X0306 4 2016-10-07 0 0000861838 IDERA PHARMACEUTICALS, INC. IDRA 0001087939 BAKER JULIAN 667 MADISON AVENUE, 21ST FLOOR NEW YORK NY 10065 1 0 0 0 0001580575 Baker Bros. Advisors (GP) LLC 667 MADISION AVENUE, 21ST FLOOR NEW YORK NY New York 1 0 0 0 0001263508 BAKER BROS. ADVISORS LP 667 MADISON AVENUE, 21ST FLOOR NEW YORK NY 10065 1 0 0 0 0001363364 Baker Brothers Life Sciences LP 667 MADISION AVENUE, 21ST FLOOR NEW YORK NY 10065 1 0 0 0 0001551138 14159, L.P. 667 MADISION AVENUE, 21ST FLOOR NEW YORK NY 10065 1 0 0 0 0001087940 BAKER FELIX 667 MADISON AVENUE, 21ST FLOOR NEW YORK NY 10065 1 0 0 0 0001551139 667, L.P. 667 MADISION AVENUE, 21ST FLOOR NEW YORK NY 10065 1 0 0 0 Common Stock 111010 I See footnote Common Stock 2016-10-07 4 P 0 321404 2.00 A 1003781 I See footnote Common Stock 2016-10-07 4 P 0 2928596 2.00 A 9309333 I See footnote As a result of Felix J. Baker's and Julian C. Baker's ownership interest in 14159 Capital (GP), LLC, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in 111,010 shares of common stock of Idera Pharmaceuticals, Inc. (the "Issuer") beneficially owned by 14159, L.P. ("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 75,905 shares issued pursuant to the Stock Incentive Plan in lieu of director retainer fees, of which the fund may be deemed to own a portion. On October 7, 2016, 667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences", and together with 667 and 14159 the "Funds") purchased 321,404 and 2,928,596 shares of the Common Stock, respectively of the Issuer, pursuant to an underwritten public offering. After giving effect to the transactions reported herein and as a result of Felix J. Baker's and Julian C. Baker's ownership interest in Baker Biotech Capital (GP), LLC, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in 1,003,781 shares of common stock of the Issuer beneficially owned 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. Includes beneficial ownership of 75,905 shares issued pursuant to the Stock Incentive Plan in lieu of director retainer fees,of which the fund may be deemed to own a portion. After giving effect to the transactions reported herein and as a result of Felix J. Baker's and Julian C. Baker's ownership interest in Baker Brothers Life Sciences Capital (GP), LLC, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest 9,309,333 shares of common stock of the Issuer beneficially owned 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. Includes beneficial ownership of 75,905 shares issued pursuant to the Stock Incentive Plan in lieu of director retainer fees, of which the fund may be deemed to own a portion. Baker Bros. Advisors LP (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. Remarks: Julian C. Baker and Dr. Kevin 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. /s/ Julian C. Baker 2016-10-11 By: Baker Bros. Advisors (GP) LLC Name: Scott L. Lessing Title: President /s/ Scott L. Lessing 2016-10-11 BAKER BROS. ADVISORS LP Name: Scott L. Lessing Title: President /s/ Scott L. Lessing 2016-10-11 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/ 2016-10-11 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 2016-10-11 /s/ Felix J. Baker 2016-10-11 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 2016-10-11