Document:

Exhibit
10.1

Portions of this Exhibit were omitted and filed
separately with the Secretary of the Commission pursuant to an application for
confidential treatment filed with the Commission pursuant to Rule 24b-2 under
the Securities Exchange Act of 1934.  Such
omissions are designated as **.

 

Execution Copy

AMENDMENT NO. 2

This Amendment No. 2 (this “Amendment No. 2”) to the
Collaboration and License Agreements effective as of July 9, 2003 between (i)
Pharmacopeia Drug Discovery, Inc. (f/k/a Pharmacopeia, Inc.) and Schering
Corporation and (ii) Pharmacopeia Drug Discovery, Inc. and Schering-Plough Ltd.
(collectively, as each has been amended by Amendment No. 1 dated July 27, 2006,
the “2003 Agreements”), is effective as of September 22nd 2006 (the “Amendment
No. 2 Effective Date”).  By agreement of
the Parties, as of the Amendment No. 2 Effective Date, this Amendment No. 2
amends the 2003 Agreements as follows:

1.             All capitalized terms
not defined in this Amendment No. 2 shall have the meanings given to them in
the 2003 Agreements.

2.             The Parties agree
that as of the Amendment No. 2 Effective Date, and notwithstanding anything in
the 2003 Agreements to the contrary:

(a)                                  The
term of the Collaboration is extended and shall continue until April 7, 2007,
on which date it shall terminate.

(b)                                 For
the period from October 8, 2006 until April 7, 2007, Pharmacopeia shall provide
ten (10) chemistry FTEs for the performance of the Collaboration.  During such period, each of Schering and SPL
shall pay to Pharmacopeia research funding for the Collaboration at a rate of **
Dollars ($**) ** (an aggregate ** Dollars ($**) **).  All such FTEs shall be dedicated to work full
time on the Collaboration.

(c)                                  The
FTEs that Pharmacopeia provides under Section 2(b) above shall work on Optimization
Programs designated by the Collaboration Committee.  For the avoidance of doubt, such FTEs shall
not be required to work on Screening Programs.

(d)                                 Payments
by each of Schering and SPL under Section 2(b) above shall be made in
accordance with Section 5.2.3 of the Agreements. 

3.             The Parties agree
that the last sentence of Section 2.2.4 of the Agreements shall not apply to
any Optimization Programs based upon Lead Compounds that are Schering Compounds
(“Extension Programs”) that Pharmacopeia works on during the period set forth
in Section 2(b) above.  For the avoidance
of doubt, the Parties agree that with respect to any Agreement Compounds
resulting from such Extension Programs, Pharmacopeia shall be entitled to
receive milestone payments under Section 5.4.1(a) of the Agreements and royalty
payments under Section 5.5 of the Agreements.

4.             The Parties agree that
from October 8, 2006 until April 7, 2007, senior management representatives of
each Party (from Pharmacopeia the Chief Scientific Officer, or equivalent; from
Schering and SPL the global head of chemistry, or equivalent) and each Party’s
primary project managers shall convene a monthly meeting or teleconference, to
discuss overall

 

performance under the Agreements in order to ensure
effective communication among the Parties.

5.             The remaining terms
of the 2003 Agreements, except to the extent modified by the terms of this
Amendment No. 2, shall remain in full force and effect.

IN WITNESS WHEREOF, the parties hereto have caused
this Amendment No. 2 to be duly executed by their authorized representatives
and delivered in triplicate originals on the Amendment No. 2 Effective Date.

	
  SCHERING CORPORATION

  	
  PHARMACOPEIA
  DRUG DISCOVERY,

  INC. (F/K/A PHARMACOPEIA, INC.)

  
	
   

  	
   

  
	
  By:

  	
  /s/ Michael
  DuBois

  	
   

  	
   

  
	
  Name: Michael
  DuBois

  	
  By:

  	
  /s/ Brian M.
  Posner

  	
   

  
	
  Title: Vice
  President

  	
  Name: Brian M.
  Posner

  
	
   

  	
  Title: Executive
  Vice President,

  
	
   

  	
  Chief Financial
  Officer and Treasurer

  
	
   

  	
   

  
	
  SCHERING-PLOUGH,
  LTD.

  	
   

  
	
   

  	
   

  
	
   

  	
   

  
	
  By:

  	
  /s/ Michael
  DuBois

  	
   

  	
   

  
	
  Name: Michael
  DuBois

  	
   

  
	
  Title: Vice
  President

  	
   

  

 

 2Exhibit
10.2

Portions of this Exhibit were
omitted and filed separately with the Secretary of the Commission pursuant to
an application for confidential treatment filed with the Commission pursuant to
Rule 24b-2 under the Securities Exchange Act of 1934.  Such omissions are designated as **.

