Document:

Registration Rights Agreement

 Exhibit 10.3 

REGISTRATION RIGHTS AGREEMENT 

This Registration Rights Agreement (this “Agreement”) is dated as of August 18, 2010 by and among
Achillion Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and the several purchasers identified in the attached Exhibit A (each a “Purchaser” and collectively, the
“Purchasers”). 
 WHEREAS, subject to the terms and conditions set forth in this Agreement and
pursuant to that certain Securities Purchase Agreement, dated as of the date hereof, among the Company and the Purchasers (the “Purchase Agreement”), the Company has agreed to provide certain registration rights under the Securities
Act of 1933, as amended, and the rules and regulations thereunder, or any similar successor statute (collectively, the “Securities Act”), and applicable state securities laws. 

NOW, THEREFORE, IN CONSIDERATION of the mutual covenants contained in this Agreement, and for other good and valuable
consideration, the receipt and adequacy of which are hereby acknowledged, the Company and the Purchasers agree as follows: 

1. Definitions. As used in this Agreement, the following terms shall have the following meanings: 

“Acceleration Request” means within three business days of the date that the Company is notified (orally
or in writing, whichever is earlier) by the Commission that a Registration Statement will not be reviewed or will not be subject to further review, a request for acceleration of effectiveness in accordance with Rule 461 promulgated under the
Exchange Act is filed with the Commission, which request shall request an effective date that is within three business days of the date of such request. 

“Advice” shall have the meaning set forth in Section 8(d). 

“Commission” means the Securities and Exchange Commission and its staff. 

“DGCL” means the General Corporation Law of the State of Delaware. 

“Effectiveness Date” means, with respect to the Mandatory Registration Statement,
(i) if there is no Commission review of the Mandatory Registration Statement, the
90th calendar day following the Closing Date or upon
effectiveness of an Acceleration Request or (ii) if there is Commission review of the Mandatory Registration Statement, the earlier of the
120th calendar day following the Closing Date or upon
effectiveness of an Acceleration Request. With respect to any other Registration Statements (i) if there is no Commission review of such Registration Statement, the
90th calendar day following the date on which the Company
first knows that such additional Registration Statement is required hereunder or (ii) if there is Commission review of such Registration Statement, the earlier of the
120th calendar day following the date on which the Company
first knows, that such Registration Statement is required hereunder or upon effectiveness of an Acceleration Request. 

“Effectiveness Period” shall have the meaning set forth in Section 2(b). 

 “Event” shall have the meaning set forth in
Section 2(d). 
 “Event Date” shall have the meaning set forth in Section 2(d).

 “Exchange Act” means the Securities Exchange Act of 1934, as amended. 

“Filing Date” means, with respect to the Mandatory Registration Statement, the 30
th calendar day following the Closing Date (as defined in
the Purchase Agreement), and, with respect to any other Registration Statements, the
30th day following the date on which the Company first
knows that such Registration Statement is required hereunder. 
 “Holder” or
“Holders” means the holder or holders, as the case may be, from time to time of Registrable Securities. 

“Indemnified Party” shall have the meaning set forth in Section 5(c). 

“Indemnifying Party” shall have the meaning set forth in Section 5(c). 

“Legal Counsel” shall have the meaning set forth in Section 2(e). 

“Losses” shall have the meaning set forth in Section 5(a). 

“Mandatory Registration Statement” shall have the meaning set forth in Section 2(a). 

“Plan of Distribution” shall have the meaning set forth in Section 2(b). 

“Proceeding” means an action, claim, suit, investigation or proceeding (including, without limitation,
an investigation or partial proceeding, such as a deposition), whether commenced or threatened. 

“Prospectus” means the prospectus included in a Registration Statement (including, without limitation, a
prospectus that includes any information previously omitted from a prospectus filed as part of an effective registration statement in reliance upon Rule 430A promulgated under the Securities Act), as amended or supplemented by any prospectus
supplement, with respect to the terms of the offering of any portion of the Registrable Securities covered by a Registration Statement, and all other amendments and supplements to the Prospectus, including post-effective amendments, and all material
incorporated by reference or deemed to be incorporated by reference in such Prospectus. 
 “Registrable
Securities” means (i) all of the Shares (as defined in the Purchase Agreement), (ii) all of the Common Warrant Shares (as defined in the Purchase Agreement), and (iii) any securities issued or issuable upon any stock split,
dividend or other distribution, recapitalization or similar event with respect to any of the foregoing referenced in clauses (i) and (ii); provided, however, that the term “Registrable Securities” shall not include any Shares or
Common Warrant Shares that are actually sold pursuant to a registration statement that has been declared effective under the Securities Act by the Commission. 
  

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 “Registration Statement” means the Mandatory Registration
Statement, any additional registration statements which may be required pursuant to Section 2(c) and any additional registration statements contemplated by Section 3(b), including (in each case) the Prospectus, amendments and supplements
to such registration statement or Prospectus, including pre- and post-effective amendments, all exhibits thereto, and all material incorporated by reference or deemed to be incorporated by reference in such registration statement. 

“Rule 415” means Rule 415 promulgated by the Commission pursuant to the Securities Act, as such Rule may
be amended from time to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same purpose and effect as such Rule. 

“Rule 424” means Rule 424 promulgated by the Commission pursuant to the Securities Act, as such Rule may
be amended from time to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same purpose and effect as such Rule. 

“Rule 461” means Rule 461 promulgated by the Commission pursuant to the Securities Act, as such Rule may
be amended from time to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same purpose and effect as such Rule. 

“Securities” shall have the meaning set forth in the Purchase Agreement. 

“Selling Shareholder Questionnaire” shall have the meaning set forth in Section 3(a). 

“Trading Day” shall have the meaning set forth in the Purchase Agreement. 

“Transaction Documents” shall have the meaning set forth in the Purchase Agreement. 

2. Registration Statements. 

(a) On or prior to the Filing Date, the Company shall prepare and file with the Commission a Mandatory Registration
Statement covering the resale of all Registrable Securities on the Filing Date for an offering to be made on a continuous basis pursuant to Rule 415 (the “Mandatory Registration Statement”). 

(b) The Mandatory Registration Statement shall be on Form S-3 (except if the Company is not then eligible to register for
resale the applicable Registrable Securities on Form S-3, in which case such registration shall be on another appropriate form in accordance herewith) and shall contain (unless otherwise directed by the Holders) substantially the “Plan of
Distribution” attached hereto as Annex A (the “Plan of Distribution”) . Subject to the terms of this Agreement, the Company shall use its best efforts to cause a Registration Statement to be declared effective under the
Securities Act as promptly as possible after the filing thereof, but in any event prior to the Effectiveness Date, and shall use its best efforts to keep such Registration Statement continuously effective under the Securities Act until the earlier
of (i) the date all of the Registrable Securities covered by such Registration Statement have been sold and (ii) the later of (A) the second anniversary of the Effectiveness Date or (B) the date upon which the Registrable
Securities may be sold without volume or manner-of-sale restrictions under Rule 144 as determined by the counsel to the Company pursuant to a written opinion letter to such effect, addressed and acceptable to the Company’s transfer agent and
the affected Holders (the 
  

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“Effectiveness Period”). The Company shall immediately notify the Holders of the effectiveness of the Mandatory Registration Statement on the same Trading Day that the Company
telephonically confirms effectiveness with the Commission. The Company shall file a final prospectus under Rule 424. 

