Alnylam Pharmaceuticals, Inc. Sample Contracts

CITIGROUP PIPER JAFFRAY
Underwriting Agreement • May 10th, 2004 • Alnylam Pharmaceuticals Inc • Pharmaceutical preparations • New York
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ALNYLAM PHARMACEUTICALS, INC. 5,000,000 Shares of Common Stock Underwriting Agreement
Underwriting Agreement • January 15th, 2019 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • New York

Alnylam Pharmaceuticals, Inc., a Delaware corporation (the “Company”), proposes to issue and sell to the several underwriters listed in Schedule I hereto (the “Underwriters”), for whom Barclays Capital Inc. is acting as representative (the “Representative”), an aggregate of 5,000,000 shares of common stock, par value $0.01 per share, of the Company (the “Underwritten Shares”) and, at the option of the Underwriters, up to an additional 750,000 shares of common stock of the Company (the “Option Shares”). The Underwritten Shares and the Option Shares are herein referred to as the “Shares”. The shares of common stock of the Company to be outstanding after giving effect to the sale of the Shares are referred to herein as the “Stock”. To the extent there are no additional Underwriters listed in Schedule I hereto, all references herein to the Underwriters shall refer just to you.

EXHIBIT 1.1 4,700,000 SHARES ALNYLAM PHARMACEUTICALS, INC. Common Stock, Par Value $0.01 Per Share UNDERWRITING AGREEMENT December 12, 2006
Underwriting Agreement • December 13th, 2006 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • New York
EXHIBIT 10.5
Registration Rights Agreement • February 27th, 2004 • Alnylam Pharmaceuticals Inc • Massachusetts
LEASE
Lease • February 27th, 2004 • Alnylam Pharmaceuticals Inc • Massachusetts
AND
Stock Purchase Agreement • September 12th, 2005 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware
ALNYLAM PHARMACEUTICALS, INC. AND THE BANK OF NEW YORK MELLON, as Trustee INDENTURE Dated as of September 15, 2022 1.00% Convertible Senior Notes due 2027
Indenture • October 27th, 2022 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • New York

INDENTURE dated as of September 15, 2022 between ALNYLAM PHARMACEUTICALS, INC., a Delaware corporation, as issuer (the “Company,” as more fully set forth in Section 1.01) and THE BANK OF NEW YORK MELLON, a New York banking corporation, as trustee (the “Trustee,” as more fully set forth in Section 1.01).

AGREEMENT
License Agreement • May 21st, 2004 • Alnylam Pharmaceuticals Inc • Pharmaceutical preparations • California
AND
Collaboration Agreement • May 16th, 2005 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware
RECITALS
Loan and Security Agreement • April 6th, 2004 • Alnylam Pharmaceuticals Inc • Pharmaceutical preparations • California
DATE: September [ ], 2022 TO: Alnylam Pharmaceuticals, Inc. 675 West Kendall Street, Henri A. Termeer Square Cambridge, Massachusetts 02142 FROM: [Insert Dealer Name] SUBJECT: [Base][Additional] Call Option Transaction
Call Option Transaction • September 16th, 2022 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations

The purpose of this letter agreement (this “Confirmation”) is to confirm the terms and conditions of the call option transaction entered into between [Dealer] (“Dealer”) and Alnylam Pharmaceuticals, Inc. (“Counterparty”) as of the Trade Date specified below (the “Transaction”). This letter agreement constitutes a “Confirmation” as referred to in the ISDA Master Agreement specified below. This Confirmation shall replace any previous agreements and serve as the final documentation for the Transaction.

AND
Collaboration and License Agreement • November 9th, 2006 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • Massachusetts
FORM OF DIRECTOR INDEMNIFICATION AGREEMENT
Director Indemnification Agreement • August 4th, 2016 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware

This Indemnification Agreement (“Agreement”) is made as of by and between Alnylam Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and (“Indemnitee”).

