Document:

Exhibit
10.4

Confidential Materials omitted and filed separately
with the

Securities and Exchange
Commission.  Asterisks denote omissions.

THIRD
AMENDMENT TO THE OCTOBER 31, 2002 LICENSE

This Third Amendment,
effective as of the date set forth above the signatures of the parties below,
pertains to the Exclusive Patent License Agreement, effective on October 31,
2002, as subsequently amended by a First Amendment on November 15, 2002
and a Second Amendment on July 17, 2004, by and between the Massachusetts Institute of Technology (“M.I.T.”) and
Momenta Pharmaceuticals, Inc. (“COMPANY”).

WHEREAS, COMPANY possesses certain non-exclusive
rights and desires to obtain certain exclusive rights to M.I.T. Case No. 6582, “A
Method for the Mass Spectrometric Determination of the Molecular Weight of
Highly Acidic (and Basic) Organic and Biological Molecules,” by Klaus Biemann
and Peter Juhasz; and

WHEREAS. M.I.T. is willing to grant such rights to
COMPANY;

NOW, THEREFORE, M.I.T. and
COMPANY hereby agree to modify the Exclusive Patent License Agreement as
follows:

1.               The first paragraph of Section 2.2, as
amended, shall be modified to read as follows:

2.2   Exclusivity.
In order to establish an exclusive period for COMPANY and its AFFILIATES,
M.I.T. agrees that it shall not grant any other license for PATENTS RIGHTS
HEPARINASE, PATENT RIGHTS MASSPEC, PATENT RIGHTS SEQUENCING and PATENT RIGHTS
ENZYMES in FIELD SEQUENCING MACHINES to develop, make, have made, use, sell,
offer to sell, lease and import LICENSED PRODUCTS during the TERM.

2.               The last sentence of Section 2.2, as amended,
shall be amended to read as follows:

Upon COMPANY’s exercise of such right, the Appendix of this Agreement
that describes the PATENT RIGHTS that dominate the IMPROVEMENT shall be deemed
to have been amended to add the invention disclosure (and any related patent
applications) covering such IMPROVEMENT, and such IMPROVEMENT and any resulting
patent applications and patents shall thereafter be included in PATENT RIGHTS
for all purposes of this Agreement, without any additional fee, other than the
one Ten Thousand Dollar fee referred to in the previous sentence, and M.I.T.
shall provide COMPANY with an updated Appendix A, B, C or E for its
records.

3.               Section 7.2(a), as amended, shall be modified
to read as follows:

COMPANY Right to Prosecute PATENT RIGHTS in Exclusive Fields.  So
long as COMPANY remains the exclusive licensee of the PATENT RIGHTS SEQUENCING,
PATENT RIGHTS MASSPEC, PATENT RIGHTS HEPARINSE and PATENT RIGHTS ENZYMES in the
FIELD SEQUENCING MACHINES in the TERRITORY, COMPANY, to the extent permitted by
law, shall have the right, under its own control and at its own expense, to
prosecute any third party infringement of the PATENT RIGHTS SEQUENCING, PATENT
RIGHTS MASSPEC, PATENT RIGHTS HEPARINASE and

 

PATENT RIGHTS ENZYMES in the FIELD SEQUENCING MACHINES in the
TERRITORY, subject to Sections 7.4 and 7.5.  If required by law, M.I.T. shall permit any
action under this Section to be brought in its name, including being joined as
a party-plaintiff, provided that COMPANY shall hold M.I.T. harmless from, and
indemnify M.I.T. against, any costs, expenses, or liability that M.I.T. incurs
in connection with such action.  Prior to
commencing any such action, COMPANY shall consult with M.I.T. and shall consider
the views of M.I.T. regarding the advisability of the proposed action and its
effect on the public interest.  COMPANY
shall not enter into any settlement, consent judgment, or other voluntary final
disposition of any infringement action under this Section without the prior
written consent of M.I.T.