(c) If for any reason the Commission does not permit all of the applicable Registrable Securities to be included in the
Mandatory Registration Statement, or for any other reason any outstanding Registrable Securities are not then covered by an effective Registration Statement(s), then the Company shall prepare and file an additional Registration Statement covering
the resale of all Registrable Securities not already covered by an existing and effective Registration Statement for an offering to be made on a continuous basis pursuant to Rule 415, on Form S-3 (or on such other form appropriate for such purpose).
Each such Registration Statement shall contain (except if otherwise required pursuant to written comments received from the Commission upon a review of such Registration Statement) the Plan of Distribution. The Company shall cause each such
Registration Statement to be declared effective under the Securities Act as soon as possible, but in any event, by its Effectiveness Date, and shall use its best efforts to keep such Registration Statement continuously effective under the Securities
Act during the entire Effectiveness Period. 
 (d) If: (i) a Registration Statement is not filed on or
prior to its Filing Date (if the Company files a Registration Statement without affording the Holders a reasonable opportunity to review and comment on the same as required by Section 3(a), the Company shall not be deemed to have satisfied this
clause (i)), or (ii) the Company fails to file with the Commission a request for acceleration in accordance with Rule 461 promulgated under the Securities Act, within five Trading Days of the date that the Company is notified (orally or in
writing, whichever is earlier) by the Commission that a Registration Statement will not be “reviewed,” or not subject to further review and comment, or (iii) a Registration Statement filed or required to be filed hereunder is not
declared effective by the Commission by its Effectiveness Date, or (iv) after the Effectiveness Date, a Registration Statement ceases to remain continuously effective as to all Registrable Securities for which it is required to be effective due
to the good faith determination of the board of directors of the Company that the existence of a pending corporate development with respect to the Company that the Company reasonably believes is material makes it not in the best interest of the
Company to allow continued availability of a Registration Statement or Prospectus, or the Holders are not permitted to utilize the Prospectus therein to resell such Registrable Securities for either: (A) more than 15 consecutive Trading Days or
(B) more than an aggregate of 45 Trading Days during any 12-month period (which need not be consecutive Trading Days), or (v) after the Effectiveness Date, a Registration Statement ceases for any reason to remain continuously effective as
to all Registrable Securities for which it is required to be effective, or the Holders are not permitted to utilize the Prospectus therein to resell such Registrable Securities for either: (A) more than 15 consecutive Trading Days or
(B) more than an aggregate of 45 Trading Days during any 12-month period (which need not be consecutive Trading Days) or (vi) any other event, condition or occurrence that is expressly identified in this Agreement as an “Event”
(any such failure or breach being referred to as an “Event”, and for purposes of clause (i) the date on which such Event occurs, or for purposes of clause (ii) the date on which such five Trading Day period is exceeded, or
for purposes of clause (iii) the date on which such Event occurs, except that if the Commission will not permit acceleration or requests withdrawal as a result of the issuance of the Securities under

  

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the Purchase Agreement or the failure of any Holder to comply with the Plan of Distribution, then such date shall be 30 Trading Days after the date such Event occurs, or for purposes of clause
(iv) the date on which such 15 or 45 Trading Day period, as applicable, is exceeded, or for purposes of clause (v) the date on which such 15 or 45 Trading Day period is exceeded being referred to as “Event Date”), then in
addition to any other rights the Holders may have hereunder or under applicable law, on each monthly anniversary of each such Event Date (if the applicable Event shall not have been cured by such date) until the applicable Event is cured, the
Company shall promptly pay to each Holder an amount in cash, as partial liquidated damages and not as a penalty, equal to 1.5% of the aggregate purchase price paid by such Holder pursuant to the Purchase Agreement for any Registrable Securities then
held by such Holder and not then registered pursuant to a Registration Statement that has been declared effective by the Commission. The partial liquidated damages pursuant to the terms hereof shall apply on a daily pro-rata basis for any portion of
a month prior to the cure of an Event. Notwithstanding the foregoing, nothing shall preclude any Holder from pursuing or obtaining any available remedies at law, specific performance or other equitable relief with respect to this Section 2(d)
in accordance with applicable law. 
 (e) Subject to Section 4 below, the Holders shall have the right to
select one legal counsel to review and oversee any registration pursuant to this Section 2 (“Legal Counsel”), which shall be Reed Smith LLP or such other counsel as thereafter designated by the holders of a majority of the
Registrable Securities. 
 3. Registration Procedures. In connection with the Company’s registration
obligations hereunder, the Company shall: 
 (a) Not less than five Trading Days prior to the filing of each
Registration Statement or any related Prospectus or any amendment or supplement thereto (including any document that would be incorporated or deemed to be incorporated therein by reference), the Company shall, (i) furnish to each Holder and
Legal Counsel copies of all such documents proposed to be filed, which documents (other than those incorporated) will be subject to the review of such Holders and Legal Counsel, and (ii) cause its officers and directors, counsel and independent
certified public accountants to respond to such inquiries as shall be reasonably necessary to conduct a reasonable investigation within the meaning of the Securities Act. The Company shall not file a Registration Statement or any such Prospectus or
any amendments or supplements thereto to which the Holders of a majority of the Registrable Securities covered by such Registration Statement shall reasonably object in good faith, provided that, the Company is notified of such objection in writing
no later than 5 Trading Days after the Holders have been so furnished copies of such documents. Each Holder agrees to furnish to the Company a completed Questionnaire in the form attached to this Agreement as Annex B (a “Selling
Shareholder Questionnaire”) not less than two Trading Days prior to the Filing Date or by the end of the fourth Trading Day following the date on which such Holder receives draft materials in accordance with this Section. 

(b)(i) Prepare and file with the Commission such amendments, including post-effective amendments, to a Registration
Statement and the Prospectus used in connection therewith as may be necessary to keep a Registration Statement continuously effective as to the applicable Registrable Securities for the Effectiveness Period and prepare and file with the

  

