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FIRST AMENDMENT TO AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT

Investors Rights Agreement

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SGX PHARMACEUTICALS, INC. | Oxford Finance Corporation

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Title: FIRST AMENDMENT TO AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT
Governing Law: California     Date: 3/31/2006
Industry: BIOTRX    

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EXHIBIT 4.9

First Amendment to
Amended and Restated Investor Rights Agreement

     This First Amendment to the Amended and Restated Investor Rights Agreement (the “Amendment”) is made effective as of October 31, 2005, and is entered into by and among SGX Pharmaceuticals, Inc., a Delaware corporation, previously known as Structural GenomiX, Inc. (the “Company”), certain holders of the Company’s Series A Preferred Stock (“Series A Preferred”), and certain holders of the Company’s Series B Preferred Stock (“Series B Preferred”) (which parties are hereinafter collectively referred to as the “Original Parties”).

     Whereas, the Original Parties have previously entered into that certain Amended and Restated Investor Rights Agreement, dated April 21, 2005 (the “Investor Rights Agreement”);

     Whereas, the Company, Silicon Valley Bank (“SVB”) and Oxford Finance Corporation (“Oxford”) have entered into a Loan and Security Agreement dated September 16, 2005 (the “Loan Agreement”); and

     Whereas, pursuant to the Loan Agreement, the Company agreed to issue certain warrants to SVB and Oxford and to solicit the requisite consent of the parties to the Investor Rights Agreement to add SVB and Oxford as parties to the Investor Rights Agreement to provide such parties with those certain incidental, or “Piggyback,” registration rights pursuant to and as set forth therein.

     Now, therefore, in consideration of the foregoing premises and the mutual covenants and conditions herein, the parties hereto hereby agree that:

1.

 

Capitalized terms not defined herein shall have the meaning ascribed to them in the Investor Rights Agreement.

 

 

 

2.

 

SVB and Oxford shall become parties to the Investor Rights Agreement and the definition of “Holder” in Section 1 of the Investor Rights Agreement shall include SVB and Oxford; provided, however, that neither SVB nor Oxford (nor any permitted transferee or assignee of SVB or Oxford) shall be deemed a Holder for purposes of Section 2.2 or 2.4 of the Investor Rights Agreement.

 

 

 

3.

 

The definition of “Registrable Securities” in Section 1.1 of the Investor Rights Agreement shall be replaced in its entirety with the following:

     ““Registrable Securities” means the (a) Common Stock of the Company issued or issuable upon conversion of the Shares; (b) Bridge Converted Common Stock; (c) Common Stock of the Company issued or issuable upon conversion of the Conversion Securities (as those securities are defined in the Convertible Promissory Note issued by the Company to mHoldings Trust (“mHoldings”) dated December 21, 2001 (the “Millennium Note”) (or in the event the Conversion Securities (as those securities are defined in the Millennium Note) consist of the Company’s Common Stock, the Conversion Securities (as those securities are defined in the Millennium Note)); (d) Common Stock of the Company issued or issuable upon conversion of the Warrant Securities (or in the event the Warrant

1.


 

Securities consist of the Company’s Common Stock, the Warrant Securities), provided, however, that any such shares of Common Stock or Warrant Securities issued upon exercise of the Lender Warrants (or upon conversion of the Warrant Securities issued upon exercise thereof) shall not be deemed Registrable Securities for purposes of Section 2.2 or 2.4 hereof; and (e) Common Stock of the Company issued as (or issuable upon the conversion or exercise of any warrant, right or other security which is issued as) a dividend or other distribution with respect to, or in exchange for or in replacement of, such above-described securities. Notwithstanding the foregoing, Registrable Securities shall not include any securities sold by a person to the public either pursuant to a registration statement or Rule 144 or sold in a private transaction in which the transferor’s rights under Section 2 of this Agreement are not assigned.”

4.

