i.    in the case of Convertible Securities
or Options for Common Stock, the only Additional Shares of Common Stock issued
were shares of Common Stock, if any, actually issued upon the exercise of such
Options or the conversion or exchange of such Convertible Securities and the
consideration received therefor was the consideration actually received by the
Corporation for the issue of all such Options, whether or not exercised, plus
the consideration actually received by the Corporation upon such exercise, or
for the issue of all such Convertible Securities which were actually converted
or exchanged, plus the additional consideration, if any, actually received by
the Corporation upon such conversion or exchange, and

                                    ii.   in the case of Options for Convertible
Securities, only the Convertible Securities, if any, actually issued upon the
exercise thereof were issued at the time of issue of such Options, and the
consideration received by the Corporation for the Additional Shares of Common
Stock deemed to have been then issued was the consideration actually received by
the Corporation for the issue of all such Options, whether or not exercised,
plus the consideration deemed to have been received by the Corporation upon the
issue of the Convertible Securities with respect to which such Options were
actually exercised;

                              (D)   no readjustment pursuant to clause (B) or
(C) above shall have the effect of increasing the applicable Conversion Price to
an amount which exceeds the lower of (i) the applicable Conversion Price on the
original adjustment date just prior to such adjustment, or (ii) the applicable
Conversion Price that would have resulted, had the original adjustment not taken
place, from an issuance(s) of Additional Shares of Common Stock, with respect to
the applicable series of Series Preferred, between the original adjustment date
and such readjustment date; and

                              (E)   in the case of any Options which expire by
their terms not more than 90 days after the date of issue thereof, no adjustment
of the applicable Conversion Price shall be made until the expiration or
exercise of all such Options.

                        (iii) ADJUSTMENT OF CONVERSION PRICE UPON ISSUANCE OF
ADDITIONAL SHARES OF COMMON STOCK. In the event this Corporation shall issue
Additional Shares of Common Stock (including Additional Shares of Common Stock
deemed to be issued pursuant to Section B.3(d)(ii)) after the Original Issue
Date without consideration or for consideration per share less than the
Conversion Price for the Series Preferred, as applicable, in effect on the date
of and immediately prior to such issue, then and in such event, the Conversion
Price for the Series Preferred, as applicable, shall be reduced, concurrently
with such issue, to a price determined by multiplying such applicable Conversion
Price by a fraction, the numerator of which shall be the number of shares of
Common Stock outstanding immediately prior to such issue (including shares
issuable upon conversion of the outstanding Series Preferred) plus the number of
shares of Common Stock which the aggregate consideration received by the

                                       8.


Corporation for the total number of Additional Shares of Common Stock so issued
would purchase at such applicable Conversion Price; and the denominator of which
shall be the number of shares of Common Stock outstanding immediately prior to
such issue (including shares issuable upon conversion of the outstanding Series
Preferred) plus the number of such Additional Shares of Common Stock so issued.
For the purpose of this Section, the number of shares of Common Stock
outstanding shall be deemed to include the Common Stock issuable upon conversion
of all outstanding Series Preferred, upon conversion of all other outstanding
Convertible Securities and upon exercise of all outstanding Options (and
assuming conversion of Convertible Securities issuable upon exercise of
Options).

                        (iv)  DETERMINATION OF CONSIDERATION. For purposes of
this Section B.3(d), the consideration received by the Corporation for the issue
of any Additional Shares of Common Stock shall be computed as follows:

                              (A)   CASH AND PROPERTY: Such consideration shall:

                                    (1)   insofar as it consists of cash, be
computed at the aggregate amount of cash received by the Corporation;

                                    (2)   insofar as it consists of property
other than cash, be computed at the fair value thereof at the time of such
issue, as determined in good faith by the Board irrespective of any accounting
treatment; and

                                    (3)   in the event Additional Shares of
Common Stock are issued together with other shares or securities or other assets
of the Corporation for consideration which covers both, be the proportion of
such consideration so received, computed as provided in clauses (1) and (2)
above, as determined in good faith by the Board of Directors.