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Commission such additional Registration Statements in order to register for resale under the Securities Act all applicable Registrable Securities; (ii) cause the related Prospectus to be
amended or supplemented by any required Prospectus supplement (subject to the terms of this Agreement), and as so supplemented or amended to be filed pursuant to Rule 424; (iii) respond as promptly as reasonably possible to any comments
received from the Commission with respect to a Registration Statement or any amendment thereto and as promptly as reasonably possible provide the Holders true and complete copies of all correspondence from and to the Commission relating to a
Registration Statement; (iv) file a final prospectus pursuant to Rule 424; and (v) comply in all material respects with the provisions of the Securities Act and the Exchange Act with respect to the disposition of all Registrable Securities
covered by a Registration Statement during the Effectiveness Period in accordance (subject to the terms of this Agreement) with the intended methods of disposition by the Holders thereof set forth in such Registration Statement as so amended or in
such Prospectus as so supplemented. 
 (c) Notify the Holders of Registrable Securities to be sold (which notice
shall, pursuant to clauses (ii) through (vi) hereof, be accompanied by an instruction to suspend the use of the Prospectus until the requisite changes have been made) as promptly as reasonably possible (and, in the case of (i)(A) below,
not less than five Trading Days prior to such filing and in the case of clause (iii) below, on the same day of receipt by the Company of such notice from the Commission or federal or state governmental authority) and (if requested by any such
Person) confirm such notice in writing no later than one Trading Day following the day (i)(A) when a Prospectus or any Prospectus supplement or post-effective amendment to a Registration Statement is proposed to be filed; (B) when the
Commission notifies the Company whether there will be a “review” of such Registration Statement and whenever the Commission comments in writing on such Registration Statement (the Company shall provide true and complete copies thereof and
all written responses thereto to each of the Holders, except to the extent the Company requests that such responses be exempt from requests under the Freedom of Information Act); and (C) with respect to a Registration Statement or any
post-effective amendment, when the same has become effective; (ii) of any request by the Commission or any other Federal or state governmental authority for amendments or supplements to a Registration Statement or Prospectus or for additional
information; (iii) of the issuance by the Commission or any other federal or state governmental authority of any stop order suspending the effectiveness of a Registration Statement covering any or all of the Registrable Securities or the
initiation of any Proceedings for that purpose; (iv) of the receipt by the Company of any notification with respect to the suspension of the qualification or exemption from qualification of any of the Registrable Securities for sale in any
jurisdiction, or the initiation or threatening of any Proceeding for such purpose; (v) of the occurrence of any event or passage of time that makes the financial statements included in a Registration Statement ineligible for inclusion therein
or any statement made in a Registration Statement or Prospectus or any document incorporated or deemed to be incorporated therein by reference untrue in any material respect or that requires any revisions to a Registration Statement, Prospectus or
other documents so that, in the case of a Registration Statement or the Prospectus, as the case may be, it will not contain any untrue statement of a material fact or omit to state any material fact required to be stated therein or necessary to make
the statements therein, in light of the circumstances under which they were made, not misleading; and (vi) of the occurrence or existence of any pending corporate development with respect to the Company that the Company reasonably believes is
material and that, in the determination of the Company, makes it not in the best interest of the Company to 
  

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allow continued availability of a Registration Statement or Prospectus; provided, that, all of such information shall remain confidential to each Holder (other than disclosure to Holder’s
employees, agents, affiliates, accountants, attorneys and advisors) until such information otherwise becomes public, unless disclosure by a Holder is required by law; provided, further, notwithstanding each Holder’s agreement to keep such
information confidential that, the Holders make no acknowledgement that any such information provided pursuant to this Section 3(c) is material, non-public information. 

If the Company notifies the Holders in accordance with clauses (ii) through (vi) of this Section 3(c) to
suspend the use of any Prospectus until the requisite changes to such Prospectus have been made, then the Holders shall suspend use of such Prospectus. The Company will use its reasonable best efforts to ensure that the use of the Prospectus may be
resumed as promptly as is practicable. The Company shall be entitled to exercise its right under Section 2(d) to suspend the availability of a Registration Statement and Prospectus, subject to the payment of partial liquidated damages pursuant
to Section 2(d), for a period not to exceed an aggregate 45 Trading Days in any 12 month period; provided, however, that no such postponement or suspension shall be permitted for more than twenty (20) consecutive Trading Days. 

(d) Use its reasonable best efforts to avoid the issuance of, or, if issued, obtain the withdrawal of (i) any order
stopping or suspending the effectiveness of a Registration Statement, or (ii) any suspension of the qualification (or exemption from qualification) of any of the Registrable Securities for sale in any jurisdiction, at the earliest practicable
moment. 
 (e) Furnish to each Holder upon request and without charge, at least one conformed copy of each such
Registration Statement and each amendment thereto, including financial statements and schedules, all documents incorporated or deemed to be incorporated therein by reference to the extent requested by such Person, and all exhibits to the extent
requested by such Person (including those previously furnished or incorporated by reference) promptly after the filing of such documents with the Commission. 

(f) Promptly deliver to each Holder, without charge, as many copies of the Prospectus or Prospectuses (including each
form of prospectus) and each amendment or supplement thereto as such Persons may reasonably request in connection with resales by the Holder of Registrable Securities. Subject to the terms of this Agreement, the Company hereby consents to the use of
such Prospectus and each amendment or supplement thereto by each of the selling Holders in connection with the offering and sale of the Registrable Securities covered by such Prospectus and any amendment or supplement thereto, except after the
giving of any notice pursuant to Section 3(c). 
 (g) If FINRA Rule 5110 requires any broker-dealer to make
a filing prior to executing a sale by a Holder, the Company shall (i) make an Issuer Filing with the FINRA Corporate Financing Department pursuant to FINRA Rule 5190, (ii) respond within five Trading Days to any comments received from
FINRA in connection therewith and (iii) and pay the filing fee required in connection therewith. 
  

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 (h) Prior to any resale of Registrable Securities by a Holder or any public
offering of Registrable Securities hereunder, use its best efforts to register or qualify or cooperate with the selling Holders in connection with the registration or qualification (or exemption from the registration or qualification) of such
Registrable Securities for the resale or sale by the Holder, as applicable, under the securities or Blue Sky laws of such jurisdictions within the United States as any Holder reasonably requests in writing, to keep each registration or qualification
(or exemption therefrom) effective during the Effectiveness Period and to do any and all other acts or things reasonably necessary to enable the disposition in such jurisdictions of the Registrable Securities covered by each Registration Statement;
provided, that the Company shall not be required to qualify generally to do business in any jurisdiction where it is not then so qualified, subject the Company to any material tax in any such jurisdiction where it is not then so subject or file a
general consent to service of process in any such jurisdiction where it is not then subject. 
 (i) Cooperate
with the Holders to facilitate the timely preparation and delivery of certificates representing Registrable Securities to be delivered to a transferee pursuant to a Registration Statement, which certificates shall be free, to the extent permitted by
the Purchase Agreement, of all restrictive legends, and to enable such Registrable Securities to be in such denominations and registered in such names as any such Holders may request. 

(j) Upon the occurrence of any event contemplated by this Section 3, as promptly as reasonably possible under the
circumstances taking into account the Company’s good faith assessment of any adverse consequences to the Company and its stockholders of the premature disclosure of such event, prepare a supplement or amendment, including a post-effective
amendment, to a Registration Statement or a supplement to the related Prospectus or any document incorporated or deemed to be incorporated therein by reference, and file any other required document so that, as thereafter delivered, neither a
Registration Statement nor such Prospectus will contain an untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make the statements therein, in light of the circumstances under which they
were made, not misleading. 
 (k) Comply with all applicable rules and regulations of the Commission.

 (l) Cause all Registrable Securities relating to a Registration Statement to be listed on the Nasdaq Global
Market, or other Trading Market on which similar securities issued by the Company are then listed. 
 (m) In
connection with the filing of a Registration Statement, the Company may require each selling Holder to furnish to the Company a certified statement as to the number of shares of Common Stock beneficially owned by such Holder and, if required by the
Commission, the person thereof that has voting and dispositive control over the Shares. During any periods that the Company is unable to meet its obligations hereunder with respect to the registration of the Registrable Securities solely because any
Holder fails to furnish such information within three Trading Days of the Company’s request, any liquidated damages that are accruing at such time as to such Holder only shall be tolled and any Event that may otherwise occur solely because of
such delay shall be suspended as to such Holder only, until such information is delivered to the Company. 
  