ALNYLAM PHARMACEUTICALS, INC. and Trustee INDENTURE Dated as of _______________ SUBORDINATED DEBT SECURITIES
Indenture • July 21st, 2011 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations

WHEREAS, the Issuer may from time to time duly authorize the issue of its unsecured subordinated debentures, notes or other evidences of indebtedness to be issued in one or more series (the “Securities”) up to such principal amount or amounts as may from time to time be authorized in accordance with the terms of this Indenture;

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LEASE by and between BMR-675 WEST KENDALL STREET LLC, a Delaware limited liability company and ALNYLAM PHARMACEUTICALS, INC., a Delaware corporation
Lease • August 7th, 2015 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations

IN WITNESS WHEREOF, Tenant has executed this Acknowledgment of Term Commencement Date and Term Expiration Date as of the date first written above.

BY AND BETWEEN
Research Collaboration and License Agreement • March 2nd, 2009 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • Massachusetts
ALNYLAM PHARMACEUTICALS, INC LICENCE AGREEMENT
Licence Agreement • May 21st, 2004 • Alnylam Pharmaceuticals Inc • Pharmaceutical preparations • London
LEASE RREEF AMERICA REIT II CORP. PPP, Landlord, and ALNYLAM PHARMACEUTICALS, INC., Tenant Riverfront Office Park Cambridge, Massachusetts
Lease • August 7th, 2015 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations

By this Lease Landlord leases to Tenant and Tenant leases from Landlord the Premises in the Building as set forth and described on the Reference Pages. The Premises are depicted on the floor plan attached hereto as Exhibit A, and the Building is depicted on the site plan attached hereto as Exhibit A-1. The Building is located on the Lot legally described on Exhibit A-2. The Reference Pages, including all terms defined thereon, are incorporated as part of this Lease.

CREDIT AGREEMENT Dated as of April 29, 2016 Among ALNYLAM U.S., INC., as the Borrower, ALNYLAM PHARMACEUTICALS, INC., as Parent and Parent Guarantor, and WELLS FARGO BANK, NATIONAL ASSOCIATION, as the Lender
Credit Agreement • August 4th, 2016 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • New York

This CREDIT AGREEMENT is entered into as of April 29, 2016, among ALNYLAM PHARMACEUTICALS, INC., a Delaware corporation (the “Parent” or the “Parent Guarantor”), ALNYLAM U.S., INC., a Delaware corporation and a wholly-owned Subsidiary of Parent (the “Borrower” and, together with the Parent Guarantor, collectively the “Loan Parties” and, each individually, a “Loan Party”), and WELLS FARGO BANK, NATIONAL ASSOCIATION, as the Lender.

BETWEEN
Rights Agreement • July 14th, 2005 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware
SETTLEMENT AGREEMENT AND GENERAL RELEASE
Settlement Agreement • February 19th, 2013 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware

This Settlement Agreement and General Release (the “Agreement”) is entered into this 12th day of November 2012 (the “Effective Date”) by and among Tekmira Pharmaceuticals Corporation, a British Columbia corporation with a principal place of business at 100-8900 Glenlyon Parkway, Burnaby, British Columbia, Canada V5J 5J8 (“TPC”), Protiva Biotherapeutics Inc., a wholly-owned subsidiary of TPC and a British Columbia corporation with a principal place of business at 100-8900 Glenlyon Parkway, Burnaby, British Columbia, Canada V5J 5J8 (“Protiva”), Alnylam Pharmaceuticals, Inc., a Delaware corporation with a principal place of business at 300 Third Street, Cambridge, MA 02142 (“Alnylam”), and AlCana Technologies, Inc., a British Columbia corporation with a principal place of business at 2714 West 31st Avenue, Vancouver, British Columbia, Canada V6L 2A1 (“AlCana”). Each of TPC, Protiva, Alnylam, and AlCana shall be considered a “Party,” and collectively they shall be considered the “Parties.”

INVESTOR AGREEMENT By and Between
Investor Agreement • August 6th, 2019 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware

THIS INVESTOR AGREEMENT (this “Agreement”) is made as of April 8, 2019, by and between Regeneron Pharmaceuticals, Inc. (the “Investor”), a New York corporation with its principal place of business at 777 Old Saw Mill River Road, Tarrytown, New York 10591, and Alnylam Pharmaceuticals, Inc. (the “Company”), a Delaware corporation with its principal place of business at 300 Third Street, Cambridge, Massachusetts 02142.

AND
Investor Rights Agreement • September 12th, 2005 • Alnylam Pharmaceuticals, Inc. • Pharmaceutical preparations • Delaware
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