**Exhibit3.1**

**AMENDEDAND RESTATED CERTIFICATE OF INCORPORATIONOFPHARMACOPEIA DRUG DISCOVERY, INC.**

Pharmacopeia Drug Discovery, Inc., a corporationorganized and existing under the laws of the State of Delaware, herebycertifies as follows:

*ONE*.The name of this corporation is “Pharmacopeia Drug Discovery, Inc.”

*TWO*.The registered office of the Corporation in the State of Delaware is to belocated at Corporation Trust Company, 1209 Orange Street, City of Wilmington,County of New Castle, Delaware, 19808. The name of the registered agent of thecorporation at such address is The Corporation Trust Company.

*THREE*.The nature of the business or purposes to be conducted or promoted is to engagein any lawful act or activity for which corporations may now or hereafter beorganized under the General Corporation Law of Delaware (the “GCL”) and topossess and exercise all of the powers and privileges granted by such law andany other law of the State of Delaware.

*FOUR*.This corporation is authorized to issue two classes of stock to be designated,respectively, “Common Stock” and “Preferred Stock.” The total number of sharesof Common Stock which the corporation is authorized to issue is FIFTY MILLION(50,000,000) shares, par value $0.01. The total number of shares of PreferredStock which the corporation is authorized to issue is TWO MILLION FIVE HUNDREDTHOUSAND (2,500,000), par value $0.01 per share.

1.     The Board of Directorsis authorized, subject to limitations prescribed by law and the provisions ofthis Article FOUR, to provide for the issuance of the shares of Preferred Stockin one or more series, and by filing a certificate pursuant to the applicablelaw of the State of Delaware, to establish from time to time the number ofshares to be included in each such series, and to fix the designation, powers,preferences, and rights of the shares of each such series and thequalifications, limitations or restrictions thereof.

2.     The authority of theBoard with respect to each series shall include, but not be limited to,determination of the following:

(a)   The number of shares constitutingthat series and the distinctive designation of that series, which number may beincreased or decreased (but not below the number of shares then outstanding)from time to time by action of the Board of Directors;

(b)   The dividend rate and the timesof payment of dividends on the shares of that series, whether dividends shallbe cumulative, and, if so, from which date;

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(c)   Whether that series shall havevoting rights, in addition to the voting rights provided by law, and, if so,the terms of such voting rights;

(d)   Whether that series shall haveconversion privileges, and, if so, the terms and conditions of such conversion,including provision for adjustment of the conversion rate in such events as theBoard of Directors shall determine;

(e)   Whether or not the shares of thatseries shall be redeemable, and, if so, the terms and conditions of suchredemption, including the date or date upon or after which they shall be redeemable,and the amount per share payable in case of redemption, which amount may varyunder different conditions and at different redemption dates;

(f)    Whether that series shallhave a sinking fund for the redemption or purchase of shares of that series,and, if so, the terms and amount of such sinking fund;

(g)   Whether or not the shares of theseries will have priority over or be on a parity with or be junior to theshares of any other series or class in any respect or will be entitled to thebenefit of limitations restricting the issuance of shares of any other seriesor class having priority over or being on a parity with the shares of suchseries in any respect, or restricting the payment of dividends on or the makingof other distributions in respect of shares of any other series or classranking junior to the shares of the series as to dividends or assets, orrestricting the purchase or redemption of the shares of any such junior seriesor class, and the terms of any such restrictions;

(h)   The rights of the shares of thatseries in the event of voluntary or involuntary liquidation, dissolution orwinding up of the corporation, and the relative rights or priority, if any, ofpayment of shares of that series; and

(i)    Any other relative rights,preferences and limitations of that series.

3.*    CommonStock.*    All shares of Common Stock willentitle the holders thereof to the following rights and privileges.

(a)*    Dividends.*    Subjectto the rights of the holders of Preferred Stock, and subject to any otherprovisions of their Amended and Restated Certificate of Incorporation, holdersof Common Stock shall be entitled to receive such dividends and otherdistributions in cash, stock of any corporation or property of the Corporationas may be declared thereon by the Board of Directors from time to time out ofassets or funds of the Corporation legally available therefor and shall shareequally on a per share basis in all such dividends and other distributions. Theright to dividends on shares of the Common Stock shall not be cumulative, andno right shall accrue to holders of Common Stock by reason of the fact thatdividends on said shares are not declared in any prior period.

(b)*    Distributionof Assets.*    Subject to the rights of theholders of Preferred Stock, in the event of the voluntary or involuntaryliquidation, dissolution or winding up of the Corporation, holders of CommonStock will be entitled to receive all of the remaining

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assets of theCorporation available for distribution to its stockholders after all amounts towhich the holders of Preferred Stock are entitled have been paid or set asidein cash for payment.