                        (v)   OPTIONS AND CONVERTIBLE SECURITIES. The
consideration per share received by the Corporation for Additional Shares of
Common Stock deemed to have been issued pursuant to Section B.3(d)(ii), relating
to Options and Convertible Securities, shall be determined by dividing:

                              (A)   the total amount, if any, received or
receivable by the Corporation as consideration for the issue of such Options or
Convertible Securities, plus the minimum aggregate amount of additional
consideration (as set forth in the instruments relating thereto, without regard
to any provision contained therein for a subsequent adjustment of such
consideration) payable to the Corporation upon the exercise of such Options or
the conversion or exchange of such Convertible Securities, or in the case of
Options for Convertible Securities, the exercise of such Options for Convertible
Securities and the conversion or exchange of such Convertible Securities by

                              (B)   the maximum number of shares of Common Stock
(as set forth in the instruments relating thereto, without regard to any
provision contained therein for a subsequent adjustment of such number) issuable
upon the exercise of such Options or the conversion or exchange of such
Convertible Securities.

                                       9.


                        (vi)  SPECIAL MANDATORY CONVERSION.

                              (A)   For purposes of this Section B.3(d)(vi), the
following definitions shall apply:

                                    (1)   An "AFFILIATE" of a Holder (i) shall
mean any person, association or entity that, directly or indirectly, through one
or more intermediaries, has voting control of, has its voting controlled by, or
is under common voting control with, such Holder and (ii) shall also include,
without limitation, (a) any partner or retired partner of such Holder, if such
Holder is a partnership, (b) any member or former member of such Holder, if such
Holder is a limited liability company, (c) all related funds, affiliated funds,
sister funds, predecessor and successor funds, annex funds and associate funds,
if such Holder is a venture capital fund and (d) any immediate family member of
such Holder and any trust for the benefit of such Holder or any immediate family
of such Holder. For purposes of this Section B.3(d)(iv), "IMMEDIATE FAMILY"
shall mean any relationship by blood, marriage or adoption, not more remote than
first cousin.

                                    (2)   "HOLDER" shall mean any purchaser of
shares of Series B Preferred pursuant to the Series B Preferred Stock Purchase
Agreement (as defined below) and any transferee of shares of Series Preferred
from such purchaser.

                                    (3)   "INITIAL CLOSING" shall mean the
Initial Closing as defined in the Series B Preferred Stock Purchase Agreement.

                                    (4)   "INITIAL CLOSING DATE" shall mean the
Initial Closing Date as defined in the Series B Preferred Stock Purchase
Agreement.

                                    (5)   "NON-PARTICIPATING HOLDER" shall mean
any Holder that is not a Participating Investor (as defined below); provided,
however, that notwithstanding anything to the contrary set forth herein, a
Holder shall not be deemed a "Non-Participating Holder" if such Holder and its
Affiliates collectively acquire at the Second Closing (as defined below) at
least the Second Closing Commitment Dollar Amount of such Holder collectively
with the Second Closing Commitment Dollar Amount of its Affiliates;

                                    (6)   "PARTICIPATING INVESTOR" shall mean
any Holder that purchases such Holder's full Second Closing Commitment Dollar
Amount of shares of Series B Preferred at the Second Closing (each as defined
below) pursuant to the Series B Preferred Stock Purchase Agreement.

                                    (7)   "SECOND CLOSING" shall mean the Second
Closing as defined in the Series B Preferred Stock Purchase Agreement.

                                    (8)   "SECOND CLOSING COMMITMENT DOLLAR
AMOUNT" shall mean the Second Closing Commitment Dollar Amount set forth on
Exhibit A to the Series B Preferred Stock Purchase Agreement.

                                    (9)   "SECOND CLOSING DATE" shall mean the
Second Closing Date as defined in the Series B Preferred Stock Purchase
Agreement.

                                      10.


                                    (10)  "SECOND CLOSING NOTICE" shall mean the
Second Closing Notice as defined in the Series B Preferred Stock Purchase
Agreement.

                                    (11)  "SERIES B FINANCING" shall mean the
sale of up to approximately 3,200,000 shares of Series B Preferred at a purchase
price of $4.71 per share pursuant to the Series B Preferred Stock Purchase
Agreement.

                                    (12)  "SERIES B PREFERRED STOCK PURCHASE
AGREEMENT" shall mean that certain Series B Preferred Stock Purchase and
Recapitalization Agreement relating to the Series B Financing, dated as of April
21, 2005, entered into by and among the Corporation and the Holders named
therein, as such may be amended from time to time.