4.               Section 7.2(c) shall be deleted in its
entirety.

5.               Section 7.7, as amended, shall be modified to
read as follows:

Right to Sublicense.  So long as COMPANY remains the
exclusive licensee of the PATENT RIGHTS SEQUENCING, PATENT RIGHTS MASSPEC,
PATENT RIGHTS HEPARINASE and PATENT RIGHTS ENZYMES in the FIELD SEQUENCING
MACHINES in the TERRITORY, COMPANY shall have the sole right to sublicense any
alleged infringer in the FIELD SEQUENCING MACHINES in the TERRITORY for future
use of the PATENT RIGHTS SEQUENCING, PATENT RIGHTS MASSPEC, PATENT RIGHTS
HEPARINASE and PATENT RIGHTS ENZYMES in accordance with the terms and
conditions of this Agreement relating to sublicenses.  Any upfront fees as part of such sublicense
shall be shared equally between COMPANY and M.I.T.; other revenues to COMPANY
pursuant to such sublicense shall be treated as set forth in Article 4.

6.               In consideration of
the exclusive license granted for PATENT RIGHTS MASSPEC in the FIELD SEQUENCING
MACHINES hereunder, COMPANY shall pay M.I.T. a license expansion fee of [**]
Dollars ($[**]), which shall be due upon the Effective Date of this Third
Amendment.

All other terms and
conditions of the License Agreement shall remain unchanged.

The
EFFECTIVE DATE of this Amendment is August 5, 2006.

Agreed
to for:

	
  MASSACHUSETTS INSTITUTE OF

  	
   

  	
  MOMENTA PHARMACEUTICALS, INC

  
	
  TECHNOLOGY

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  By

  	
    /s/Lita
  L. Nelsen

  	
   

  	
   

  	
  By

  	
    /s/Susan
  K. Whoriskey, Ph.D.

  	
   

  
	
  Name:

  	
  Lita L. Nelsen

  	
   

  	
   

  	
  Name:

  	
  Susan K. Whoriskey, Ph.D.

  	
   

  
	
  Title:

  	
  Director,
  Technology Licensing Office

  	
   

  	
   

  	
  Title:

  	
  Vice President, Licensing &

  	
   

  
	
  Date :

  	
  August 3, 2006

  	
   

  	
   

  	
  Business Development

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
  Date:

  	
  August 3, 2006

  	
   

  
													

 

 2Exhibit
10.5

Confidential Materials omitted and filed separately
with the

Securities and Exchange
Commission.  Asterisks denote omissions.

FIFTH
AMENDMENT TO THE NOVEMBER 1, 2002 LICENSE

This Fifth Amendment, effective as of the date set
forth above the signatures of the parties below, pertains to the Amended and
Restated Exclusive Patent License Agreement, effective on November 1, 2002, as
subsequently amended by a First Amendment on November 15, 2002, a Letter
Agreement on September 12, 2003, a Letter Agreement on October 22, 2003, a
Second Amendment on November 19, 2003, a Third Amendment on April 2, 2004, and
a Fourth Amendment on July 17, 2004, by and between the Massachusetts Institute
of Technology (“M.I.T.”) and Momenta Pharmaceuticals, Inc. (“COMPANY’)

WHEREAS, COMPANY possesses certain non-exclusive
rights and desires to obtain certain exclusive rights to M.I.T. Case No. 6582, “A
Method for the Mass Spectrometric Determination of the Molecular Weight of
Highly Acidic (and Basic) Organic and Biological Molecules,” by Klaus Biemann
and Peter Juhasz; and

WHEREAS. M.I.T. is willing to grant such rights to
COMPANY;

NOW, THEREFORE, M.I.T. and COMPANY hereby agree to
modify the Amended and Restated Exclusive Patent License Agreement as follows:

1.               The
following definitions shall be added to Section 1:

“ANDA”
shall mean a United States abbreviated new drug application, or any successor
form or foreign equivalent.

“ANTICOAGULANT
PRODUCT” shall mean any product that prevents, hinders or slows the
clotting of blood, including, but not limited to, unfractionated heparins, low
molecular weight heparins and ultra-low molecular weight heparins.

“BLA” shall
mean a United States new biologics application, or any successor form or
foreign equivalent.

“ENOXAPARIN
PRODUCT” shall mean a generic version of Lovenox®.