(c)*    VotingRights.*    Except as otherwise expresslyrequired by law or provided in this Amended and Restated Certificate ofIncorporation, (i) the holders of any outstanding shares of Common Stockshall vote together as a single class on all matters with respect to whichstockholders are entitled to vote under applicable law, this Amended andRestated Certificate of Incorporation or the Bylaws of the Corporation, or uponwhich a vote of stockholders is otherwise duly called for by the Corporation,and (ii) at each annual or special meeting of stockholders, each holder ofrecord of shares of Common Stock on the relevant record date shall be entitledto cast one (1) vote in person or by proxy for each share of the CommonStock standing in such holder’s name on the Corporation’s stock transferrecords. No holder of any shares of capital stock or other securities of theCorporation, whether now or hereafter authorized, shall have any preemptiveright to subscribe for or to purchase any shares of capital stock or othersecurities of the Corporation. Holders of Common Stock shall not be permittedto cumulate their votes.

*FIVE*.The corporation is to have perpetual existence.

*SIX*.In furtherance and not in limitation of the powers conferred by statute, theBoard of Directors of the Corporation is expressly authorized to adopt, amendor repeal the Bylaws of the Corporation. The stockholders shall also have powerto adopt, amend or repeal the Bylaws of the Corporation.

*SEVEN*.The number of directors of the corporation shall be from five to ten asprovided from time to time exclusively by the Board of Directors pursuant to aresolution duly adopted by a majority of the Entire Board. For purposes of thisAmended and Restated Certificate of Incorporation, the term “Entire Board”shall mean the total number of authorized directors regardless of whether thereexist any vacancies in such authorized directorships.

1.     The Board of Directorsshall be and is divided into three classes:

(a)   Class I, Class II andClass III, which shall be as nearly equal in number as possible. Eachdirector shall serve for a term ending on the date of the third annual meetingof stockholders following the annual meeting at which the director was elected;provided, however, that each initial director in Class I shall hold officeuntil the annual meeting of stockholders in 2005; each initial director inClass II shall hold office until the annual meeting of stockholders in2006; and each initial director in Class III shall hold office until theannual meeting of stockholders in 2007. Notwithstanding the foregoingprovisions of this Article, each director shall serve until his successor isduly elected and qualified or until his death, resignation or removal.

(b)   In the event of any increase ordecrease in the authorized number of directors, (i) each director thenserving as such shall nevertheless continue as a director of the class

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ofwhich he is a member until the expiration of his current term, or his earlierresignation, removal from office or death, and (ii) the newly created oreliminated directorship resulting from such increase or decrease shall beapportioned by the Board of Directors among the three classes of directors soas to maintain such classes as nearly equal as possible.

(c)   Election by Ballot. The electionof directors need not be by written ballot unless the Bylaws of the Corporationshall so provide.

(d)   Any director may be removed fromoffice at any time only for cause by the affirmative vote of the holders of atleast a majority of the voting power of all then outstanding shares of capitalstock of the Corporation entitled to vote generally in the election ofdirectors voting together as a single class. Directors may not be removed fromoffice without cause.

*EIGHT*.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 toany provisions contained in the statutes) outside the State of Delaware at suchplace or places as may be designated from time to time by the Board ofDirectors or in the Bylaws of the Corporation.

*NINE*.

(a)   The Corporation shall indemnifyeach of the Corporation’s directors and officers in each and every situationwhere, under Section 145 of the GCL, as amended from time to time (“Section 145”),the Corporation is permitted or empowered to make such indemnification. TheCorporation may, in the sole discretion of the Board of Directors of thecorporation, indemnify any other person who may be indemnified pursuant toSection 145 to the extent the Board of Directors deems advisable, aspermitted by Section 145. The Corporation shall promptly make or cause tobe made any determination required to be made pursuant to Section 145.

(b)   The directors of the Corporationshall be entitled to the benefits of all limitations on the liability ofdirectors generally that are now or hereafter become available under the GCL.Without limiting the generality of the foregoing, to the fullest extent fromtime to time permitted by law, no person shall be personally liable to theCorporation or its stockholders for monetary damages for breach of fiduciaryduty as a director, provided, however, that the foregoing shall not eliminateor limit the liability of a director (i) for any breach of the director’sduty of loyalty to the corporation or its stockholders, (ii) for acts oromissions not in good faith or which involve intentional misconduct or aknowing violation of law, (iii) under Section 174 of the GCL or(iv) for any transaction from which the director derived an improperpersonal benefit. If the GCL is subsequently amended to further eliminate orlimit the liability of a director, then a director of the corporation, inaddition to the circumstances in which a director is not personally liable asset forth in the preceding sentence, shall not be liable to the fullest extentpermitted by the amended GCL. For purposes of this Article NINE, “fiduciaryduty as a director” shall include any fiduciary duty arising out of serving atthe

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corporation’srequest as a director of another corporation, partnership, joint venture orother enterprise, and “personal liability to the corporation or itsstockholders” shall include any liability to such other corporation,partnership, joint venture, trust or other enterprise, and any liability to thecorporation in its capacity as a security holder, joint venturer, partner,beneficiary, creditor or investor of or in any such other corporation,partnership, joint venture, trust or other enterprise.