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 4. Registration Expenses. All fees and expenses incident to the
performance of or compliance with this Agreement by the Company shall be borne by the Company whether or not any Registrable Securities are sold pursuant to a Registration Statement. The fees and expenses referred to in the foregoing sentence shall
include, without limitation, (i) all registration and filing fees (including, without limitation, fees and expenses (A) with respect to filings required to be made with the Commission and with the Trading Market on which the Common Stock
is then listed for trading, (B) in compliance with applicable state securities or Blue Sky laws reasonably agreed to by the Company in writing (including, without limitation, fees and disbursements of counsel for the Company in connection with
Blue Sky qualifications or exemptions of the Registrable Securities and determination of the eligibility of the Registrable Securities for investment under the laws of such jurisdictions as requested by the Holders) and (C) if not previously
paid by the Company in connection with an Issuer Filing, with respect to any filing that may be required to be made by any broker through which a Holder intends to make sales of Registrable Securities with FINRA pursuant to FINRA Rule 5110, so long
as the broker is receiving no more than a customary brokerage commission in connection with such sale, (ii) printing expenses (including, without limitation, expenses of printing certificates for Registrable Securities and of printing
prospectuses if the printing of prospectuses is reasonably requested by the holders of a majority of the Registrable Securities included in a Registration Statement), (iii) messenger, telephone and delivery expenses, (iv) fees and
disbursements of counsel and auditors for the Company, and (v) fees and expenses of all other Persons retained by the Company in connection with the consummation of the transactions contemplated by this Agreement. In addition, the Company shall
be responsible for all of its internal expenses incurred in connection with the consummation of the transactions contemplated by this Agreement (including, without limitation, all salaries and expenses of its officers and employees performing legal
or accounting duties), the expense of any annual audit and the fees and expenses incurred in connection with the listing of the Registrable Securities on any securities exchange as required hereunder. In no event shall the Company be responsible for
any broker or similar commissions or, except to the extent provided for in the Transaction Documents, any legal fees or other costs of the Holders. 

5. Indemnification. 

(a) Indemnification by the Company. The Company shall, notwithstanding any termination of this Agreement, indemnify
and hold harmless each Holder, the officers, directors, members, general and limited partners, managers, agents, brokers (including brokers who offer and sell Registrable Securities as principal as a result of a pledge or any failure to perform
under a margin call of Common Stock), investment advisors and employees (and any other Persons with a functionally equivalent role of a Person holding such titles, notwithstanding a lack of such title or any other title) of each of them, each Person
who controls any such Holder (within the meaning of Section 15 of the Securities Act or Section 20 of the Exchange Act) and the officers, directors, members, general and limited partners, managers, agents and employees (and any other
Persons with a functionally equivalent role of a Person holding such titles, notwithstanding a lack of such title or any other title) of each such controlling Person, to the fullest extent permitted by applicable law, from and against any and all
losses, claims, damages, liabilities, costs (including, without limitation, reasonable attorneys’ fees) and reasonable expenses (collectively, “Losses”), as incurred, arising out of or relating to (1) any untrue or alleged
untrue statement of a material fact contained in a Registration Statement, any Prospectus or any form of prospectus or in any amendment or supplement thereto or in any preliminary 

 

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prospectus, or arising out of or relating to any omission or alleged omission of a material fact required to be stated therein or necessary to make the statements therein (in the case of any
Prospectus or form of prospectus or supplement thereto, in light of the circumstances under which they were made) not misleading or (2) any violation or alleged violation by the Company of the Securities Act, the Exchange Act or any state
securities law, or any rule or regulation thereunder, in connection with the performance of its obligations under this Agreement, except to the extent, but only to the extent, that (i) such untrue statements or omissions are based solely upon
information regarding such Holder furnished in writing to the Company by such Holder expressly for use therein, or to the extent that such information relates to such Holder or such Holder’s proposed method of distribution of Registrable
Securities and was reviewed and expressly approved in writing by such Holder expressly for use in a Registration Statement, such Prospectus or such form of Prospectus or in any amendment or supplement thereto (it being understood that the Holder has
approved Annex A hereto for this purpose) or (ii) in the case of an occurrence of an event of the type specified in Section 3(c)(ii)-(vi), the use by such Holder of an outdated or defective Prospectus after the Company has notified
such Holder in writing that the Prospectus is outdated or defective and prior to the receipt by such Holder of the Advice contemplated in Section 8(d). The Company shall notify the Holders promptly of the institution, threat or assertion of any
Proceeding arising from or in connection with the transactions contemplated by this Agreement of which the Company is aware. 

(b) Indemnification by Holders. Each Holder shall, severally and not jointly, indemnify and hold harmless the
Company, its directors, officers, agents and employees, each Person who controls the Company (within the meaning of Section 15 of the Securities Act and Section 20 of the Exchange Act), and the directors, officers, agents or employees of
such controlling Persons, to the fullest extent permitted by applicable law, from and against all Losses, as incurred, to the extent arising solely out of or based solely upon: (x) such Holder’s failure to comply with the prospectus
delivery requirements of the Securities Act or (y) any untrue statement of a material fact contained in any Registration Statement, any Prospectus, or any form of prospectus, or in any amendment or supplement thereto or in any preliminary
prospectus, or arising solely out of or based solely on to any omission or alleged omission of a material fact required to be stated therein or necessary to make the statements therein not misleading (in the case of any Prospectus or form of
prospectus or supplement thereto, in the light of the circumstances under which they were made) (i) to the extent, but only to the extent, that such untrue statement or omission is contained in any information so furnished in writing by such
Holder to the Company specifically for inclusion in such Registration Statement or such Prospectus or (ii) to the extent that (1) such untrue statements or omissions are based solely upon information regarding such Holder furnished in
writing to the Company by such Holder expressly for use therein, or to the extent that such information relates to such Holder or such Holder’s proposed method of distribution of Registrable Securities and was reviewed and expressly approved in
writing by such Holder expressly for use in a Registration Statement (it being understood that the Holder has approved Annex A hereto for this purpose), such Prospectus or such form of Prospectus or in any amendment or supplement thereto or
(2) in the case of an occurrence of an event of the type specified in Section 3(c)(ii)-(vi), the use by such Holder of an outdated or defective Prospectus after the Company has notified such Holder in writing in accordance with
Section 3(c) that the Prospectus is outdated or defective and prior to the receipt by such Holder of the Advice contemplated in Section 8(d). In no event shall the liability of any selling Holder hereunder be greater in amount than the
dollar amount of the net proceeds received by such Holder upon the sale of the Registrable Securities giving rise to such indemnification obligation. 
  

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 (c) Conduct of Indemnification Proceedings. If any Proceeding shall
be brought or asserted against any Person entitled to indemnity hereunder (an “Indemnified Party”), such Indemnified Party shall promptly notify the Person from whom indemnity is sought (the “Indemnifying Party”) in
writing, and the Indemnifying Party shall have the right to assume the defense thereof, including the employment of counsel reasonably satisfactory to the Indemnified Party and the payment of all fees and expenses incurred in connection with defense
thereof; provided, that the failure of any Indemnified Party to give such notice shall not relieve the Indemnifying Party of its obligations or liabilities pursuant to this Agreement, except (and only) to the extent that it shall be finally
determined by a court of competent jurisdiction (which determination is not subject to appeal or further review) that such failure shall have materially prejudiced the Indemnifying Party. 