“FIELD
ANTICOAGULANT” shall mean (a) use in the discovery, characterization and
development of ANTICOAGULANT PRODUCTS and (b) the pre-clinical and clinical
testing, regulatory filing and approval, use, manufacture, quality control,
commercial release specification, distribution and sale of ANTICOAGULANT
PRODUCTS.

“GENERIC
ANTICOAGULANT PRODUCT” shall mean a generic version of a
particular branded ANTICOAGULANT PRODUCT.

 

“INNOVATIVE
ANTICOAGULANT PRODUCT” shall mean a new chemical entity
marketed as a branded ANTICOAGULANT PRODUCT.

“MARKETING
APPROVAL FILING” shall mean an ANDA, BLA, NDA or SNDA.

“SNDA”
shall mean a United States supplementary new drug application, or any successor
form or foreign equivalent.

“TERRITORY”
shall mean the world.

2.               The
last sentence of Section 2.1, as amended, shall be modified to read as follows:

Upon COMPANY’s
exercise of such right, the Appendix of this Agreement that describes the
PATENT RIGHTS that dominate the IMPROVEMENT shall be deemed to have been
amended to add the invention disclosure (and any related patent applications)
covering such IMPROVEMENT, and such IMPROVEMENT and any resulting patent
applications and patents shall thereafter be included in PATENT RIGHTS for all
purposes of this Agreement, without any additional fee, other than the one Ten
Thousand Dollar fee referred to in the previous sentence, and M.I.T. shall
provide COMPANY with an updated Appendix C, D, E or H for its records.

3.               Section 2.2, as
amended, shall be modified to read as follows:

Exclusivity.  In order to establish an exclusive period for
COMPANY and its AFFILIATES, M.I.T. agrees that it shall not grant any other
license for

(a)  PATENT RIGHTS HEPARIN in FIELD ALL BUT
MACHINES, (b) PATENT RIGHTS HEPARINASE in FIELD MANUFACTURING, (c)  PATENT RIGHTS ENZYMES IN FIELD ENZYMES, but
specifically excluding FIELD RESEARCH REAGENTS, and (d) PATENT RIGHTS MASSPEC
in FIELD ANTICOAGULANT, in each case to develop, make, have made, use, sell,
offer to sell, lease and import LICENSED PRODUCTS or to develop and perform
LICENSED PROCESSES during the TERM.

4.               Section 2.5(a)
shall be modified to read as follows:

M.I.T.  M.I.T. retains the right to practice under
the PATENT RIGHTS for research, teaching, and educational purposes.  In addition, in accordance with the NIH
Guidelines for Patenting of Research Tools, M.I.T. retains the right to grant
to not-for-profit institutions, nonexclusive, non-transferable licenses under
the PATENT RIGHTS HEPARIN and PATENT RIGHTS MASSPEC for use as research tools
and for research purposes only, specifically not including manufacturing,
quality assurance, quality control, and clinical

 2
 

 

testing of
commercial products or characterization of a marketed product for commercial
purposes.

5.               Section 7.2(a), as
amended, shall be modified to read as follows:

COMPANY Right to
Prosecute PATENT RIGHTS in Exclusive Fields.  So long as COMPANY remains the exclusive
licensee of PATENT RIGHTS HEPARIN in FIELD ALL BUT MACHINES, COMPANY, to the
extent permitted by law, shall have the right, under its own control and at its
own expense, to prosecute any third party infringement of PATENT RIGHTS HEPARIN
in FIELD ALL BUT MACHINES, subject to Sections 7.4 and 7.5.  So long as COMPANY remains the exclusive
licensee of PATENT RIGHTS HEPARINASE in FIELD MANUFACTURING, COMPANY, to the
extent permitted by law, shall have the right, under its own control and at its
own expense, to prosecute any third party infringement of PATENT RIGHTS
HEPARINASE in FIELD MANUFACTURING, subject to Sections 7.4 and 7.5.  So long as COMPANY remains the exclusive
licensee of PATENT RIGHTS ENZYMES in FIELD ENZYMES excluding FIELD RESEARCH
REAGENTS, COMPANY, to the extent permitted by law, shall have the right, under
its own control and at its own expense, to prosecute any third party
infringement of PATENT RIGHTS ENZYMES in FIELD ENZYMES excluding FIELD RESEARCH
REAGENTS, subject to Sections 7.4 and 7.5. 
Lastly, so long as COMPANY remains the exclusive licensee of PATENT
RIGHTS MASSPEC in FIELD ANTICOAGULANT, COMPANY, to the extent permitted by law,
shall have the right, under its own control and at its own expense, to
prosecute any third party infringement of PATENT RIGHTS MASSPEC in FIELD
ANTICOAGULANT, subject to Sections 7.4 and 7.5. 
If required by law, M.I.T. shall permit any action under this Section to
be brought in its name, including being joined as a party-plaintiff, provided
that COMPANY shall hold M.I.T. harmless from, and indemnify M.I.T. against, any
costs, expenses, or liability that M.I.T. incurs in connection with such
action.  Prior to commencing any such
action, COMPANY shall consult with M.I.T. and shall consider the views of
M.I.T. regarding the advisability of the proposed action and its effect on the
public interest.  COMPANY shall not enter
into any settlement, consent judgment, or other voluntary final disposition of
any infringement action under this Section without the prior written consent of
M.I.T.