                              (B)   In the event:

                                    (1)   after the completion of the Initial
Closing and delivery by the Corporation of the Second Closing Notice to each
Holder as set forth in Section 2.2(a) of the Series B Preferred Stock Purchase
Agreement not less than ten (10) nor more than forty-five (45) calendar days
prior to the proposed Second Closing Date;

                                    (2)   the Corporation does not receive or
has not received from such Holder on or prior to the Second Closing Date such
Holder's Second Closing Commitment Dollar Amount (each such Holder that fails to
deliver or has not delivered to the Corporation such funds being deemed a
Non-Participating Holder);

then all of such Non-Participating Holder's shares of Series Preferred (and any
right to any dividend, payment or other distribution thereon) shall
automatically and without further action on the part of such holder be
converted, effective immediately following such Second Closing into shares of
Common Stock at the applicable Conversion Price then in effect.

                              (C)   The holder of any shares of Series Preferred
converted into shares of Common Stock pursuant to this Section B.3(d)(vi) shall
deliver to the Corporation during regular business hours at the office of any
transfer agent of the Corporation for the Series Preferred, or at such other
place as may be designated by the Corporation, the certificate or certificates
for the shares so converted, duly endorsed or assigned in blank or to the
Corporation. As promptly as practicable thereafter, the Corporation shall issue
and deliver to such Non-Participating Holder, at the place designated by such
Non-Participating Holder, a certificate or certificates for the whole number of
shares of Common Stock to be issued hereunder. Such conversion shall be deemed
to have occurred, and such Non-Participating Holder shall be deemed to have
become a stockholder of record of Common Stock, immediately upon the
consummation of the Second Closing. Upon such conversion of any shares of Series
Preferred to Common Stock pursuant to this Section B.3(d)(vi), all rights of the
holder of such shares as a holder of Series Preferred shall cease and terminate
with respect to such shares so converted even if the holder fails to deliver the
certificate or certificates for the shares so converted duly endorsed or
assigned in blank or to the Corporation. Immediately following such conversion
to Common Stock and until such time as the holder surrenders to the Corporation
the duly endorsed and assigned certificate or certificates for the shares so
converted, the certificate

                                      11.


or certificates representing such holder's shares of Series Preferred shall be
deemed a certificate representing that number of shares of Common Stock into
which such shares of Series Preferred were converted pursuant to this
B.3(d)(vi). Following the Second Closing, the Corporation shall provide written
notice to each Non-Participating Holder whose shares of Series Preferred were
converted to Common Stock pursuant to this Section B.3(d)(vi).

                  (e)   FRACTIONAL SHARES. In lieu of any fractional shares to
which the holder of Series Preferred would otherwise be entitled, the
Corporation shall pay cash equal to such fraction multiplied by the fair market
value of one share of such Series Preferred as determined by the Board of
Directors. Whether or not fractional shares are issuable upon such conversion
shall be determined on the basis of the total number of shares of Series
Preferred of each holder at the time converting into Common Stock and the number
of shares of Common Stock issuable upon such aggregate conversion.

                  (f)   ADJUSTMENT OF CONVERSION PRICE. The Conversion Price of
each share of Series Preferred shall be subject to adjustment from time to time
as follows:

                        (i)   If the number of shares of Common Stock
outstanding at any time after the date hereof is increased by a stock dividend
payable in shares of Common Stock or by a subdivision or split-up of shares of
Common Stock, then, on the date such payment is made or such change is
effective, the Conversion Prices applicable to the Series Preferred shall be
appropriately decreased so that the number of shares of Common Stock issuable on
conversion of any shares of Series Preferred shall be increased in proportion to
such increase of outstanding shares.

                        (ii)  If the number of shares of Common Stock
outstanding at any time after the date hereof is decreased by a combination of
the outstanding shares of Common Stock, then, on the effective date of such
combination, the Conversion Prices applicable to the Series Preferred shall be
appropriately increased so that the number of shares of Common Stock issuable on
conversion of any shares of Series Preferred shall be decreased in proportion to
such decrease in outstanding shares.

                        (iii) In case the Corporation shall distribute to
holders of its Common Stock shares of its capital stock or other property of the
Corporation other than Common Stock (excluding any distribution in which the
Series Preferred participate on an as-converted basis, and any distribution for
which adjustment is otherwise made pursuant to this Section), then in such case
the holders of the Series Preferred shall, concurrent with the distribution to
holders of Common Stock, receive a like distribution based upon the number of
shares of Common Stock into which such Series Preferred is then convertible.