An Indemnified Party shall have the right to employ separate counsel in any such Proceeding and to participate in the
defense thereof, but the fees and expenses of such counsel shall be at the expense of such Indemnified Party or Parties unless: (1) the Indemnifying Party has agreed in writing to pay such fees and expenses; (2) the Indemnifying Party
shall have failed promptly to assume the defense of such Proceeding and to employ counsel reasonably satisfactory to such Indemnified Party in any such Proceeding; or (3) the named parties to any such Proceeding (including any impleaded
parties) include both such Indemnified Party and the Indemnifying Party, and such Indemnified Party shall reasonably believe that a material conflict of interest is likely to exist if the same counsel were to represent such Indemnified Party and the
Indemnifying Party (in which case, if such Indemnified Party notifies the Indemnifying Party in writing that it elects to employ separate counsel at the expense of the Indemnifying Party, the Indemnifying Party shall not have the right to assume the
defense thereof and the reasonable fees and expenses of one separate counsel shall be at the expense of the Indemnifying Party). The Indemnifying Party shall not be liable for any settlement of any such Proceeding effected without its written
consent, which consent shall not be unreasonably withheld or delayed. No Indemnifying Party shall, without the prior written consent of the Indemnified Party, effect any settlement of any pending or threatened Proceeding in respect of which any
Indemnified Party is a party, unless such settlement includes an unconditional release of such Indemnified Party from all liability on claims that are the subject matter of such Proceeding. 

Subject to the terms of this Agreement, all reasonable fees and expenses of the Indemnified Party (including reasonable
fees and expenses to the extent incurred in connection with investigating or preparing to defend such Proceeding in a manner not inconsistent with this Section) shall be paid to the Indemnified Party, as incurred, within ten Trading Days of written
notice thereof to the Indemnifying Party; provided, that the Indemnified Party shall promptly reimburse the Indemnifying Party for that portion of such fees and expenses applicable to such actions for which it is finally judicially determined (not
subject to appeal) such Indemnified Party is not entitled to indemnification hereunder, determined based upon the relative faults of the parties. 
  

 11 

 (d) Contribution. If the indemnification under Section 5(a) or
5(b) is unavailable to an Indemnified Party for any reason or insufficient to hold an Indemnified Party harmless for any Losses, then each Indemnifying Party shall contribute to the amount paid or payable by such Indemnified Party, in such
proportion as is appropriate to reflect the relative fault of the Indemnifying Party and Indemnified Party in connection with the actions, statements or omissions that resulted in such Losses as well as any other relevant equitable considerations.

 The relative fault of such Indemnifying Party and Indemnified Party shall be determined by reference to,
among other things, whether any action in question, including any untrue or alleged untrue statement of a material fact or omission or alleged omission of a material fact, has been taken or made by, or relates to information supplied by, such
Indemnifying Party or Indemnified Party, and the parties’ relative intent, knowledge, access to information and opportunity to correct or prevent such action, statement or omission. The amount paid or payable by a party as a result of any
Losses shall be deemed to include, subject to the limitations set forth in this Agreement, any reasonable attorneys’ or other reasonable fees or expenses incurred by such party in connection with any Proceeding to the extent such party would
have been indemnified for such fees or expenses if the indemnification provided for in this Section was available to such party in accordance with its terms. 

The parties hereto agree that it would not be just and equitable if contribution pursuant to this Section 5(d) were
determined by pro rata allocation or by any other method of allocation that does not take into account the equitable considerations referred to in the immediately preceding paragraph. Notwithstanding the provisions of this Section 5(d), in no
event shall any selling Holder be required to contribute an amount under this Section 5(d) in excess of the net proceeds received by such Holder upon sale of such Holder’s Registrable Securities pursuant to the Registration Statement
giving rise to such contribution obligation, except in the case of fraud by such Holder. 
 The indemnity and
contribution agreements contained in this Section are in addition to any liability that the Indemnifying Parties may have to the Indemnified Parties. 

6. Reports Under Exchange Act. With a view to making available to the Holder the benefits of Rule 144 promulgated
under the Securities Act and any other rule or regulation of the Commission that may at any time permit a Holder to sell Registrable Shares of the Company to the public without registration, the Company agrees to: 

(a) Make and keep public information available, as those terms are used in Rule 144, at all times; 

(b) File with the Commission in a timely manner all reports and other documents required of the Company under the
Securities Act, the Exchange Act and the rules and regulations of the Trading Market; 
 (c) Furnish to any
Holder, so long as the Holder owns any Registrable Securities, forthwith on request, (i) a written statement by the Company that it has complied with the reporting requirements of Rule 144, the Securities Act and the Exchange Act, (ii) a
copy of the most recent annual or quarterly report of the Company and such other reports and documents so filed by the Company, and (iii) such other information as may be reasonably requested in availing any Holder of any rule or regulation of
the Commission that permits the selling of any such securities without registration; and 
  

 12 

 (d) Undertake any additional actions reasonably necessary to maintain the
availability of the use of Rule 144, the Company’s eligibility to file and maintain continuously effective Form S-3 registration statements and any future rules adopted by the Commission permitting the resale of the Registrable Securities.

 7. Transferees and Assignees. If any of the Registrable Securities are transferred or assigned by a Holder in
accordance with the terms of the Transaction Documents, then, upon request by the transferring Holder, the Company shall use its best efforts (to the greatest extent and at the earliest opportunity practicable and in any event not later than 20 days
after the earliest practicable date permitted under applicable guidance of the Commission and the Trading Market upon which the Registrable Securities are listed and traded) to enable such transferee or assignee to resell such transferred or
assigned Registrable Securities using the Registration Statement filed and made effective pursuant to this Agreement and the related Prospectus by filing a post-effective amendment or prospectus supplement, naming such transferee or assignee as a
selling holder under such Registration Statement and Prospectus. 
 8. Miscellaneous. 

(a) Remedies. In the event of a breach by the Company or by a Holder, of any of their obligations under this
Agreement, each Holder or the Company, as the case may be, in addition to being entitled to exercise all rights granted by law and under this Agreement, including recovery of damages, will be entitled to specific performance of its rights under this
Agreement. The Company and each Holder agree that monetary damages would not provide adequate compensation for any losses incurred by reason of a breach by it of any of the provisions of this Agreement and hereby further agrees that, in the event of
any action for specific performance in respect of such breach, it shall waive the defense that a remedy at law would be adequate. 

(b) No Piggyback on Holder Registrations. No Person has any right to cause the Company to effect a registration
under the Securities Act of any securities of the Company or to include securities of the Company in the Mandatory Registration Statement other than the Registrable Securities, except for rights that have been duly waived. Neither the Company nor
any of its security holders (other than the Holders in such capacity pursuant hereto) may include securities of the Company in the Mandatory Registration Statement other than the Registrable Securities. 

(c) Compliance. Each Holder covenants and agrees that it will comply with the prospectus delivery requirements of
the Securities Act as applicable to it in connection with sales of Registrable Securities pursuant to a Registration Statement. 