6.               Section 7.2(b), as
amended, shall be modified to read as follows:

M.I.T. Right to
Prosecute PATENT RIGHTS in Exclusive Fields.  In the event that COMPANY is unsuccessful in
persuading the alleged infringer of PATENT RIGHTS HEPARIN in FIELD ALL BUT
MACHINES, PATENT RIGHTS HEPARINASE in FIELD MANUFACTURING, PATENT RIGHTS ENZYMES
in FIELD ENZYMES excluding FIELD RESEARCH REAGENTS, or PATENT RIGHTS MASSPEC in
FIELD

 3
 

 

ANTICOAGULANT to
desist or fails to have initiated an infringement action within a reasonable
time after COMPANY first becomes aware of the basis for such action, M.I.T.
shall have the right, to prosecute such infringement under its sole control and
at its sole expense, and any recovery obtained shall belong to M.I.T. If
required by law, COMPANY hereby agrees that M.I.T. may include COMPANY as a
party-plaintiff in any such suit, without expense to COMPANY.  Prior to commencing any such action, M.I.T.
shall consult with COMPANY and shall consider the views of COMPANY regarding
the advisability of the proposed action. 
Further, M.I.T. shall not enter into any settlement, consent judgment,
or other voluntary final disposition of any infringement action under this
Section without first consulting with and considering the views of
COMPANY.  Notwithstanding the forgoing,
any action taken under this Section shall be at the sole discretion of M.I.T.

7.               Section 7.2(c), as
amended, shall be modified to read as follows:

M.I.T. Right to
Prosecute PATENT RIGHTS in Non-Exclusive Fields.  M.I.T. shall have the right, but shall not be
obligated, to prosecute at its sole control and sole expense all infringements
of PATENT RIGHTS other than PATENT RIGHTS HEPARIN in FIELD ALL BUT MACHINES,
PATENT RIGHTS HEPARINASE in FIELD MANUFACTURING, PATENT RIGHTS ENZYMES in FIELD
ENZYMES excluding FIELD RESEARCH REAGENTS, or PATENT RIGHTS MASSPEC in FIELD
ANTICOAGULANT, and M.I.T. shall keep any recovery or damages derived therefrom,
whether compensatory for past infringement or punitive. If required by law,
COMPANY hereby agrees that M.I.T. may include COMPANY as a party plaintiff in
any such suit, without expense to COMPANY. 
Prior to commencing any such action, M.I.T. shall consult with COMPANY
and shall consider the views of COMPANY regarding the advisability of the
proposed action.  Further, M.I.T. shall
not enter into any settlement, consent judgment, or other voluntary final
disposition of any infringement action under this Section without first
consulting with and considering the views of COMPANY. Lastly, in the event that
COMPANY approaches M.I.T. and requests that M.I.T. commence the prosecution of
an infringement of any of the PATENT RIGHTS other than the PATENT RIGHTS
HEPARIN in FIELD ALL BUT MACHINES, the PATENT RIGHTS HEPARINASE in FIELD
MANUFACTURING, the PATENT RIGHTS ENZYMES in FIELD ENZYMES excluding FIELD
RESEARCH REAGENTS, and the PATENT RIGHTS MASSPEC in FIELD ANTICOAGULANT, M.I.T.
agrees to give due consideration to the views of the COMPANY. Notwithstanding
the forgoing, any action taken under this Section shall be at the sole
discretion of M.I.T.