(c)   Neither any amendment nor repealof this Article NINE, nor the adoption of any provision of this Amended andRestated Certificate of Incorporation inconsistent with this Article NINE,shall eliminate or reduce the effect of this Article NINE in respect of anymatter occurring, or any cause of action, suit or claim that, but for thisrepeal or adoption of an inconsistent provision, would have been subject to anylimitation on liability or indemnification or advancement of expensespreviously contained herein with respect to matters involving any occurrence oralleged occurrence of any action or omission to act that took place prior tosuch amendment or repeal.

*TEN*.Advance notice of new business and stockholder nominations for the election ofdirectors shall be given in the manner and to the extent provided in the Bylawsof the corporation.

*ELEVEN*.Whenever a compromise or arrangement is proposed between this corporation andits creditors or any class of them and/or between this corporation and itsstockholders or any class of them, any court of equitable jurisdiction withinthe State of Delaware may, on the application in a summary way of thiscorporation or of any creditor or stockholder thereof or on the application ofany receiver or receivers appointed for this corporation under the provisionsof Section 291 of Title B of the Delaware Code or on the application oftrustees in dissolution or of any receiver or receivers appointed for thiscorporation under the provisions of Section 279 of Title 8 of the DelawareCode, order a meeting of the creditors or class of creditors, and/or of thestockholders or class of stockholders of this corporation, as the case may be,to be summoned in such manner as the said court directs. If a majority innumber representing three-fourths in value of the creditors or class ofcreditors, and/or of the stockholders or class of stockholders of thiscorporation, as the case may be, agree to any compromise or arrangements and toany reorganization of this corporation as consequence of such compromise orarrangement, the said compromise or arrangement and the said reorganizationshall, if sanctioned by the court to which the said application has been made,be binding on all the creditors or class of creditors, and/or on all thestockholders or class of stockholders, of this corporation, as the case may be,and also on this corporation.

*TWELVE*.The Corporation reserves the right to amend, alter, change or repeal anyprovisions contained in this Certificate, in the manner now or hereafterprescribed by statute, and all rights conferred upon stockholders herein aregranted subject to this reservation.

*THIRTEEN*.Any action required or permitted to be taken by the stockholders of theCorporation must be effected at a duly called annual or special meeting ofstockholders of the Corporation and may not be effected by any consent inwriting in lieu of a meeting by such stockholders. Special meeting ofstockholders of the Corporation may be called only by the

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Chairman of the Board of Directors, or by the Board ofDirectors acting pursuant to a resolution adopted by a majority of the EntireBoard.

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**CERTIFICATE OF AMENDMENT**

**OF THE**

**AMENDED AND RESTATED CERTIFICATEOF INCORPORATION**

**OF**

**PHARMACOPEIADRUG DISCOVERY, INC.**

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**PHARMACOPEIADRUG DISCOVERY, INC.**, a corporation organized and existingunder the General Corporation Law of the State of Delaware (the “Corporation”),does hereby certify:

**FIRST: **That by written consent ofthe board of directors dated March 16, 2007, resolutions were duly adoptedsetting forth a proposed amendment to the Amended and Restated Certificate ofIncorporation of the Corporation, declaring said amendment to be advisable andcalling for consideration of said proposed amendment by the stockholders of theCorporation at the next annual meeting of stockholders. The resolution settingforth the amendment is as follows:

RESOLVED, that it is hereby proposed that Article One of the Amendedand Restated Certificate of Incorporation of the Corporation be amended andrestated in its entirety to read as follows:

“*ONE*. The name of this corporation is ‘Pharmacopeia,Inc.’”

**SECOND: **That thereafter, pursuantto the resolutions of the board of directors, the proposed amendment wasapproved by the stockholders of the Corporation at a meeting held on May 3,2007.

**THIRD: **That said amendment wasduly adopted in accordance with the provisions of Section 242 of the GeneralCorporation Law of the State of Delaware.

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**INWITNESS WHEREOF,** the Corporation has caused this Certificateto be signed by Stephen C. Costalas, its Executive Vice President, GeneralCounsel and Secretary, this 3rd day of May, 2007.
|            | **PHARMACOPEIA DRUG DISCOVERY, INC.** |
|------------|---------------------------------------|
| ** ** |                                  |
| ** ** |                                  |
|       | By:                                   | /s/ Stephen C.  Costalas |   |
|       |                                  | Stephen C. Costalas |   |
|       |                                  | Executive Vice President, General |   |
|       |                                  | Counsel and  Secretary |   |

 

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