(d) Discontinued Disposition. Each Holder agrees by its acquisition of such Registrable Securities that, upon
receipt of a notice from the Company of the occurrence of any event of the kind described in Section 3(c), such Holder will forthwith discontinue disposition of such Registrable Securities under a Registration Statement until such Holder’s
receipt of the 
  

 13 

 
copies of the supplemented Prospectus and/or amended Registration Statement, or until it is advised in writing (the “Advice”) by the Company that the use of the applicable
Prospectus may be resumed, and, in either case, has received copies of any additional or supplemental filings that are incorporated or deemed to be incorporated by reference in such Prospectus or Registration Statement. The Company will use its best
efforts to ensure that the use of the Prospectus may be resumed as promptly as it practicable. The Company agrees and acknowledges that any periods during which the Holder is required to discontinue the disposition of the Registrable Securities
hereunder shall be subject to the provisions of Section 2(d). 
 (e) Piggy-Back Registrations. If at
any time during the period from the Closing Date (as defined in the Purchase Agreement) to the second anniversary of the Closing Date, any Registrable Securities are not able to be resold pursuant to an effective Registration Statement and the
Company shall determine to prepare and file with the Commission a registration statement relating to an underwritten offering or a “registered direct” offering to be placed by a placement agent, either for the Company’s own account or
the account of others under the Securities Act of any of its equity securities, other than on Form S-4 or Form S-8 (each as promulgated under the Securities Act) or their then equivalents relating to equity securities to be issued solely in
connection with any acquisition of any entity or business or equity securities issuable in connection with stock option or other employee benefit plans, then the Company shall send to the Holder written notice of such determination and, if within
ten days after receipt of such notice, the Holder shall so request in writing, the Company shall include in such registration statement all or any part of the Registrable Securities such Holder requests to be registered, subject to customary
underwriter or placement agent cutbacks applicable to all holders of registration rights, if any, due to a reasonable objection from the underwriters or placement agents that the inclusion of such Registrable Securities would materially adversely
affect the contemplated offering; provided, however, that no other stockholder’s securities are included in any offering in which a Holder’s Registrable Securities are cutback. All Holders requesting registration of their securities
through such underwritten offering or “registered direct” offering shall (together with the Company and the other holders registering their securities through such offering) enter into an underwriting agreement or placement agent
agreement, as applicable, with the underwriters or placement agents for such offering. 
 (f) Amendments and
Waivers. The provisions of this Agreement, including the provisions of this sentence, may not be amended, modified or supplemented, and waivers or consents to departures from the provisions hereof may not be given, unless the same shall be in
writing and signed by the Company and the Holders of a majority of the then outstanding Registrable Securities. Notwithstanding the foregoing, a waiver or consent to depart from the provisions hereof with respect to a matter that relates exclusively
to the rights of Holders and that does not directly or indirectly affect the rights of other Holders may be given by Holders of all of the Registrable Securities to which such waiver or consent relates; provided, however, that the provisions of this
sentence may not be amended, modified, or supplemented except in accordance with the provisions of the immediately preceding sentence. 

(g) Notices. Any and all notices or other communications or deliveries required or permitted to be provided
hereunder shall be delivered as set forth in the Purchase Agreement. 
  

 14 

 (h) Successors and Assigns. This Agreement shall inure to the benefit
of and be binding upon the successors and permitted assigns of each of the parties and shall inure to the benefit of each Holder. The Company may not assign its rights or obligations hereunder without the prior written consent of all of the Holders
of the then outstanding Registrable Securities. Each Holder may assign their respective rights hereunder in the manner and to the Persons as permitted under the Purchase Agreement, including, without limitation, to affiliates of any Holder or any
general partner, limited partners or members of a Holder or of such Holder’s affiliates. 
 (i) No
Inconsistent Agreements. Neither the Company nor any of its subsidiaries has entered, as of the date hereof, nor shall the Company or any of its subsidiaries, on or after the date of this Agreement, enter into any agreement with respect to its
securities, that would have the effect of impairing the rights granted to the Holders in this Agreement or otherwise conflicts with the provisions hereof. Neither the Company nor any of its subsidiaries has previously entered into any agreement
granting any registration rights with respect to any of its securities to any Person that have not been satisfied in full or waived. 

(j) Execution and Counterparts. This Agreement may be executed in any number of counterparts, each of which when
so executed shall be deemed to be an original and, all of which taken together shall constitute one and the same Agreement. In the event that any signature is delivered by facsimile transmission (or electronic transmission of a PDF file), such
signature shall create a valid binding obligation of the party executing (or on whose behalf such signature is executed) the same with the same force and effect as if such facsimile signature (or PDF file) were the original thereof. 

(k) Governing Law. All questions concerning the construction, validity, enforcement and interpretation of this
Agreement shall be determined in accordance with the provisions of the Purchase Agreement. 
 (l) Cumulative
Remedies. The remedies provided herein are cumulative and not exclusive of any other remedies provided by law. 

(m) Severability. If any term, provision, covenant or restriction of this Agreement is held by a court of
competent jurisdiction to be invalid, illegal, void or unenforceable, the remainder of the terms, provisions, covenants and restrictions set forth herein shall remain in full force and effect and shall in no way be affected, impaired or invalidated,
and the parties hereto shall use their best efforts to find and employ an alternative means to achieve the same or substantially the same result as that contemplated by such term, provision, covenant or restriction. It is hereby stipulated and
declared to be the intention of the parties that they would have executed the remaining terms, provisions, covenants and restrictions without including any of such that may be hereafter declared invalid, illegal, void or unenforceable. 

(n) Headings. The headings in this Agreement are for convenience of reference only and shall not limit or
otherwise affect the meaning hereof. 
  

 15 

 (o) Independent Nature of Holders’ Obligations and Rights. The
obligations of each Holder hereunder are several and not joint with the obligations of any other Holder hereunder, and no Holder shall be responsible in any way for the performance of the obligations of any other Holder hereunder. Nothing contained
herein or in any other agreement or document delivered at any closing, and no action taken by any Holder pursuant hereto or thereto, shall be deemed to constitute the Holders as a partnership, an association, a joint venture or any other kind of
entity, or create a presumption that the Holders are in any way acting in concert with respect to such obligations or the transactions contemplated by this Agreement. Each Holder shall be entitled to protect and enforce its rights, including without
limitation the rights arising out of this Agreement, and it shall not be necessary for any other Holder to be joined as an additional party in any proceeding for such purpose. 

(p) Aggregation of Stock. All shares of Registrable Securities held or acquired by affiliated entities (including
affiliated venture capital funds) or persons shall be aggregated together for the purpose of determining the availability of any rights under this Agreement. 

[Signature Pages Follow] 
  

 16 

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	ACHILLION PHARMACEUTICALS, INC.
		
	By:	 	 /s/ Mary Kay Fenton

		 	Name: Mary Kay Fenton
		 	Title: CFO

 [REMAINDER OF PAGE
INTENTIONALLY LEFT BLANK 
 SIGNATURE PAGE FOR PURCHASERS FOLLOW] 

 

 17 

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	DOMAIN PARTNERS VIII, L.P.
		
	By:	 	One Palmer Square Associates VIII, L.L.C.
	Its:	 	General Partner
		
	By:	 	 /s/ Kathleen Schoemaker

		 	Name: Kathleen Schoemaker
		 	Title: Managing Member

  

			
	DP VIII ASSOCIATES, L.P.
		
	By:	 	One Palmer Square Associates VIII, L.L.C.
	Its:	 	General Partner
		
	By:	 	 /s/ Kathleen Schoemaker

		 	Name: Kathleen Shoemaker
		 	Title: Managing Member

  

 18 

			
	CLARUS LIFESCIENCES II, L.P.
		
	By:	 	Clarus Ventures II GP, LP
	Its:	 	General partner
		
	By:	 	Clarus Ventures, II LLC
	Its:	 	General partner
		
	By:	 	 /s/ Robert Liptak

		 	Name: Robert Liptak
		 	Title: Managing Director

  

 19 

			
	QUAKER BIOVENTURES II, L.P.
		
	By:	 	Quaker Bioventures Capital II, L.P.
		 	its general partner
		
	By:	 	Quaker Bioventures Capital II, L.L.C.
		 	its general partner
		
	By:	 	 /s/ Adele C. Oliva

		 	Name: Adele C. Oliva
		 	Title: Vice President

  

 20 

			
	A.M. PAPPAS LIFE SCIENCE VENTURES IV, L.P.
		