                        (iv)  In case, at any time after the date hereof, of any
capital reorganization, or any reclassification of the stock of the corporation
(other than as a result of a stock dividend or subdivision, split-up or
combination of shares), or the consolidation or merger of the Corporation with
or into another person (other than a consolidation or merger in which the
corporation is the continuing entity and which does not result in any change in
the Common Stock), the shares of Series Preferred shall, after such
reorganization, reclassification, consolidation, merger, sale or other
disposition, be convertible into the kind and number of

                                      12.


shares of stock or other securities or property of the Corporation or otherwise
to which a holder of such Series Preferred would have been entitled if
immediately prior to such reorganization, reclassification, consolidation,
merger, sale or other disposition such holder had converted its shares of such
Series Preferred into Common Stock. The provisions of this clause C.3(f)(iv)
shall similarly apply to successive reorganizations, reclassification,
consolidations, mergers, sales or other dispositions.

                        (v)   All calculations under this Section B.3(f) shall
be made to the nearest cent or to the nearest one hundredth (1/100) of a share,
as the case may be.

                  (g)   MINIMAL ADJUSTMENTS. No adjustment in the Conversion
Price for any series of Series Preferred need be made if such adjustment would
result in a change in the Conversion Price of less than $0.01. Any adjustment of
less than $0.01 which is not made shall be carried forward and shall be made at
the time of and together with any subsequent adjustment which, on a cumulative
basis, amounts to an adjustment of $0.01 or more in the Conversion Price.

                  (h)   NO IMPAIRMENT. The Corporation will not, by amendment of
its Certificate of Incorporation or through any reorganization,
recapitalization, transfer of assets, consolidation, merger, dissolution, issue
or sale of securities or any other voluntary action, avoid or seek to avoid the
observance or performance of any of the terms to be observed or performed
hereunder by the Corporation, but will at all times in good faith assist in the
carrying out of all the provisions of this Section B.3 and in the taking of all
such action as may be necessary or appropriate in order to protect the
Conversion Rights of the holders of Series Preferred against impairment. This
provision shall not restrict the Corporation's right to amend its Certificate of
Incorporation with the requisite board and stockholder consent.

                  (i)   CERTIFICATE AS TO ADJUSTMENTS. Upon the occurrence of
each adjustment or readjustment of the Conversion Price pursuant to Section
B.3(d), the Corporation at its expense shall promptly compute such adjustment or
readjustment in accordance with the terms hereof and prepare and furnish to each
applicable holder of Series Preferred a certificate setting forth such
adjustment or readjustment and showing in detail the facts upon which such
adjustment or readjustment is based. The Corporation shall, upon written request
at any time of any holder of Series Preferred, furnish or cause to be furnished
to such holder a like certificate setting forth (i) all such adjustments and
readjustments, (ii) the Series A Conversion Rate and the Series B Conversion
Rate (as applicable) at the time in effect, and (iii) the number of shares of
Common Stock and the amount, if any, of other property which at the time would
be received upon the conversion of such holder's shares of Series Preferred.

                  (j)   NOTICES OF RECORD DATE. In the event the Corporation
shall propose at any time to (i) declare any dividend or other distribution upon
its Common Stock, (ii) other than with respect to a transaction contemplated by
Section B.3(d)(vi), which transaction shall be governed by the provisions of
Section B.3(d)(vi), declare any right to subscribe for, purchase or otherwise
acquire any shares of stock of any class or any other securities or property,
(iii) effect any capital reorganization, reclassification of its Common Stock,
consolidation or merger with or into any other corporation or transfer of all or
substantially all of its assets or (iv) liquidate, dissolve or wind up the
Corporation, the Corporation shall mail to each holder of

                                      13.


Series Preferred at least twenty (20) days prior to the date on which a record
shall be taken for such dividend, distribution or subscription rights or the
effective date of such reorganization, reclassification, consolidation, merger,
liquidation, dissolution or winding up, as applicable, a notice containing such
record date or effective date, as applicable.

