**Exhibit 31.1**

**CERTIFICATION OF PRINCIPAL EXECUTIVE OFFICER**

(Pursuant to Rule 13a-14(a) of the Securities Exchange Act of 1934,as amended,as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002)

I,Leslie J. Browne, Ph.D., certify that:

1.      I have reviewed this quarterly report on Form 10-Q ofPharmacopeia, Inc.;

2.      Based on my knowledge, this report does not contain any untrue statementof a material fact or omit to state a material fact necessary to make thestatements made, in light of the circumstances under which such statements weremade, not misleading with respect to the period covered by this report;

3.      Based on my knowledge, the consolidated financial statements, and otherfinancial information included in this report, fairly present in all materialrespects the financial condition, results of operations and cash flows of theregistrant as of, and for, the periods presented in this report;

4.      The registrant’s other certifying officers and I are responsible forestablishing and maintaining disclosure controls and procedures (as defined inExchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant andhave:

a)        designedsuch disclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that materialinformation relating to the registrant, including its consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this quarterly report is being prepared;

b)       evaluatedthe effectiveness of the registrant’s disclosure controls and procedures andpresented in this report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by thisreport based on such evaluation; and

c)        disclosedin this report any change in the registrant’s internal control over financialreporting that occurred during the registrant’s most recent fiscal quarter thathas materially affected, or is reasonably likely to materially affect, theregistrant’s internal control over financial reporting; and

5.      The registrant’s other certifying officers and I have disclosed, basedon our most recent evaluation of internal control over financial reporting, tothe registrant’s auditors and the audit committee of the registrant’s board ofdirectors (or persons performing the equivalent functions):

a)        allsignificant deficiencies and material weaknesses in the design or operation ofinternal control over financial reporting which are reasonably likely toadversely affect the registrant’s ability to record, process, summarize andreport financial information; and

b)       anyfraud, whether or not material, that involves management or other employees whohave a significant role in the registrant’s internal control over financialreporting.
| Date:  May 10, 2007 |   |                                             |
|--------------------------|--------|--------------------------------------------------|
|                     |   |                                             |
|                     | By:    | /s/ Leslie J. Browne,  Ph.D.                |   |
|                     |   | Leslie J. Browne, Ph.D.                          |
|                     |   | President, Chief Executive  Officer and Director |
|                     |   | (Principal Executive  Officer)                   |

 

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