8.               Section 7.7, as
amended, shall be modified to read as follows:

 4
 

 

Right to
Sublicense.  So long as
COMPANY remains the exclusive licensee of the PATENT RIGHTS HEPARIN in FIELD
ALL BUT MACHINES, PATENT RIGHTS HEPARINASE in FIELD MANUFACTURING, PATENT
RIGHTS ENZYMES in FIELD ENZYMES excluding FIELD RESEARCH REAGENTS, or PATENT
RIGHTS MASSPEC in FIELD ANTICOAGULANT, COMPANY shall have the sole right to
sublicense to any alleged infringer for future use of PATENT RIGHTS HEPARIN in
FIELD ALL BUT MACHINES, PATENT RIGHTS HEPARINASE in FIELD MANUFACTURING, PATENT
RIGHTS ENZYMES in FIELD ENZYMES excluding FIELD RESEARCH REAGENTS, or PATENT
RIGHTS MASSPEC in FIELD ANTICOAGULANT, as the case may be, in accordance with
the terms and conditions of this Agreement relating to sublicenses.  Any upfront fees as part of such sublicense
shall be shared equally between COMPANY and M.I.T.; other revenues to COMPANY
pursuant to such sublicense shall be treated as set forth in Article 4.

9.   In consideration of the exclusive license
granted for PATENT RIGHTS MASSPEC in FIELD ANTICOAGULANT hereunder, COMPANY
shall make the payments set forth in paragraphs 10 through 14 of this Fifth
Amendment to M.I.T.

10.  COMPANY shall pay M.I.T. a license expansion
fee of [**] Dollars ($[**]), which shall be due upon the Effective Date of this
Fifth Amendment.

11.  If COMPANY, or any of its AFFILIATES,
SUBLICENSEES or CORPORATE PARTNERS, submits a MARKETING APPROVAL FILING for a
GENERIC ANTICOAGULANT PRODUCT other than an ENOXAPARIN PRODUCT in the TERRITORY
or submits an IND for an INNOVATIVE ANTICOAGULANT PRODUCT in the TERRITORY
which, in either case, includes any data generated through the practice of the
PATENT RIGHTS MASSPEC, then COMPANY shall pay M.I.T. [**] Dollars ($[**])
within thirty (30) days of the first such submission for each such
ANTICOAGULANT PRODUCT.

12. If
COMPANY, or any of its AFFILIATES, SUBLICENSEES or CORPORATE PARTNERS, is the
first party to sell a GENERIC ANTICOAGULANT PRODUCT other than an ENOXAPARIN
PRODUCT in the TERRITORY and any data generated through the practice of the
PATENT RIGHTS MASSSPEC is included in the MARKETING APPROVAL FILING for such
GENERIC ANTICOAGULANT PRODUCT, then COMPANY shall pay M.I.T.:

(a)            [**]
Dollars ($[**]) within thirty (30) days of the first sale of each such GENERIC
ANTICOAGULANT PRODUCT;

 5
 

 

(b)           [**]
Dollars ($[**]) upon the first anniversary of the first sale of each such
GENERIC ANTICOAGULANT PRODUCT;

(c)            [**]
Dollars ($[**]) upon the second anniversary of the first sale of each such
GENERIC ANTICOAGULANT PRODUCT; and

(d)           [**]
Dollars ($[**]) upon the third anniversary of the first sale of each such
GENERIC ANTICOAGULANT PRODUCT

provided,
however, that if an additional GENERIC ANTICOAGULANT PRODUCT has been marketed
or sold in the TERRITORY by a party other than COMPANY, or its AFFILIATES,
SUBLICENSEES or CORPORATE PARTNERS, at the time any payment referenced in the
foregoing clauses (b) through (d) is due, such payment for such GENERIC
ANTICOAGULANT PRODUCT shall be reduced by [**] percent ([**]%).