                  (k)   NOTICES. Any notice required by the provisions of this
Section B.3 to be given to any holder of Series Preferred shall be deemed given
if deposited in the United States mail, postage prepaid, and addressed to each
holder of record at such holder's address appearing on the Corporation's books;
provided, however that any notice required by the provisions of Section
B.3(d)(vi) shall also be deemed effectively given when sent by confirmed
electronic mail or facsimile if sent during normal business hours of the
recipient (or, if not, then on the next business day), or one (1) day after
deposit with a nationally recognized overnight courier, specifying next day
delivery.

      C.    VOTING RIGHTS.

            1.    Except as otherwise required by law or as set forth herein,
the holder of each share of Common Stock issued and outstanding shall have one
vote for each share of Common Stock held by such holder, and the holder of each
share of Series Preferred shall be entitled to the number of votes equal to the
number of shares of Common Stock into which such share of Series Preferred could
be converted at the record date for determination of the stockholders entitled
to vote on such matters, or, if no such record date is established, at the date
such vote is taken or any written consent of stockholders is solicited, such
votes to be counted together with all other shares of stock of the Corporation
having general voting power and not counted separately as a class, except with
respect to those matters required by law to be submitted to a class vote and
except as otherwise set forth herein. Holders of Series Preferred, voting
together as a separate class, shall be entitled to elect four (4) members of the
Board of Directors and the holders of Series Preferred and Common Stock, voting
together on an as-converted basis, shall elect the remaining directors. Holders
of Common Stock and Series Preferred shall be entitled to notice of any
stockholders' meeting in accordance with the Bylaws of the Corporation.
Fractional votes by the holders of Series Preferred shall not, however, be
permitted and any fractional voting rights shall (after aggregating all shares
into which shares of Series Preferred held by each holder could be converted) be
rounded to the nearest whole number.

            2.    In the case of any vacancy (other than a vacancy caused by
removal) in the office of a director occurring among the directors elected by
the holders of a series and/or class or classes (as applicable) of stock
pursuant to this Section C, the remaining directors so elected by that series
and/or class or classes (as applicable) may by affirmative vote of a majority
thereof (or the remaining director so elected if there be but one, or if there
are no such directors remaining, by the affirmative vote of the holders of a
majority of the shares of that class and/or series), elect a successor or
successors to hold office for the unexpired term of the director or directors
whose place or places shall be vacant. Any director who shall have been elected
by the holders of a series and/or class or classes (as applicable) of stock or
by any directors so elected as provided in the immediately preceding sentence
hereof may be removed during the aforesaid term of office, either with or
without cause, by, and only by, the affirmative vote of the holders of the
shares of the series and/or class or classes (as applicable) of stock entitled
to elect such

                                      14.


director or directors, given either at a special meeting of such stockholders
duly called for that purpose or pursuant to a written consent of stockholders,
and any vacancy thereby created may be filled by the holders of that class
and/or classes or series (as applicable) of stock represented at the meeting or
pursuant to unanimous written consent.

      D.    REDEMPTION.

            1.    If requested by the holders of not less than sixty-six and two
thirds percent (66 2/3%) of the outstanding shares of Series Preferred, the
Corporation shall, on any date after April 21, 2008 and on each of the first and
second anniversaries thereof, redeem the Series Preferred in three annual
installments (the date of each such annual installment a "REDEMPTION DATE"),
from any funds legally available for such purpose. The number of shares to be
redeemed from each holder on each Redemption Date shall equal the total number
of shares of Series Preferred held by such holder on the date of the Redemption
Notice (as defined below), divided by the number of Redemption Dates remaining
as of the date of the Redemption Notice, minus the number of shares of Series
Preferred that such holder converts into Common Stock after the date of the
Redemption Notice and prior to such Redemption Date, provided that for a holder
of more than one series of Series Preferred, such number of shares to be
redeemed shall be allocated pro rata to each such series of Series Preferred in
proportion to the total number of shares of each such series of Series Preferred
held by such holder just prior to the Redemption Date. The Corporation shall
effect redemptions by paying cash in an amount equal to $2.4632352 per share of
Series A Preferred and $4.71 per share of Series B Preferred (each as adjusted
for any stock dividends, combinations, splits, recapitalizations, or other
similar events with respect to such shares) plus declared but unpaid dividends
on such shares (the "REDEMPTION PRICES"). Upon the Corporation's default in the
payment of any required redemption of an installment hereunder, the unpaid
balance shall accrue interest at the rate of eight percent (8%) per annum,
payable quarterly in arrears.

