AKAO 2017 Annual Report

143 EXHIBIT INDEX Incorporated by Reference from Provided Herewith Exhibit Number Description of Document Registrant's Form File No. Date Filed with the SEC Exhibit Number 1.1 Common Stock Sales Agreement, dated February 27, 2018, by and between the Company and Cowen and Company, LLC. X 3.1 Amended and Restated Certificate of Incorporation of Achaogen, Inc. 8-K 001-36323 3/17/2014 3.1 3.2 Amended and Restated Bylaws of Achaogen, Inc. 8-K 001-36323 3/17/2014 3.2 4.1 Form of Common Stock Certificate. S-1/A 333-193559 2/25/2014 4.1 4.2 Warrant issued to Oxford Finance LLC on November 1, 2011. S-1 333-193559 1/24/2014 4.4 4.3 Warrant issued to Oxford Finance LLC on April 30, 2012 (Term A Loan (2)). S-1 333-193559 1/24/2014 4.6 4.4 Warrant issued to Oxford Finance LLC on April 30, 2012 (Term B Loan). S-1 333-193559 1/24/2014 4.7 4.5 Form of Warrant, issued pursuant to the Securities Purchase Agreement, dated June 1, 2016, by and among Achaogen, Inc. and the purchasers named therein S-3 333-212253 6/24/2016 4.3 5.1 Opinion of Latham & Watkins LLP. X 10.1(A)† License Agreement, dated January 25, 2006, by and between the registrant and Ionis Pharmaceuticals, Inc. S-1/A 333-193559 2/27/2014 10.5(A) 10.1(B)† Letter Agreement, dated January 25, 2006, by and between the registrant and Ionis Pharmaceuticals, Inc. S-1 333-193559 1/24/2014 10.5(B) 10.2 Loan and Security Agreement, dated November 1, 2011, by and among the registrant, Oxford Finance LLC and Silicon Valley Bank. S-1 333-193559 1/24/2014 10.8 10.3 Third Amended and Restated Investors’ Rights Agreement, dated March 6, 2013, by and among the registrant and certain stockholders. S-1 333-193559 1/24/2014 10.15 10.4(A) Amended and Restated Lease Agreement, dated December 29, 2010, by and between the registrant and ARE- San Francisco No. 17, LLC. S-1 333-193559 1/24/2014 10.9(A) 10.4(B) Letter Agreement, dated January 4, 2011, by and between the registrant and ARE- San Francisco No. 17, LLC. S-1 333-193559 1/24/2014 10.9(B) 10.4(C) Letter Agreement, dated June 15, 2011, by and between the registrant and ARE- San Francisco No. 17, LLC. S-1 333-193559 1/24/2014 10.9(C)