 

The definition of “Shares” in Section 1.1 of the Investor Rights Agreement shall be replaced in its entirety with the following:

     ““Shares” shall mean (a) the Series A Stock and Series B Stock now held or hereafter acquired by the Investors listed on Exhibit A hereto and their permitted assigns; (b) the Pre-Series B Conversion Preferred Stock held by the Investors listed on Exhibit A hereto and their permitted assigns; (c) the Company securities issuable upon exercise of the Warrant and the Lenders Warrants (the “Warrant Securities”); and (d) the Conversion Securities (as those securities are defined in the Millennium Note) issued pursuant to the Millennium Note to mHoldings (or its permitted assigns).”

5.

 

The following definition shall be added to Section 1.1 of the Investor Rights Agreement immediately following the definition of “Initial Offering”:

     ““Lender Warrants” shall mean those certain warrants issued to Silicon Valley Bank and Oxford Finance Corporation (or their respective permitted assigns) pursuant to that certain Loan and Security Agreement dated as of September 16, 2005 by and among the Company, Silicon Valley Bank and Oxford Finance Corporation.”

6.

 

By executing this Amendment, each of SVB and Oxford agree to be bound by the provisions of the Investor Rights Agreement, as amended by this Amendment (and as may be subsequently amended from time to time), including without limitation the provisions of Section 2.13 thereof.

 

 

 

7.

 

This Amendment may be executed in any number of counterparts, each of which shall be an original, but all of which together shall constitute one instrument. Except as specifically amended by this Amendment, the terms and conditions of the Investor Rights Agreement shall remain unchanged and in full force and effect. This Amendment shall be governed by and construed in accordance with the laws of the State of California as applied to contracts among California residents entered into and performed entirely within California.

2.


 

     In Witness Whereof, the parties hereto have executed this First Amendment to the Amended and Restated Investor Rights Agreement effective as of the day and year first set forth above.

Company:

 

 

 

 

 

 

 

SGX Pharmaceuticals, Inc.

 

 

 

 

 

 

 

 

 

By:

 

/s/ Michael Grey

 

 

 

 

 

 

 

 

 

Name:

 

Michael Grey

 

 

 

 

Title:

 

President and Chief Executive Officer

 

 

[Signature Page to First Amendment to Amended and Restated Investor Rights Agreement]

 


 

     In Witness Whereof, the parties hereto have executed this First Amendment to the Amended and Restated Investor Rights Agreement effective as of the day and year first set forth above.

 

 

 

 

 

 

 

Investors/Holders:

 

 

 

 

 

 

 

 

 

ALEXANDRIA REAL ESTATE EQUITIES, L.P.,

 

 

a Delaware limited partnership

 

 

 

 

 

 

 

 

 

By:

 

ARE-QRS CORP.,

 

 

 

 

a Maryland corporation, general partner

 

 

 

 

 

 

 

 

 

 

 

By:

 

/s/ Etsuko Mason

 

 

 

 

 

 

 

Etsuko Mason

 

 

 

 

 

 

Vice President, Treasurer and

 

 

 

 

 

 

Assistant Secretary

 

 

[Signature Page to First Amendment to Amended and Restated Investor Rights Agreement]

 


 

     In Witness Whereof, the parties hereto have executed this First Amendment to the Amended and Restated Investor Rights Agreement effective as of the day and year first set forth above.

 

 

 

 

 

Investors /

 

Holders:

 

 

 

 

 

 

 

Name :

 

*

 

 

 

 

 

 

 

 

 

 

 

 

By:

 

/s/ Jeanne Larkin Henry

 

 

 

 

 

 

 

 

 

 

 

 

Print Name:

 

Jeanne Larkin Henry

 

 

 

 

 

 

 

 

 

 

 

 

Title:

 

Vice-President

 

 

 

 

 

 

 

 

 

 

 

 

ATLAS VENTURE FUND III, L.P.

 

 

ATLAS VENTURE ENTREPRENEURS’ FUND III, L.P.