            2.    If the funds of the Corporation legally available for
redemption of shares of Series Preferred on any Redemption Date are insufficient
to redeem the total number of shares of Series Preferred to be redeemed on such
date, those funds which are legally available will be used to redeem shares from
the holders of Series Preferred ratably in proportion to the aggregate
Redemption Prices that would be payable to each holder if all shares required to
be redeemed were being redeemed. The shares of Series Preferred not redeemed
shall remain outstanding and entitled to all the rights and preferences provided
herein, including the rights of conversion set forth herein. If any time
thereafter additional funds become legally available for the redemption, such
funds will immediately be used to redeem the balance of the shares which the
Corporation has become obliged to redeem on any Redemption Date but which it has
not redeemed.

            3.    At least thirty (30) days prior to each Redemption Date, the
Corporation shall mail a Redemption Notice, first class postage prepaid, to each
holder of record of Series Preferred as of the close of business two business
days preceding the mailing date, at the address last shown on the records of the
Corporation for such holder. The Redemption Notice shall specify the number of
shares to be redeemed from such holder, the Redemption Date, the Redemption
Price and the place at which payment may be obtained, and shall call upon such
holder to surrender to the Corporation, in the manner and at the place
designated, the certificate or certificates representing the shares to be
redeemed. On or after the Redemption Date, each

                                      15.


holder of Series Preferred to be redeemed shall surrender to the Corporation the
certificate or certificates representing such shares, in the manner and at the
place designated in the Redemption Notice. Each surrendered certificate shall be
canceled, and the Redemption Price for such shares shall then be payable to the
order of the person whose name appears on such certificate or certificates as
the owner thereof. If less than all the shares represented by any such
certificate are redeemed, a new certificate shall be issued representing the
unredeemed shares. Nothing herein shall be deemed to prevent a holder of Series
Preferred from converting all or part of such holder's shares into Common Stock
in accordance with the terms of Section B.3(a) hereof at any time prior to a
Redemption Date covering such shares, and the provisions of this section shall
not apply to any shares so converted.

            4.    From and after the Redemption Date, unless there has been a
default in payment of the Redemption Price, the shares of Series Preferred
designated for redemption in the Redemption Notice shall cease to be outstanding
and shall no longer be transferred on the books of the Corporation, and all
rights of the holders with respect to such shares shall cease, except the right
to receive the Redemption Price without interest upon surrender of their
certificate or certificates.

      E.    PROTECTIVE PROVISIONS.

            1.    In addition to any other class vote that may be required by
law and without limiting any such required vote, so long as at least thirty-five
percent (35%) of the Series Preferred outstanding as of the Original Issue Date
remains outstanding, this Corporation shall not (by amendment, merger,
consolidation or otherwise) without first obtaining the approval (by vote or
written consent, as provided by law) of the holders of a majority of the then
outstanding shares of Series Preferred, voting together as a single class:

                  (a)   create any new class or series of shares having any
rights, preferences, or privileges senior to or on a parity with the Series
Preferred;

                  (b)   adversely alter or change the rights, preferences or
privileges of the Series Preferred or amend the Corporation's Certificate of
Incorporation or Bylaws in a manner that would have such effect;

                  (c)   increase or decrease the aggregate number of authorized
shares of Series Preferred;

                  (d)   sell, convey, or otherwise dispose of all or
substantially all of its property or business or merge into or consolidate with
any other corporation (other than a wholly-owned subsidiary corporation) or
effect any transaction or series of related transactions in which more than
fifty percent (50%) of the voting power of this corporation is disposed of;

                  (e)   redeem, repurchase, or make other distributions with
respect to Common Stock or Series Preferred (except for acquisitions of Common
Stock by the Corporation pursuant to agreements which permit the Corporation to
repurchase such shares upon termination of services to the Corporation or in
exercise of the Corporation's right of first refusal upon a proposed transfer or
redemptions under the terms of the Corporation's Certificate of Incorporation,
as amended from time to time);

                                      16.


                  (f)   declare any dividends on the Common Stock or Series
Preferred;

                  (g)   increase or decrease the size of the Board of Directors;
or

                  (h)   voluntarily liquidate or dissolve.

            2.    The consent of the holders of a majority of the outstanding
shares of a particular series of the Series Preferred, voting as a separate
series, shall be required to amend or repeal any provision of, or add any
provision to, the Corporation's Certificate of Incorporation or Bylaws that
adversely changes the rights, preferences or privileges of such series of the
Series Preferred in a manner different from other series of Series Preferred.

