X0202 4 2006-04-25 0 0000861838 IDERA PHARMACEUTICALS, INC. IDP 0001307729 Baker Brothers Life Sciences Capital (GP), LLC 667 MADISON AVENUE 17TH FLOOR NEW YORK NY 10021 0 0 1 0 0001244386 Baker Biotech Capital II (GP), LLC 667 MADISON AVE 17TH FLOOR NEW YORK NY 10021 0 0 1 0 0001307726 Baker Biotech Capital II (Z) (GP), LLC 667 MADISON AVENUE 17TH FLOOR NEW YORK NY 10021 0 0 1 0 0001307728 Baker Biotech Capital III (Z) (GP), LLC 667 MADISON AVENUE 17TH FLOOR NEW YORK NY 10021 0 0 1 0 0001087939 BAKER JULIAN 667 MADISON AVENUE NEW YORK NY 10021 0 0 1 0 0001087940 BAKER FELIX 667 MADISON AVENUE NEW YORK NY 10021 0 0 1 0 Common Stock 2006-04-25 4 J 0 5094924 0 D 0 I See Footnote Common Stock 2006-04-25 4 J 0 674120 0 D 0 I See Footnote Common Stock 2006-04-25 4 J 0 811124 0 D 0 I See Footnote Common Stock 2006-04-25 4 J 0 6580168 0 A 11175900 I See Footnote Warrant .65 2006-04-25 4 J 0 3821193 0 D 2006-09-26 2011-09-26 Common Stock 3821193 0 I See footnote Warrant .65 2006-04-25 4 J 0 505590 0 D 2006-09-26 2011-09-26 Common Stock 505590 0 I See footnote Warrant .65 2006-04-25 4 J 0 608343 0 D 2006-09-26 2011-09-26 Common Stock 608343 0 I See footnote Warrant .65 2006-04-25 4 J 0 4935126 0 A 2006-09-26 2011-09-26 Common Stock 4935126 8381925 I See footnote In addition to Baker Brothers Life Sciences Capital (GP), LLC (formerly known as Baker Biotech Capital III (GP), LLC), this form is being filed jointly by Julian C. Baker, Felix J. Baker, Baker Biotech Capital II (GP), LLC, Baker Biotech Capital II (Z)(GP), LLC, and Baker Biotech Capital III (Z)(GP), each of whom has the same business address as Baker Brothers Life Sciences Capital (GP), LLC. Each of the reporting persons disclaims beneficial ownership of the securities reported hereon except to the extent of his or its pecuniary interest, if any, therein. On April 25, 2006, Baker Biotech Fund II, L.P., Baker Biotech Fund II (Z), L.P. and Baker Biotech Fund III (Z), L.P. were merged with and into Baker Biotech Fund III, L.P. which changed its name simultaneously therewith to Baker Brothers Life Sciences, L.P. Simultaneously therewith, Baker Biotech Capital II, L.P., Baker Biotech Capital II (Z), L.P., and Baker Biotech Capital III (Z), L.P., the general partners of Baker Biotech Fund II, L.P., Baker Biotech Fund II (Z), L.P. and Baker Biotech Fund III (Z), L.P., respectively, were merged with and into Baker Biotech Capital III, L.P., the general partner of Baker Biotech Fund III, L.P., and Baker Biotech Capital III, L.P. changed its name simultaneously therewith to Baker Brothers Life Sciences Capital, L.P. (Continued in footnote 3.) In addition, simultaneously therewith, Baker Biotech Capital II (GP), LLC, Baker Biotech Capital II (Z)(GP), LLC, and Baker Biotech Capital III (Z)(GP), LLC, the general partners of Baker Biotech Capital II, L.P., Baker Biotech Capital II (Z), L.P., and Baker Biotech Capital III (Z), L.P., respectively, were merged with and into Baker Biotech Capital III (GP), LLC, the general partner of Baker Biotech Capital III, L.P. and Baker Biotech Capital III (GP), LLC changed its name simultaneously therewith to Baker Brothers Life Sciences Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the controlling members of Baker Biotech Capital II (GP), LLC, Baker Biotech Capital II (Z)(GP), LLC, Baker Biotech Capital III (Z)(GP), LLC and Baker Brothers Life Sciences Capital (GP), LLC, and may have a pecuniary interest in shares held by them. Such pecuniary interest, if any, was unchanged as a result of the mergers referred to herein. (Continued in footnote 4.) Julian C. Baker and Felix J. Baker disclaim beneficial ownership of the shares reported herein except to the extent of their pecuniary interest, if any, therein. Represents securities owned directly by Baker Biotech Fund II, L.P., which is no longer subject to Section 16 of the Securities Exchange Act of 1934. Represents securities owned directly by Baker Biotech Fund II (Z), L.P., which is no longer subject to Section 16 of the Securities Exchange Act of 1934. Represents securities owned directly by Baker Biotech Fund III(Z), L.P., which is no longer subject to Section 16 of the Securities Exchange Act of 1934. Represents securities owned directly by Baker Brothers Life Sciences, L.P. (formerly known as Baker Biotech Fund III, L.P.). /s/ Julian C. Baker, as Managing Member of Baker Biotech Capital II (GP), LLC 2006-08-17 /s/ Julian C. Baker, as Managing Member of Baker Biotech Capital II (Z) (GP), LLC 2006-08-17 /s/ Julian C. Baker, as Managing Member of Baker Biotech Capital III (GP), LLC 2006-08-17 /s/ Julian C. Baker, as Managing Member of Baker Biotech Capital III (Z) (GP), LLC 2006-08-17 s/ Julian C. Baker, as Managing Member of Baker Brothers Life Sciences Capital (GP), LLC 2006-08-17 /s/ Julian C. Baker 2006-08-17 /s/ Felix J. Baker 2006-08-17