 

 

By:

 

Atlas Venture Associates III, L.P.

 

 

 

 

its general partner

 

 

By:

 

Atlas Venture Associates III, L.P.

 

 

 

 

its general partner

 

 

 

 

 

 

 

ATLAS VENTURE FUND IV, L.P.

 

 

ATLAS VENTURE PARALLEL FUND IV — A, C.V.

 

 

ATLAS VENTURE PARALLEL FUND IV — B, C.V.

 

 

ATLAS VENTURE ENTREPRENEURS’ FUND IV, L.P.

 

 

By:

 

Atlas Venture Associates IV, L.P.

 

 

 

 

its general partner

 

 

By:

 

Atlas Venture Associates IV, Inc.

 

 

 

 

its general partner

 

 


[Signature Page to First Amendment to Amended and Restated Investor Rights Agreement]

 


 

     In Witness Whereof, the parties hereto have executed this First Amendment to the Amended and Restated Investor Rights Agreement effective as of the day and year first set forth above.

 

 

 

 

 

Investors/Holders:

 

 

 

 

 

 

 

Name :

 

Bavp, L.P.

 

 

 

 

 

 

 

 

By:

 

/s/ Louis C. Bock

 

 

 

 

 

 

 

 

 

 

 

 

Print Name:

 

Louis C. Bock

 

 

 

 

 

 

 

Title:

 

Managing Director

 

 

[Signature Page to First Amendment to Amended and Restated Investor Rights Agreement]

 


 

     In Witness Whereof, the parties hereto have executed this First Amendment to the Amended and Restated Investor Rights Agreement effective as of the day and year first set forth above.

 

 

 

 

 

Investors/Holders:

 

 

 

 

 

 

 

Name :

 

Caduceus Private Investments, LP

 

 

 

 

 

 

 

 

By:

 

/s/ Eric A. Bittelman

 

 

 

 

 

 

 

 

 

 

 

 

Print Name:

 

Eric A. Bittelman

 

 

 

 

 

 

 

Title:

 

CFO, OrbiMed Capital LLC, General Partner

 

 

[Signature Page to First Amendment to Amended and Restated Investor Rights Agreement]

 


 

     In Witness Whereof, the parties hereto have executed this First Amendment to the Amended and Restated Investor Rights Agreement effective as of the day and year first set forth above.

 

 

 

 

 

Investors/Holders:

 

 

 

 

 

 

 

Coleman Swenson Hoffman Booth IV L.P.

 

 

By:

 

Its General Partner,

 

 

 

 

CSHB Ventures IV L.P.

 

 

 

 

 

 

 

By:

 

/s/ Larry H. Coleman

 

Its: General Partner

 

 

 

 

 

 

 

Print Name:

 

Larry H. Coleman

 

 

 

 

 

 

 

Title:

 

General Partner

 

 

[Signature Page to First Amendment to Amended and Restated Investor Rights Agreement]

 


 

     In Witness Whereof, the parties hereto have executed this First Amendment to the Amended and Restated Investor Rights Agreement effective as of the day and year first set forth above.

 

 

 

 

 

Investors/Holders:

 

 

 

 

 

 

 

Name :

 

Walter T. Dec

 

 

 

 

 

 

 

 

By:

 

/s/ Walter T. Dec

 

 

 

 

 

 

 

 

 

 

 

 

Print Name:

 

Walter T. Dec

 

 

 

 

 

 

 

Title:

 

Sir

 

 

[Signature Page to First Amendment to Amended and Restated Investor Rights Agreement]

 


 

     In Witness Whereof, the parties hereto have executed this First Amendment to the Amended and Restated Investor Rights Agreement effective as of the day and year first set forth above.

 

 

 

 

 

Investors/Holders:

 

 

 

 

 

 

 

Name :

 

/s/ Ken Dill Joland Schreurs

 

 

 

 

 

 

 

 

By:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Print Name:

 

Ken Dill Joland Schreurs