X0306 4 2018-03-15 0 0000861838 IDERA PHARMACEUTICALS, INC. IDRA 0001263508 BAKER BROS. ADVISORS LP 860 WASHINGTON STREET 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001551138 14159, L.P. 860 WASHINGTON STREET, 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001551139 667, L.P. 860 WASHINGTON STREET, 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001580575 Baker Bros. Advisors (GP) LLC 860 WASHINGTON STREET 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001363364 Baker Brothers Life Sciences LP 860 WASHINGTON STREET 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001087940 BAKER FELIX 860 WASHINGTON STREET 3RD FLOOR NEW YORK NY 10014 1 0 1 0 0001087939 BAKER JULIAN 860 WASHINGTON STREET, 3RD FLOOR NEW YORK NY 10014 1 0 1 0 Common Stock 2018-03-15 4 M 0 2250846 0.47 A 4102796 I See footnotes Common Stock 2018-03-15 4 M 0 17626445 0.47 A 34193251 I See footnotes Common Stock 2018-03-15 4 M 0 439036 0.47 A 602867 I See footnotes Common Stock Warrant (right to buy) 0.47 2018-03-15 4 M 0 2250846 D 2013-05-07 2018-05-07 Common Stock 2250846 0 I See Footnotes Common Stock Warrant (right to buy) 0.47 2018-03-15 4 M 0 17626445 D 2013-05-07 2018-05-07 Common Stock 17626445 0 I See Footnotes Common Stock Warrant (right to buy) 0.47 2018-03-15 4 M 0 439036 D 2013-05-07 2018-05-07 Common Stock 439036 0 I See Footnotes On March 15, 2018, 667, L.P. ("667"), Baker Brothers Life Sciences, L.P. ("Life Sciences") and 14159, L.P. ("14159", and together with 667 and Life Sciences the "Funds") exercised a warrant to purchase 2,250,846, 17,626,445 and 439,036 shares of the common stock of Idera Pharmaceuticals, Inc. (the "Issuer") for $0.47 per share ("2018 Warrants"). After giving effect to the transactions reported herein, and as a result of their ownership interest in Baker Biotech Capital (GP), LLC, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the Issuer's shares of common stock reported in column 5 of Table I directly held by 667, a limited partnership of which the sole general partner is Baker Biotech Capital, L.P., a limited partnership of which the sole general partner is Baker Biotech Capital (GP), LLC, due to Baker Biotech Capital, L.P.'s right to receive an allocation of a portion of the profits from 667. After giving effect to the transactions reported herein, and as a result of their ownership interest in Baker Brothers Life Sciences Capital (GP), LLC, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the Issuer's shares of common stock reported in column 5 of Table I directly held by Life Sciences, a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital, L.P., a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital (GP), LLC, due to Baker Brothers Life Sciences Capital, L.P.'s right to receive an allocation of a portion of the profits from Life Sciences. After giving effect to the transactions reported herein, and as a result of their ownership interest in 14159 Capital (GP), LLC, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the Issuer's shares of common stock reported in column 5 of Table I directly held by 14159, a limited partnership of which the sole general partner is 14159 Capital, L.P., a limited partnership of which the sole general partner is 14159 Capital (GP), LLC, due to 14159 Capital, L.P.'s right to receive an allocation of a portion of the profits from 14159. Includes beneficial ownership of 128,726 shares issued pursuant to the Stock Incentive Plan to Julian C. Baker and Kelvin M. Neu, respectively, a principal and an employee of Baker Bros. Advisors LP (the "Adviser") in lieu of director retainer fees, of which the fund may be deemed to own a portion. The shares of Common Stock are fully vested. Julian C. Baker and Dr. Neu serve on the Issuer's Board of Directors (the "Board") as representatives of the Funds . Dr. Neu also serves on the Compensation Committee of the Board for which he receives additional director retainer fees. Pursuant to the policies of the Adviser, Julian C. Baker and Dr. Neu do not have any right to the pecuniary interest in the Issuer's securities issued in lieu of director retainer fees and the Funds are entitled to an indirect proportionate pecuniary interest in the securities issued in lieu of director fees. The Funds each own an indirect proportionate pecuniary interest in the shares of Common Stock. Solely as a result of their ownership interest in the general partners of the general partners of the Funds, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in the shares of Common Stock issued in lieu of director retainer fees (i.e., no direct pecuniary interest). The Adviser serves as the Investment Adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held by the Funds. Baker Bros. Advisors (GP) LLC (the "Adviser GP") is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are principals of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held by the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held by the Funds. Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose. Pursuant to Instruction 4(c)(iii), this response has been left blank. Remarks: Julian C. Baker and Dr. Kelvin M. Neu, respectively, a principal and an employee of Baker Bros. Advisors LP (the "Adviser") are directors of Idera Pharmaceuticals, Inc. ("the Issuer"). By virtue of their representation on the Board of Directors of the Issuer, for purposes of Section 16 of the Securities Exchange Act of 1934, as amended, the reporting persons are deemed directors by deputization of the Issuer. By: Baker Bros. Advisors LP, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 2018-03-15 Baker Bros. Advisors LP, Mgmt. Co. and Inv. Adviser to 14159, L.P., pursuant to authority granted by 14159 Capital, L.P., GP to 14159, L.P. Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 2018-03-15 Baker Bros. Advisors LP, Mgmt. Co. and Inv. Adviser to 667, L.P., pursuant to authority granted by Baker Biotech Capital, L.P., GP to 667, L.P. Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 2018-03-15 By: Baker Bros. Advisors (GP) LLC, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 2018-03-15 Baker Bros. Advisors LP, Mgmt. Co. and Inv. Adviser to BAKER BROTHERS LIFE SCIENCES, L.P., pursuant to authority granted by Baker Brothers Life Sciences Capital, L.P., GP to Baker Brothers Life Sciences, L.P., Name: Scott L. Lessing, Title: President /s/ 2018-03-15 /s/ Felix J. Baker 2018-03-15 /s/ Julian C. Baker 2018-03-15