	By:	 	AMP&A Management IV, LLC
	Its:	 	General Partner
		
	By:	 	 /s/ Ford S. Worthy

		 	Name: Ford S. Worthy
		 	Title: Partner & CFO

  

			
	PV IV CEO FUND, L.P.
		
	By:	 	AMP&A Management IV, LLC
	Its:	 	General Partner
		
	By:	 	 /s/ Ford S. Worthy

		 	Name: Ford S. Worthy
		 	Title: Partner & CFO

  

 21 

 EXHIBIT A 

Schedule of Purchasers 
  

	
	Purchaser Name and Address
	 
	
Domain Partners VIII, L.P.
 One Palmer Square

 Suite 515
 Princeton, NJ
08542

	 
	
DP VIII Associates, L.P.
 One Palmer
Square
 Suite 515
 Princeton, NJ 08542

	 
	
Clarus Lifesciences II, L.P.
 c/o Clarus
Ventures, LLC
 101 Main Street, Suite 1210

Cambridge, MA 02142

	 
	
Quaker Bioventures II, L.P.
 Cira
Centre
 2929 Arch Street
 Philadelphia,
PA 19104-2868

	 
	
A.M. Pappas Life Science Ventures IV, L.P.
 c/o
Pappas Ventures
 P.O. Box 110287

Research Triangle Park, NC 27709

	 
	
PV IV CEO Fund L.P.
 c/o Pappas
Ventures
 P.O. Box 110287
 Research
Triangle Park, NC 27709

  

 22 

 ANNEX A 

Plan of Distribution 

Each Selling Stockholder (the “Selling Stockholders”) of the common stock (“Common
Stock”) of Achillion Pharmaceuticals, Inc., a Delaware corporation (the “Company”) and any of their pledgees, assignees and successors-in-interest may, from time to time, sell any or all of their shares of Common Stock on
the Trading Market or any other stock exchange, market or trading facility on which the shares are traded or in private transactions. These sales may be at fixed or negotiated prices. A Selling Stockholder may use any one or more of the following
methods when selling shares: 
  

	 	•	 	 ordinary brokerage transactions and transactions in which the broker-dealer solicits purchasers; 

 

	 	•	 	 block trades in which the broker-dealer will attempt to sell the shares as agent but may position and resell a portion of the block as principal to
facilitate the transaction; 

  

	 	•	 	 purchases by a broker-dealer as principal and resale by the broker-dealer for its account; 

 

	 	•	 	 an exchange distribution in accordance with the rules of the applicable exchange; 

 

	 	•	 	 privately negotiated transactions; 

  

	 	•	 	 settlement of short sales entered into after the effective date of the registration statement of which this prospectus is a part;

  

	 	•	 	 broker-dealers may agree with the Selling Stockholders to sell a specified number of such shares at a stipulated price per share;

  

	 	•	 	 a combination of any such methods of sale; 

  

	 	•	 	 through the writing or settlement of options or other hedging transactions, whether through an options exchange or otherwise; or

  

	 	•	 	 any other method permitted pursuant to applicable law. 

The Selling Stockholders may also sell shares under Rule 144 under the Securities Act of 1933, as amended (the
“Securities Act”), if available, rather than under this prospectus. The Selling Stockholders have the sole and absolute discretion not to accept any purchase offer or make any sale of shares if they deem the purchase price to be
unsatisfactory at any particular time. 
 Broker-dealers engaged by the Selling Stockholders may arrange for
other brokers-dealers to participate in sales. Broker-dealers may receive commissions or discounts from the Selling Stockholders (or, if any broker-dealer acts as agent for the purchaser of shares, from the purchaser) in amounts to be negotiated,
but, except as set forth in a supplement to this Prospectus, in the case of an agency transaction not in excess of a customary brokerage commission in compliance with NASDR Rule 2440; and in the case of a principal transaction a markup or markdown
in compliance with NASDR IM-2440. 
  

 23 

 In connection with the sale of the Common Stock or interests therein, the
Selling Stockholders may enter into hedging transactions with broker-dealers or other financial institutions, which may in turn engage in short sales of the Common Stock in the course of hedging the positions they assume. The Selling Stockholders
may also sell shares of the Common Stock short and deliver these securities to close out their short positions, or loan or pledge the Common Stock to broker-dealers that in turn may sell these securities. The Selling Stockholders may also enter into
option or other transactions with broker-dealers or other financial institutions or the creation of one or more derivative securities which require the delivery to such broker-dealer or other financial institution of shares offered by this
prospectus, which shares such broker-dealer or other financial institution may resell pursuant to this prospectus (as supplemented or amended to reflect such transaction). 

The Selling Stockholders and any broker-dealers or agents that are involved in selling the shares may be deemed to be
“underwriters” within the meaning of the Securities Act in connection with such sales. In such event, any commissions received by such broker-dealers or agents and any profit on the resale of the shares purchased by them may be deemed to
be underwriting commissions or discounts under the Securities Act. Each Selling Stockholder has informed the Company that it does not have any written or oral agreement or understanding, directly or indirectly, with any person to distribute the
Common Stock. 
 The Company is required to pay certain fees and expenses incurred by the Company incident to
the registration of the shares. The Company has agreed to indemnify the Selling Stockholders against certain losses, claims, damages and liabilities, including liabilities under the Securities Act. 

[Because Selling Stockholders may be deemed to be “underwriters” within the meaning of the Securities Act,
they will be subject to the prospectus delivery requirements of the Securities Act.] In addition, any securities covered by this prospectus which qualify for sale pursuant to Rule 144 under the Securities Act may be sold under Rule 144 rather
than under this prospectus. Each Selling Stockholder has advised us that they have not entered into any written or oral agreements, understandings or arrangements with any underwriter or broker-dealer regarding the sale of the resale shares. There
is no underwriter or coordinating broker acting in connection with the proposed sale of the resale shares by the Selling Stockholders. 

We agreed to keep this prospectus effective until the earlier of (i) the date all of the Registrable Securities
covered by such Registration Statement have been sold and (ii) the later of (A) the second anniversary of the Effectiveness Date or (B) the date upon which the Registrable Securities may be sold without volume or manner-of-sale
restrictions under Rule 144 as determined by the counsel to the Company pursuant to a written opinion letter to such effect, addressed and acceptable to the Company’s transfer agent and the affected Holders. The resale shares will be sold only
through registered or licensed brokers or dealers if required under applicable state securities laws. In addition, in certain states, the resale shares may not be sold unless they have been registered or qualified for sale in the applicable state or
an exemption from the registration or qualification requirement is available and is complied with. 
  

 24 

 Under applicable rules and regulations under the Exchange Act, any person
engaged in the distribution of the resale shares may not simultaneously engage in market making activities with respect to the Common Stock for the applicable restricted period, as defined in Regulation M, prior to the commencement of the
distribution. In addition, the Selling Stockholders will be subject to applicable provisions of the Exchange Act and the rules and regulations thereunder, including Regulation M, which may limit the timing of purchases and sales of shares of the
Common Stock by the Selling Stockholders or any other person. We will make copies of this prospectus available to the Selling Stockholders and have informed them of the need to deliver a copy of this prospectus to each purchaser at or prior to the
time of the sale. 
  

 25 

 ANNEX B 

ACHILLION PHARMACEUTICALS, INC. 