Execution
Version

AMENDMENT
NO. 1 

to

PRODUCT DEVELOPMENT AND

COMMERCIALIZATION AGREEMENT

This Amendment No. 1 (this “Amendment”), effective as of August 1, 2006 (the “Amendment
Effective Date”), is entered into by
and between SmithKline Beecham Corporation, doing business as GlaxoSmithKline,
a Pennsylvania corporation having a principal place of business at One Franklin
Plaza, 200 N 16th Street, Philadelphia, PA 19102 (“SB Corp”),
and Glaxo Group Limited, a company existing under the laws of England and
Wales, having its registered office at Glaxo Wellcome House, Berkeley Avenue,
Greenford, Middlesex, UB6 0NN, England (“GGL”), SB Corp and GGL being
collectively referred to hereinafter as “GSK”; and Pharmacopeia Drug Discovery,
Inc., a Delaware corporation having a principal place of business at 3000 Eastpark Boulevard, Cranbury, New Jersey
08512 (“Pharmacopeia”).  Pharmacopeia and GSK are each referred to
herein by name or as a “Party” or, collectively, as the “Parties.”  The Parties do hereby enter into this
Amendment in order to amend that certain Product Development and Commercialization Agreement by and
between the Parties which was executed as of March 24, 2006 (the “Agreement”).

The Parties do hereby amend the Agreement as follows:

1.             All capitalized
terms not defined in this Amendment shall have the meanings given to them in
the Agreement.

2.             Add new Section
1.32(a) as follows:

“1.32(a)  ‘GSK TOOL COMPOUND’ shall mean any compound (and any isomers, esters, salts, hydrates,
or solvates thereof) provided hereunder by GSK to Pharmacopeia (as
documented by a “GSK Tool Compound Transfer Record” which shall describe the
compound being transferred and the amount and date provided and the purpose for
which the compound is provided) which (i) has been documented by GSK, at the
time of transfer to Pharmacopeia, to modulate the activity of an Initial
Target, (ii) is described in any know-how or pending or issued patent
Controlled by GSK, and (iii) is neither in the public domain nor available to Pharmacopeia
from any Third Party having the legal right to provide such compound, and which
is provided to Pharmacopeia for use under the Agreement only as a positive
control in biological assays for
activity with respect to the applicable Initial Target, and not for any other
use or purpose.”

3.                                       Add new Section
1.32(b) as follows:

“1.32(b)  ‘GSK TOOL COMPOUND IP’
shall mean any Know-how or pending or issued Patent, pertaining specifically to
a GSK Tool Compound, which (i) exists as of the date such GSK Tool Compound is
supplied to Pharmacopeia and is owned or Controlled by GSK or (ii) is conceived
solely by GSK and reduced to practice by Pharmacopeia in the course of
performing a

 

Program.  Any
GSK Tool Compound IP shall be assigned to GSK as the sole owner thereof, and
GSK shall have sole control over all matters pertaining to the prosecution,
defense and enforcement of any Patents included in GSK Tool Compound IP.  In the event that Pharmacopeia conceives an
invention based on its use of any GSK Tool Compound as expressly
permitted pursuant to this Amendment and
obtains patent protection therefor, such patent shall not fall within the GSK
Tool Compound IP defined in this paragraph. 
However, Pharmacopeia hereby grants to GSK a non-exclusive, ** license,
under all of **, to ** of the Agreement.”

4.             Revise Section 2.2.2(a) to
read in its entirety as follows:

“(a)  determine
the ** (**) ** (other than the ** (**) **, which shall be determined prior to
the Effective Date pursuant to Section 3.2.1) which shall be pursued via
Programs pursuant to this Agreement.  The
JSC may, at its discretion, agree to revise the schedule for the transfer of
reagents and assays from GSK to Pharmacopeia described in paragraph (c) below,
or the JSC may for any reason agree to substitute an alternative Target for the
applicable Initial Target;”

5.             Revise Section 3.2.3 to read
in its entirety as follows:

“3.2.3      Provision
of Reagents and Assays.  The reagents and
assays for screening of the Initial Targets shall be provided by GSK to
Pharmacopeia on a reasonable schedule to be established by the JSC, except with
respect to any Initial Targets for which Pharmacopeia has or can readily
generate reagents and assays, at Pharmacopeia’s reasonable discretion.  GSK will complete transfer of reagents and
assays to Pharmacopeia for the ** (**) ** in accordance with a schedule to be
mutually agreed by the Parties after the Effective Date.  In the event GSK determines that, for any
reason, it will be unable to complete the transfer of such reagents and assays
in accordance with such schedule, the JSC may agree to revise the schedule or
to substitute an alternative Target for the applicable Initial Target.”