13. If
COMPANY, or any of its AFFILIATES, SUBLICENSEES or CORPORATE PARTNERS, is the
first party to sell an INNOVATIVE ANTICOAGULANT PRODUCT in the TERRITORY and
any data generated through the practice of the PATENT RIGHTS MASSPEC is
included in the MARKETING APPROVAL FILING for such INNOVATIVE ANTICOAGULANT
PRODUCT, then COMPANY shall pay M.I.T.:

(a)            [**]
Dollars ($[**]) within thirty (30) days of the first sale of each such
INNOVATIVE ANTICOAGULANT PRODUCT;

(b)           [**]
Dollars ($[**]) upon the first anniversary of the first sale of each such
INNOVATIVE ANTICOAGULANT PRODUCT;

(c)            [**]
Dollars ($[**]) upon the second anniversary of the first sale of each such
INNOVATIVE ANTICOAGULANT PRODUCT; and

(d)           [**]
Dollars ($[**]) upon the third anniversary of the first sale of each such
INNOVATIVE ANTICOAGULANT PRODUCT

provided,
however, that if a generic version of any such INNOVATIVE ANTICOAGULANT PRODUCT
has been marketed or sold in the TERRITORY by a party other than COMPANY, or
its AFFILIATES, SUBLICENSEES or CORPORATE PARTNERS, at the time any payment
referenced in the foregoing clauses (b) through (d) is due, such payment for
such INNOVATIVE ANTICOAGULANT PRODUCT shall be reduced by [**] percent ([**]%).

14. If
COMPANY, or any of its AFFILIATES, SUBLICENSEES or CORPORATE PARTNERS, is the
first party to sell an ENOXAPARIN PRODUCT in the TERRITORY and any data
generated through the practice of the PATENT RIGHTS MASS SPEC is included in
the MARKETING

 6
 

 

APPROVAL
FILING for such ENOXAPARIN PRODUCT, then COMPANY shall pay M.I.T.:

(a)            [**]
Dollars ($[**]) within thirty (30) days of the first sale of such ENOXAPARIN
PRODUCT;

(b)           [**]
Dollars ($[**]) upon the first anniversary of the first sale of such ENOXAPARIN
PRODUCT;

(c)            [**]
Dollars ($[**]) upon the second anniversary of the first sale of such ENOXAPARIN
PRODUCT; and

(d)           [**]
Dollars ($[**]) upon the third anniversary of the first sale of such ENOXAPARIN
PRODUCT;

provided,
however, that if an additional ENOXAPARIN PRODUCT has been marketed or sold in
the TERRITORY by a party other than COMPANY, or its AFFILIATES, SUBLICENCEES or
CORPORATE PARTNERS, at the time any payment referenced in the foregoing clauses
(b) through (d) is due, such payment for such ENOXAPARIN PRODUCT shall be
reduced by [**] percent ([**]%).

All other terms and
conditions of the License Agreement shall remain unchanged.

The
EFFECTIVE DATE of this Amendment is August 5, 2006.

Agreed to for:

 

	
    MASSACHUSETTS INSTITUTE OF

    TECHNOLOGY

  	
   

  	
  MOMENTA PHARMACEUTICALS, INC.

  
	
   

  	
   

  	
   

  
	
   By

  	
     /s/Lita
  L. Nelsen

  	
   

  	
   

  	
  By

  	
  /s/ Susan K. Whoriskey, Ph.D.

  	
   

  
	
   

  	
   

  	
   

  
	
   Name:

  	
  Lita L. Nelsen

  	
   

  	
   

  	
  Name:

  	
  Susan K. Whoriskey, Ph.D.

  	
   

  
	
   

  	
   

  	
   

  
	
   Title:

  	
  Director,
  Technology Licensing Office

  	
   

  	
   

  	
  Title:

  	
  Vice President, Licensing & 

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
  Business Development

  	
   

  
	
   Date :

  	
  August 3, 2006

  	
   

  	
   

  	
   

  	
   

  
	
   

  	
  Date :

  	
  August 3, 2006

  	
   

  
														

 

 7

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