      F.    STATUS OF CONVERTED STOCK. In the event any shares of Series
Preferred shall be converted pursuant to Section B.3 hereof, the shares so
converted shall be canceled and shall not be issuable by the Corporation.

      G.    COMMON STOCK. The rights, preferences, privileges and restrictions
granted to and imposed on the Common Stock are as set forth below:

            1.    DIVIDEND RIGHTS. Subject to the prior rights of holders of all
classes of stock at the time outstanding having prior rights as to dividends,
the holders of the Common Stock shall be entitled to receive, when and as
declared by the Board of Directors, out of any assets of this corporation
legally available therefor, such dividends as may be declared from time to time
by the Board of Directors.

            2.    LIQUIDATION RIGHTS. Upon the liquidation, dissolution or
winding up of this Corporation, the assets of this corporation shall be
distributed as provided in Section B hereof.

            3.    REDEMPTION. The Common Stock is not redeemable.

            4.    VOTING RIGHTS. The holder of each share of Common Stock shall
have the right to one vote for each such share, and shall be entitled to notice
of any stockholders' meeting in accordance with the bylaws of this Corporation,
and shall be entitled to vote upon such matters and in such manner as may be
provided by law.

      FIVE. The Corporation is to have perpetual existence.

      SIX. In furtherance and not in limitation of the powers conferred by
statute, the Board of Directors is expressly authorized to make, alter, amend or
repeal the Bylaws of the Corporation.

      SEVEN. The number of directors which will constitute the whole Board of
Directors of the Corporation shall be as specified in the Bylaws of the
Corporation.

      EIGHT. The election of directors need not be by written ballot unless the
Bylaws of the Corporation shall so provide.

                                      17.


      NINE. Meetings of stockholders may be held within or without the State of
Delaware, as the Bylaws may provide. The books of the Corporation may be kept
(subject to any provisions contained in the statutes) outside the State of
Delaware at such place or places as may be designated from time to time by the
Board of Directors or in the Bylaws of the Corporation.

      TEN. To the fullest extent permitted by the Delaware General Corporation
Law as the same exists or as may hereafter be amended, a director of the
Corporation shall not be personally liable to the Corporation or its
stockholders for monetary damages for breach of fiduciary duty as a director.
The Corporation may indemnify to the fullest extent permitted by law any person
made or threatened to be made a party to an action or proceeding, whether
criminal, civil, administrative or investigative, by reason of the fact that
such person or his or her testator or intestate is or was a director, officer or
employee of the Corporation, or any predecessor of the Corporation, or serves or
served at any other enterprise as a director, officer or employee at the request
of the Corporation or any predecessor to the Corporation. Neither any amendment
nor repeal of this Article, nor the adoption of any provision of this Amended
and Restated Certificate of Incorporation inconsistent with this Article, shall
eliminate or reduce the effect of this Article in respect of any matter
occurring, or any cause of action, suit or claim that, but for this Article,
would accrue or arise, prior to such amendment, repeal or adoption of an
inconsistent provision.

      ELEVEN. Advance notice of new business and stockholder nomination for the
election of directors shall be given in the manner and to the extent provided in
the Bylaws of the Corporation.

      TWELVE. The Corporation reserves the right to amend, alter, change or
repeal any provision contained in this Amended and Restated Certificate of
Incorporation, in the manner now or hereafter prescribed by statute, and all
rights conferred upon stockholders herein are granted subject to this
reservation.

                                       18.


      IN WITNESS WHEREOF, the Corporation has caused this Amended and Restated
Certificate of Incorporation to be signed by its President and Chief Executive
Officer in San Diego, California, this 25th day of July 2005.

                                          /s/ Michael Grey
                                          ______________________________________
                                          Michael Grey
                                          President and Chief Executive Officer

                                       19.


                           CERTIFICATE OF AMENDMENT OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                            STRUCTURAL GENOMIX, INC.

            STRUCTURAL GENOMIX, INC., a Delaware corporation (the
"CORPORATION"), does hereby certify that:

      FIRST: The name of the Corporation is Structural GenomiX, Inc.

      SECOND: The date on which the Certificate of Incorporation of the
Corporation was originally filed with the Secretary of State of the State of
Delaware is July 16, 1998.