6.             Add new Section 3.2.4 as follows:

“3.2.4      Supply of GSK Tool
Compounds.

(a)                                                          Pursuant to the
decision of the JSC, GSK will supply to Pharmacopeia a GSK Tool Compound in
reasonable quantities as determined by the JSC, provided that such quantities
are readily available to GSK, for use by Pharmacopeia only as a positive
control for determining activity in biological assays to support the conduct of
one or more Screening Programs.  All such
transfers of GSK Tool Compounds shall be documented in writing by a “GSK Tool
Compound Transfer Record”, which shall record the name of the compound and the
amount and date transferred and the permitted purpose for use by
Pharmacopeia.  At the time GSK provides a
GSK Tool Compound to Pharmacopeia, GSK shall grant, and hereby does grant to
Pharmacopeia, a non-exclusive license to use the GSK Tool Compound under the
relevant GSK Tool Compound IP owned or Controlled by GSK for use only in
biological assays pursuant to a Program (i) as a positive control in an assay
to modulate the activity of the applicable Target and/or (ii) to find
non-active site inhibitors, and for no other purpose.  For avoidance of doubt, Pharmacopeia shall
not be permitted to transfer or disclose any GSK Tool 

 2
 

 

Compound or any GSK Tool
Compound IP or any information regarding the chemical structure of any GSK Tool
Compound to a Third Party without GSK’s prior written consent.  In addition, the Parties understand and agree
that Pharmacopeia shall not use the GSK Tool Compound or the GSK Tool Compound
IP as a starting point or as an intermediate in any chemistry efforts or any
structure-activity-relationship studies (SAR studies) under a Program to
identify or optimize any chemical compound or series to be progressed by
Pharmacopeia pursuant to any Program.

(b)                                                         In addition,
pursuant to a request from the JSC, GSK may, at its sole discretion, elect to
supply to Pharmacopeia (for Pharmacopeia’s convenience), and Pharmacopeia may,
at its sole discretion, accept for screening, certain tool compounds which do
not qualify under the definition of GSK Tool Compounds, but which may be useful
as a positive control in a biological assay under a Program for one of the
Initial Targets.  Any such tool compound
provided by GSK to Pharmacopeia shall be subject to all of the same
restrictions upon permitted use and disclosure as are described above in paragraph
(a) of this Section 3.2.4 for the GSK Tool Compounds.  To the extent that Pharmacopeia uses any
compound supplied by GSK pursuant to this Section 3.2.4(b), Pharmacopeia agrees
to do so at its own risk.

7.             Add a new sentence at the
end of Section 3.3.1 as follows:

“In addition, GSK and
Pharmacopeia hereby agree that the provisions of this Section 3.3 (“Restrictions
on Targets/Noncompete”) shall not apply to restrict or prohibit the pursuit by
either Party outside of Programs under the Agreement, whether independently or
for/with a Third Party, of the discovery, research, development or
commercialization of any **, wherein such ** is an Initial Target under the
Agreement.

8.             All the terms of the
Agreement, except as expressly modified by this Amendment, shall remain
unchanged and in full force and effect.

 3
 

 

IN WITNESS WHEREOF, each of the
parties hereto has caused this Amendment to be duly executed by its duly
authorized representatives as of the Amendment Effective Date.

	
  SMITHKLINE BEECHAM CORPORATION,

  	
  PHARMACOPEIA DRUG

  
	
  d/b/a
  GLAXOSMITHKLINE

  	
  DISCOVERY, INC.

  
	
   

  	
   

  
	
  By:

  	
  /s/ Donald E.
  Parman

  	
   

  	
  By:

  	
  /s/ Leslie J. Browne

  	
   

  
	
   

  	
   

  
	
  Name: Donald E.
  Parman

  	
  Name: Leslie J. Browne, Ph.D.

  
	
   

  	
   

  
	
  Title: Vice
  President and Secretary

  	
  Title: President and Chief Executive Officer

  
	
   

  	
   

  
	
  Date:   August
  10, 2006

  	
  Date: August 8, 2006

  
	
   

  	
   

  
	
  GLAXO
  GROUP LIMITED

  	
   

  
	
   

  	
   

  
	
  By:

  	
  /s/ V.A. Whyte

  	
   

  	
   

  
	
   

  	
   

  
	
  Name: V.A. Whyte

  	
   

  
	
   

  	
   

  
	
  Title: Assistant
  Company Secretary

  	
   

  
	
   

  	
   

  
	
  Date: 10 August
  2006

  	
   

  
							

 

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