SecProbe.io

<DOCUMENT>
<TYPE>LETTER
<SEQUENCE>1
<FILENAME>filename1.txt
<TEXT>

Mail Stop 6010

									November 8, 2005

Mr. Michael Grey
President and Chief Executive Officer
SGX Pharmaceuticals, Inc.
10505 Roselle Street
San Diego, CA  92121

Re:  	SGX Pharmaceuticals, Inc.
Amendments No. 1 and 2 to Form S-1 Registration Statement
	File No. 333-128059

Dear Mr. Grey:

      We have reviewed your filing and have the following
comments.
Where indicated, we think you should revise your document in
response
to these comments.  If you disagree, we will consider your
explanation as to why our comment is inapplicable or a revision is
unnecessary.  Please be as detailed as necessary in your
explanation.
In some of our comments, we may ask you to provide us with
supplemental information so we may better understand your
disclosure.
After reviewing this information, we may or may not raise
additional
comments.

      Please understand that the purpose of our review process is
to
assist you in your compliance with the applicable disclosure
requirements and to enhance the overall disclosure in your filing.
We look forward to working with you in these respects.  We welcome
any questions you may have about our comments or on any other
aspect
of our review.  Feel free to call us at the telephone numbers
listed
at the end of this letter.

 Prospectus Summary

1. Please revise the discussion of the Phase I/II trial to clearly
state that later stage clinical trials might not support these
results.

2. Much of the discussion of the Phase II/III clinical trial of
Troxatyl is too detailed for the summary.  Please revise to move
the
following information to the Business section where these details
are
more appropriate:

"Because there is currently no approved therapy or standard of
care
for this patient population, we will compare the results of this
trial to historical results observed at M.D. Anderson Center in
similar patients.  The clinical trial has been designed to enroll
a
sufficient number of patients to reliably detect a doubling of the
historical complete response rate of 4.7% derived from the M.D.
Anderson Cancer Center database.  The Phase II/III patient
population
is similar to that studied in our recently completed Phase I/II
Troxatyl clinical trial.  Clinical response will be measured up to
approximately 60 days after dosing in each patient."

3. We note you statement that you expect to complete enrollment in
the third quarter of 2006 and announce the results shortly
thereafter.  What is the duration of the trial?

Management`s Discussion and Analysis of Financial Condition and
Results of Operations - page 38

Financial Operations Overview

Research and Development Expense, page 39

4. We have reviewed your response to comment 31 and your revised
disclosures.  As you have only characterized approximately 20% of
your research and development expense for each year presented,
please
revise your disclosure to include additional information regarding
the focus of management`s research and development efforts.
Please
quantify this information, as appropriate.

Liquidity and Capital Resources

Cash Flows, page 45

5. We note your response to comment 37 and your revised
disclosures.
It does not appear that your disclosure addresses the material
changes in the underlying drivers including the specific inflows
and
outflows generated, but merely describes items identified on the
face
of the statement of cash flows.  Please note that the expanded
disclosures should be included in the cash flow discussion for all
periods presented.  In addition, please address the trend of cash
being used in operations and include a discussion and analysis of
known trends and uncertainties.

Contractual Obligations, page 47

6. We note your response to comment 38.  We also note that you
changed the disclosure for contractual obligations to be as of
September 30, 2005.  In accordance with Item 303 of Regulation S-
K,
the information in the contractual obligation table should be as
of
the latest fiscal year end balance sheet date.  Please revise.

7. We have reviewed your response to comment 38 and the additional
disclosures included in your filing.  Please quantify the
aggregate
amount of milestone payments contingently payable to Shire.

Business - page 50

Troxatyl - page 51

8. We note your response to comment 41.  Please provide the
aggregate
amount of potential  milestone payments to Shire as we previously
requested.  Also disclose the aggregate minimum royalty payments.
While we are often willing to grant confidential treatment
requests
for the individual milestone amounts and the royalty percentage,
we
are not willing to grant confidential treatment to the aggregate
potential milestones or the minimum royalty payments.

Collaborations, Commercial Agreements and Grants - page 59

9. We note your response to comment 48.  Please make the revisions
we
previously requested.  The revisions should also be consistent
with
the disclosure requested in our comment letter on your application
for confidential treatment.

Consolidated Financial Statements

Notes to Consolidated Financial Statements

Note 4. Commitments and Collaborative Research and Development
Agreements

Note Payable, page F-19

10. We have reviewed your response to comment number 59.  It would
appear that paragraph 23 and 24 of SFAS 150 requires initial
measurement of the liability at fair market value and that
subsequent
change in fair market value should be recognized through earnings.
As such, please provide to us management`s justification for
classification of this obligation as debt and why the provisions
of
APB 21 are appropriate or revise your financial statements to
comply
with SFAS 150.  Additionally, please describe to us your
methodology
for determining the fair market value of this financial
instrument.

Note 5. Redeemable Convertible Preferred Stock, page F-21

11. We note your response to comment 58.  Please provide a roll-
forward of the balance of redeemable convertible preferred shares
outstanding for each class of preferred shares for the period from
December 31, 2004 to September 30, 2005.

*	*	*	*	*

	As appropriate, please amend your registration statement in
response to these comments.  You may wish to provide us with
marked
copies of the amendment to expedite our review.  Please furnish a
cover letter with your amendment that keys your responses to our
comments and provides any requested supplemental information.
Detailed cover letters greatly facilitate our review.  We may have
additional comments after reviewing your amendment and responses
to
our comments.

      You may contact Vanessa Robertson at 202-551-3649 or Kevin
Woody at 202-551-3629 if you have questions regarding comments on
the
financial statements and related matters.  Please contact Mary K.
Fraser at 202-551-3609 or me at 202-551-3610 with any other
questions.

								Regards,

								Jeffrey P. Riedler
								Assistant Director

Cc:	Frederick T. Muto, Esq.
	Cooley Godward LLP
	4401 Eastgate Mall
	San Diego, CA  92121
??

??

??

??

Mr. Michael Grey
SGX Pharmaceuticals, Inc.
November 8, 2005
Page 4

</TEXT>
</DOCUMENT>