SGX PHARMACEUTICALS, INC. INDEMNITY AGREEMENT

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EXHIBIT 10.1

SGX PHARMACEUTICALS, INC.

INDEMNITY AGREEMENT

THIS INDEMNITY AGREEMENT (this "AGREEMENT") is made and entered into this

[__] day of [_______], 2005 by and between SGX PHARMACEUTICALS, INC., a Delaware

corporation (the "COMPANY"), and [_____________] ("AGENT").

RECITALS

WHEREAS, Agent performs a valuable service to the Company in [HIS/HER]

capacity as [_____________] of the Company;

WHEREAS, the Company's Amended and Restated Bylaws (the "BYLAWS"), which

were approved by the stockholders of the Company, provide for the

indemnification of the directors, officers, employees and other agents of the

Company, including persons serving at the request of the Company in such

capacities with other corporations or enterprises, as authorized by the Delaware

General Corporation Law (the "DGCL");

WHEREAS, the Bylaws and the DGCL, by their non-exclusive nature, permit

contracts between the Company and its agents, officers, employees and other

agents with respect to indemnification of such persons; and

WHEREAS, in order to induce Agent to continue to serve as [_____________]

of the Company, the Company has determined and agreed to enter into this

Agreement with Agent.

NOW, THEREFORE, in consideration of Agent's continued service as

[_____________] of the Company after the date hereof, the parties hereto agree

as follows:

AGREEMENT

1. SERVICES TO THE COMPANY. Agent will serve, at the will of the Company

or under separate contract, if any such contract exists, as [_____________] of

the Company or as a director, executive officer or other fiduciary of an

affiliate of the Company (including any employee benefit plan of the Company)

faithfully and to the best of Agent's ability so long as Agent is duly elected

and qualified in accordance with the provisions of the Bylaws or other

applicable charter documents of the Company or such affiliate; provided,

however, that Agent may at any time and for any reason resign from such position

(subject to any contractual obligation that Agent may have assumed apart from

this Agreement) and that the Company or any affiliate shall have no obligation

under this Agreement to continue Agent in any such position.

2. INDEMNITY OF AGENT. The Company hereby agrees to hold harmless and

indemnify Agent to the fullest extent authorized or permitted by the provisions

of the Bylaws and the DGCL, as the same may be amended from time to time (but

only to the extent that such amendment permits the Company to provide broader

indemnification rights than the Bylaws or the DGCL permitted prior to adoption

of such amendment).

1.

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EXHIBIT 10.1

3. ADDITIONAL INDEMNITY. In addition to and not in limitation of the

indemnification otherwise provided for herein, and subject only to the

exclusions set forth in Section 4 hereof, the Company hereby further agrees to

hold harmless and indemnify Agent:

(a) against any and all expenses (including attorneys' fees),

witness fees, damages, judgments, fines and amounts paid in settlement and any

other amounts that Agent becomes legally obligated to pay because of any claim

or claims made against or by Agent in connection with any threatened, pending or

completed action, suit or proceeding, whether civil, criminal, arbitrational,

administrative or investigative (including an action by or in the right of the

Company) to which Agent is, was or at any time becomes a party, or is threatened

to be made a party, by reason of the fact that Agent is, was or at any time

becomes a director, officer, employee or other agent of the Company, or is or

was serving or at any time serves at the request of the Company as a director,

officer, employee or other agent of another corporation, partnership, joint

venture, trust, employee benefit plan or other enterprise; and

(b) otherwise to the fullest extent as may be provided to Agent by

the Company under the non-exclusivity provisions of the DGCL and Section 43 of

the Bylaws.

4. LIMITATIONS ON ADDITIONAL INDEMNITY. No indemnity pursuant to Section 3

hereof shall be paid by the Company:

(a) on account of any claim against Agent solely for an accounting

of profits made from the purchase or sale by Agent of securities of the Company

pursuant to the provisions of Section 16(b) of the Securities Exchange Act of

1934, as amended, or similar provisions of any federal, state or local statutory

law;

(b) on account of Agent's conduct that is established by a final

judgment as knowingly fraudulent or deliberately dishonest or that constituted

willful misconduct;

(c) on account of Agent's conduct that is established by a final

judgment as constituting a breach of Agent's duty of loyalty to the Company or

resulting in any personal profit or advantage to which Agent was not legally

entitled;

(d) for which payment is actually made to Agent under a valid and

collectible insurance policy or under a valid and enforceable indemnity clause,

bylaw or agreement, except in respect of any excess beyond payment under such

insurance, clause, bylaw or agreement;

(e) if indemnification is not lawful (and, in this respect, both the

Company and Agent have been advised that the Securities and Exchange Commission

believes that indemnification for liabilities arising under the federal

securities laws is against public policy and is, therefore, unenforceable and

that claims for indemnification should be submitted to appropriate courts for

adjudication); or

(f) in connection with any proceeding (or part thereof) initiated by

Agent, or any proceeding by Agent against the Company or its directors,

officers, employees or other agents, unless (i) such indemnification is

expressly required to be made by law, (ii) the proceeding was authorized by the

Board of Directors of the Company, (iii) such indemnification is provided by the

Company, in its sole discretion, pursuant to the powers vested in the Company

2.

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EXHIBIT 10.1

under the DGCL or any other applicable law, or (iv) the proceeding is initiated

pursuant to Section 9 hereof.

5. CONTINUATION OF INDEMNITY. All agreements and obligations of the

Company contained herein shall continue during the period Agent is a director,

officer, employee or other agent of the Company (or is or was serving at the

request of the Company as a director, officer, employee or other agent of

another corporation, partnersh