ACHN 2018 Proxy Statement

Except as otherwise indicated in the footnotes to this table, the address for each person is to the care of Achillion Pharmaceuticals, Inc., 300 George Street, New Haven, Connecticut 06511. Name and Address of Beneficial Owner Number of Shares Beneficially Owned Percentage of Shares Beneficially Owned 5% Stockholders RTW Investments, LP(1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250 West 55 th Street, 16 th Floor Suite A New York, NY 10019 13,546,902 9.82% BlackRock, Inc.(2) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 East 52 nd Street New York, NY 10022 11,572,015 8.39% Vanguard Group, Inc.(3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 Vanguard Blvd. Malvern, PA 19355 10,808,995 7.83% OrbiMed Advisors, LLC(4) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601 Lexington Avenue, 54 th Floor New York, NY 10022 8,170,973 5.92% Directors and Named Executive Officers Jason Fisherman, M.D.(5) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281,500 * Gary Frashier(6) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173,750 * Kurt Graves(7) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277,709 * Michael D. Kishbauch(8) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106,250 * David I. Scheer(9) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303,249 * Robert L. Van Nostrand(10) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240,000 * Frank Verwiel, M.D.(11) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80,000 * Nicole Vitullo(12) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3,664,972 2.65% Milind S. Deshpande, Ph.D(13) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1,871,513 1.34% Mary Kay Fenton(14) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 931,062 * Martha Manning(15) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99,687 * Joseph Truitt(16) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 926,812 * David Apelian(17) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . — * Joel Barrish(18) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2,500 * All current executive officers and directors as a group (12 individuals)(19) . . . . . . . 8,956,504 6.25% * Represents holdings of less than one percent of our outstanding stock. (1) Consists of 12,839,071 shares of common stock held by RTW Master Fund, Ltd. and shares of common stock held by one or more other funds (together the “Funds”), which are managed by RTW Investments, LP (the “Adviser”). The Adviser, in its capacity as the investment manager of the Funds, has the power to vote and the power to direct the disposition of all Shares held by the Funds. Accordingly, the Adviser may be deemed to beneficially own an aggregate of 13,546,902 Shares. Roderick Wong is the Managing Partner of the Adviser. This information is from a Schedule 13G/A filed on February 14, 2018. (2) Consists of 11,572,015 shares of common stock held by BlackRock, Inc., which has sole voting power with respect to 11,223,198 shares and sole dispositive power with respect to 11,572,015 shares. This information is from a Schedule 13G/A filed by BlackRock, Inc. on January 29, 2018. (3) Consists of 10,808,995 shares of common stock held by The Vanguard Group, Inc. (“The Vanguard Group”), which has sole dispositive power with respect to 10,681,249 shares and shared dispositive power with respect to 127,746 shares. Vanguard Fiduciary Trust Company, a wholly-owned subsidiary of The Vanguard Group, is the beneficial owner of 121,865 shares as a result of its serving as investment manager of collective trust accounts, and Vanguard Investments Australia, Ltd., a wholly-owned subsidiary of The Vanguard Group, is the beneficial owner of 11,361 shares as a result of its serving as investment manager of Australian investment offerings. This information is from a Schedule 13G/A filed by the Vanguard group on February 8, 2018. 7