**Exhibit 10.4(d)**

 

**Amendment No. 4 to Research, License andRoyalty Agreement**

 

This AmendmentNo. 4 to Research, License and Royalty Agreement (the “Amendment”) is enteredinto on July 22, 1998 by and between Pharmacopeia, Inc. (“Pharmacopeia”)and Berlex Laboratories, Inc. (“Berlex”), effective as of February 15,1998 (the “Amendment Effective Date”), and amends that certain Research,License and Royalty Agreement entered into by Pharmacopeia and Berlex effectiveas of February 15, 1995 (the “Agreement”), as amended by AmendmentNo. 1 to Research, License and Royalty Agreement effective as ofNovember 27, 1996, Amendment No. 2 to Research, License and RoyaltyAgreement effective as of June 30, 1997, and Amendment No. 3 to ResearchLicense and Royalty Agreement effective as of November 21, 1997.

 

WHEREAS, underthe terms of the Agreement, as amended, Pharmacopeia and Berlex have conductedcertain research activities under the Research Plan concerning identificationof compounds [*];

 

WHEREAS, underthe terms of the Agreement, as amended, Pharmacopeia has identified a LeadCompound for [*]; and

 

WHEREAS,Berlex would like Pharmacopeia to conduct certain activities to optimize theLead Compound for [*] and Pharmacopeia is willing to conduct such activities onthe terms and conditions set forth herein;

 

NOW THEREFORE,the parties hereby amend the Agreement as follows:

 

1.             All capitalized termsnot defined in this Amendment shall have the meanings given to them in theAgreement, as amended.

 

2.             The following newSections 1.51, 1.52 and 1.53 are added following Section 1.50:

 

1.51        “[*]Term” means the period commencing on the Effective Date and ending thirty-six(36) months after the Effective Date.

 

1.52        “[*]Term” shall mean the period commencing on July 1, 1998 and, unless earlierterminated, ending February 28, 1999.

 

1.53        “ResearchTerm” means the [*] Term and the [*] Term.

 

3.             Section 1.47 isamended to read in its entirety as follows:

 

----

* Information omitted and filed separately with the Commission underRule 24b-2.

 

----

 

1.47        “Termof the Agreement” is defined in Section 14.1.

 

4.             The words “during the[*] Term” are added to the end of Section 2.2.

 

5.             Section 5.1 isamended to read in its entirety as follows:

 

5.1          [*] Term.

 

(a)           Subject to Article XIVand Sections 3.2 and 3.5 (as amended herein), the [*] Term for screeningactivities under the Research Plan shall extend until [*].  The [*] Term may be further extended withthe written agreement of the Parties.

 

(b)           Berlex shall, at least[*] prior to the end of the [*] Term, notify Pharmacopeia in writing whetherBerlex wishes to negotiate an extension of the [*] Term.  Such written notice shall include at leastthe following information: (i) whether Berlex wishes to continue conductingresearch in the Field or wishes to conduct research with respect to additionalor different targets, (ii) an identification of any such proposed additional ordifferent targets, (iii) the length of the proposed extended [*] Term, and (iv)the proposed amount of funding for such extended [*] Term.

 

(c)           (i)  Berlex shall make a payment to Pharmacopeia,in addition to the payments due under Section 5.2, on or before the last day ofthe [*] Term (the “Wind-Down Payment”). The amount of the Wind-Down Payment shall be [*].  In the event Berlex fails to providePharmacopeia written notice as provided under Section 5.1(b), then the amountof the Wind-Down Payment shall be [*]. However, to the extent that Pharmacopeia’s activities pursuant to theResearch Plan utilize fewer than an average of [*] full time equivalents(“FTE’s”) between [*] and [*], any research funding paid by Berlex which isunexpended as of the end of the [*] Term (based on a value of [*] per year perFTE actually utilized, prorated over the period between [*] and [*]) may becredited against (x) the Wind-Down Payment, up to the amount of the Wind-DownPayment, to reduce or eliminate such Wind-Down Payment, or (y) any researchpayments due with respect to an extension of the [*] Term beyond [*].

 

(ii) In exchange for the Wind-Down Payment, Pharmacopeia shall provide suchnumber of FTE’s as the Research Committee reasonably agrees, in order tocomplete certain activities previously commenced pursuant to the Research Plan.

 

2

----

 

6.             Section 5.2(1) isamended to read in its entirety as follows:

 

(1)           [*] within [*] ofreceipt of the final written report on the research done during the [*] Termpursuant to the Research Plan.

 

7.             The following newSection 5.3 is added after Section 5.2:

 

5.3          [*]Funding. The parties understand and agree that Berlex has made all paymentspursuant to Section 5.1 and 5.2 for the [*] Term. With respect to the [*] Term,on or before [*], Berlex shall pay to Pharmacopeia [*]. On or before [*],Berlex shall pay to Pharmacopeia an amount equal to: [*] less an unused portionof the Wind-Down Payment to be calculated by Pharmacopeia and communicated toBerlex by [*].

 

8.             Section 14.1 isamended to read in its entirety as follows:

 

14.1        Termof the Agreement. The Term of the Agreement shall commence on the EffectiveDate and, unless terminated earlier as provided in this Section 14, shallcontinue in full force and effect on a country-by-country basis andcompound-by-compound basis until Berlex and its Sublicensees have no remainingroyalty obligations in a country, at which time this Agreement shall terminatein such country.

 

9.             Section 1.6, 1.40,3.2(a), 3.8, 4.9, 4.14, 5.2, 6.2, and 7.3 are amended by replacing eachinstance of the word “Term” with the words “[*] Term.” Section 3.2(e) isamended by replacing the words “Term of the Agreement” with the words “[*]Term.”

 

10.           Sections 1.5, 1.12,1.19, 1.37, 3.3, 3.9, 4.5(c), 4.6, 4.8(b), 4.13(d), 10.1(b), 13.1, 13.2,14.2(e) and 14.3(d) are amended by replacing each instance of the word “Term”with the words “Research Term.” Sections 4.6 and 13.6 are amended by replacingthe words “Term of this Agreement” with the words “Research Term.”

 

11.           Section 8.1 is amended by replacing eachinstance of the word “Term” with the words “Term of this Agreement.”

 

12.           Except as specifically modified or amendedhereby, the Agreement shall remain in full force and effect and, as modified oramended, is hereby ratified, confirmed and approved.  No

 

3

----

 

provision ofthis Amendment may be modified or amended except expressly in a writing signedby both parties nor shall any terms be waived except expressly in a writingsigned by the party charged therewith. This Amendment shall be governed in accordance with the laws of theState of Delaware, without regard to principles of conflicts of laws.

 

IN WITNESSWHEREOF, each of the parties has executed this Amendment as of the dateindicated on this Amendment.

 
| BERLEX LABORATORIES, INC. |                  | PHARMACOPEIA, INC. |
|---------------------------|-----------------------|--------------------|
|                      |                  |               |
|                      |                  |               |
| By:                       | /s/ Dale Stringfellow |               | By: | /s/ Joseph A. Mollica |
| Name:                     | Dale Stringfellow     |               | Name: | Joseph A. Mollica, Ph.D. |
| Title:                    | President             |               | Title: | Chairman and CEO |
| Date:                     | July 21, '98          |               | Date: | July 20, 1998 |

 

4

----