      THIRD: The Board of Directors of the Corporation, acting in accordance
with the provisions of Sections 141 and 242 of the General Corporation Law of
the State of Delaware, adopted resolutions amending its Certificate of
Incorporation as follows:

      Article ONE of the Company's Amended and Restated Certificate of
      Incorporation shall be amended and restated to read in its entirety as
      follows:

            "The name of the corporation is SGX Pharmaceuticals, Inc. (the
            "CORPORATION")."

      FOURTH: Thereafter, pursuant to a resolution of the Board of Directors,
this Certificate of Amendment was submitted to the stockholders of the
Corporation for their approval, and was duly adopted in accordance with the
provisions of Section 242 of the General Corporation Law of the State of
Delaware.

      IN WITNESS WHEREOF, Structural GenomiX, Inc. has caused this Certificate
of Amendment to be signed by its President and Chief Executive officer this 30th
day of August, 2005.


                                       STRUCTURAL GENOMIX, INC.


                                       By: /s/ Michael Grey
                                           -------------------------------------
                                           Michael Grey
                                           President and Chief Executive Officer


                           CERTIFICATE OF AMENDMENT OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                            SGX PHARMACEUTICALS, INC.

        SGX PHARMACEUTICALS, INC., a Delaware corporation (the "CORPORATION"),
does hereby certify that:

        FIRST: The name of the Corporation is SGX Pharmaceuticals, Inc.

        SECOND: The Corporation was originally incorporated under the name
Protarch, Inc., and the date on which the Certificate of Incorporation of the
Corporation was originally filed with the Secretary of State of the State of
Delaware is July 16, 1998.

        THIRD: Section A.1. of Article Four of the Corporation's Amended and
Restated Certificate of Incorporation shall be amended to become Section A.2 of
Article Four and a new Section A.1 shall be inserted before Section A.2 as
follows:

                "1. Effective at the time of filing of this Certificate of
                Amendment with the Secretary of State of the State of Delaware,
                each two (2) shares of Common Stock issued and outstanding
                shall, automatically and without any action on the part of the
                respective holders thereof, be combined and converted into one
                (1) share of Common Stock (the "REVERSE SPLIT"); provided,
                however, that this Corporation shall issue no fractional shares
                of Common Stock as a result of the Reverse Split, but shall
                instead pay to any stockholder who would be entitled to receive
                a fractional share as a result of the actions set forth herein a
                sum in cash equal to the fair market value of the shares
                constituting such fractional share as determined by the Board of
                Directors of the Corporation. The Reverse Split shall occur
                whether or not the certificates representing such shares of
                Common Stock are surrendered to the Corporation or its transfer
                agent. The Reverse Split shall be effected on a record
                holder-by-record holder basis, such that any fractional shares
                of Common Stock resulting from the Reverse Split shall be
                aggregated."

        FOURTH: Section B.3(d)(i)(A) of Article Four of the Corporation's
Amended and Restated Certificate of Incorporation shall be amended to remove the
word "or" at the end of subsection (6) and replace the "." at the end of
subsection (7) with the following:

                "; or

                        (8) shares of common stock issued (or, pursuant to
                Section B.3(d)(ii), deemed to be issued) upon the closing of a
                firm commitment underwritten initial public offering, pursuant
                to an effective registration statement under the Act covering
                the offer and sale of shares of the Corporation's Common Stock
                (an "IPO"), whether or not such IPO


                                       1.





                constitutes a Qualified Initial Public Offering, provided that
                the price per share of the Common Stock sold in such IPO to the
                public is approved by the Board of Directors or a Pricing
                Committee of the Board of Directors."

        FIFTH: This Certificate of Amendment has been duly approved by the
Corporation's Board of Directors in accordance with the provisions of Sections
141 and 242 of the General Corporation Law of the State of Delaware (the "DGCL")
and was duly adopted by the stockholders of the Corporation in accordance with
the provisions of Section 242 of the DGCL.

        IN WITNESS WHEREOF, SGX Pharmaceuticals, Inc. has caused this
Certificate of Amendment to be signed by its President and Chief Executive
officer this 3rd day of January, 2006.


                                SGX PHARMACEUTICALS, INC.


                                By: /s/ Michael Grey
                                   ------------------------------------------
                                   Michael Grey
                                   President and Chief Executive Officer



                                       2.