Selling Securityholder Notice and Questionnaire 

The undersigned beneficial owner of common stock, par value $0.001 per share (the “Common Stock”), of
Achillion Pharmaceuticals, Inc., a Delaware corporation (the “Company”), (the “Registrable Securities”) understands that the Company has filed or intends to file with the Securities and Exchange Commission (the
“Commission”) a registration statement on Form S-3 or other form as may be available for use by the Company (the “Registration Statement”) for the registration and resale under Rule 415 of the Securities Act of
1933, as amended (the “Securities Act”), of the Registrable Securities, in accordance with the terms of the Registration Rights Agreement, dated as of August 18, 2010 (the “Registration Rights Agreement”),
among the Company and the Purchasers named therein. A copy of the Registration Rights Agreement is available from the Company upon request at the address set forth below. All capitalized terms not otherwise defined herein shall have the meanings
ascribed thereto in the Registration Rights Agreement. 
 Certain legal consequences arise from being named as a
selling securityholder in the Registration Statement and the related prospectus. Accordingly, holders and beneficial owners of Registrable Securities are advised to consult their own securities law counsel regarding the consequences of being named
or not being named as a selling securityholder in the Registration Statement and the related prospectus. 
 NOTICE

 The undersigned beneficial owner (the “Selling Securityholder”) of Registrable
Securities hereby elects to include the Registrable Securities owned by it and listed below in Item 3 (unless otherwise specified under such Item 3) in the Registration Statement. 

The undersigned hereby provides the following information to the Company and represents and warrants that such
information is accurate: 
 QUESTIONNAIRE 

 

	 	1.	Name. 

  

	 	(a)	Full Legal Name of Selling Securityholder: 

  

					
		  	  
	  	

  

 26 

 (b) Full Legal Name of Registered Holder (if not the same as (a) above)
through which Registrable Securities Listed in Item 3 below are held: 
  

			
		  	  

(c) Full Legal Name of Natural Control Person (which means a natural person who directly or indirectly alone or with
others has power to vote or dispose of the securities covered by the questionnaire): 
  

	 	2.	Address for Notices to Selling Securityholder: 

  

			
		 	  

		 	  

		 	  

		 	 Telephone:

		 	 Fax:

		 	 Contact Person:

 

	 	3.	Beneficial Ownership of Registrable Securities: 

  

	 	(a)	 Type and Principal Amount of Registrable Securities beneficially owned (not including the Registrable Securities that are issuable pursuant to the
Purchase Agreement): 

  

			
		 	  

		 	  

		 	  

 

	 	4.	Broker-Dealer Status: 

  

	 	(a)	Are you a broker-dealer? 

Yes   ̈    No  
 ̈ 
  

	 	(b)	 If “yes” to Section 4(a), did you receive your Registrable Securities as compensation for investment banking services to the Company.

Yes   ̈    No  
 ̈ 
  

 27 

	 	Note:	 If no, the Commission’s staff has indicated that you should be identified as an underwriter in the Registration Statement.

  

	 	(c)	Are you an affiliate of a broker-dealer? 

Yes   ̈    No  
 ̈ 
  

	 	(d)	 If you are an affiliate of a broker-dealer, do you certify that you bought the Registrable Securities in the ordinary course of business, and at the
time of the purchase of the Registrable Securities to be resold, you had no agreements or understandings, directly or indirectly, with any person to distribute the Registrable Securities? 

Yes   ̈    No  
 ̈ 
  

	 	Note:	 If no, the Commission’s staff has indicated that you should be identified as an underwriter in the Registration Statement.

  

	 	5.	Beneficial Ownership of Other Securities of the Company Owned by the Selling Securityholder. 

Except as set forth below in this Item 5, the undersigned is not the beneficial or registered owner of any securities
of the Company other than the Registrable Securities listed above in Item 3. 
  

	 	(a)	Type and Amount of Other Securities beneficially owned by the Selling Securityholder: 

 

			
		 	  

		 	  

		 	  

 

	 	6.	Relationships with the Company: 

Except as set forth below, neither the undersigned nor any of its affiliates, officers, directors or principal equity
holders (owners of 5% of more of the equity securities of the undersigned) has held any position or office or has had any other material relationship with the Company (or its predecessors or affiliates) during the past three years. 

State any exceptions here: 
  

			
		 	  

		 	  

		 	  

  

 28 

 The undersigned agrees to promptly notify the Company of any inaccuracies or
changes in the information provided herein that may occur subsequent to the date hereof at any time while the Registration Statement remains effective. 

By signing below, the undersigned consents to the disclosure of the information contained herein in its answers to Items
1 through 6 and the inclusion of such information in the Registration Statement and the related prospectus and any amendments or supplements thereto. The undersigned understands that such information will be relied upon by the Company in connection
with the preparation or amendment of the Registration Statement and the related prospectus. 
 IN WITNESS
WHEREOF the undersigned, by authority duly given, has caused this Notice and Questionnaire to be executed and delivered either in person or by its duly authorized agent. 

 

					
	Dated:	 	  
	 	

  

					
	Beneficial Owner:	 	  
	 	

  

					
	By:	 	  
	 	
		 	Name:	 	
		 	Title:	 	

 PLEASE FAX A COPY OF THE COMPLETED AND EXECUTED NOTICE AND 

QUESTIONNAIRE, AND RETURN THE ORIGINAL BY OVERNIGHT MAIL, TO: 

Achillion Pharmaceuticals, Inc. 
 300
George Street 
 New Haven, CT 06511 

Attention: Mary Kay Fenton 
 Fax:
(203) 624-7003 
  

 29Amendment No. 1 to Third Amended and Restated Investor Rights Agreement

 Exhibit 10.4 

AMENDMENT NO. 1 TO THIRD AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

This Amendment No. 1 (the “Amendment”) to Third Amended and Restated Investor Rights Agreement is made
as of this 20th day of August, 2010, by and among
Achillion Pharmaceuticals, Inc. (the “Company”), and certain holders of the Company’s common stock, $.001 par value per share (the “Holders”), who are parties to the Third Amended and Restated Investor Rights Agreement,
dated as of August 11, 2008 (the “IRA”). 
 WHEREAS, the Company wishes to terminate several provisions of the
IRA; and 
 WHEREAS, the parties hereto wish to facilitate the termination but provide for certain rights as set forth herein to
survive such termination. 
 NOW, THEREFORE, in consideration of the mutual covenants herein contained and other valuable
consideration, the receipt and sufficiency of which is hereby acknowledged, the Company and the undersigned, who represent holders of at least two-thirds of the Conversion Shares (as defined in the IRA) held by the Holders, hereby agree as
follows: 
  

	1.	The definition of “Registration Rights Agreement” in Section 1 of the IRA is hereby deleted in its entirety and the following is inserted in lieu
thereof: 

 ““Registration Rights Agreement” means that certain Registration Rights Agreement,
dated on or about August 18, 2010, by and among the Company and the parties named therein (the “Purchasers”).” 
  

	2.	The following definition is hereby added to Section 1 of the Agreement: 

““Effective Date” means the date all of the Registrable Securities (as defined in the Registration Rights Agreement) have
been registered pursuant to effective registration statements filed pursuant to the Registration Right Agreement.”” 
  

	3.	Sections 4, 5, 10 and 11 of the IRA are hereby deleted in their entirety and shall have no further force or effect. 

 

	4.	Section 14(f) of the Agreement is hereby deleted in its entirety and the following is inserted in lieu thereof: 

“(f) The Company shall have no obligations pursuant to Section 6 with respect to any request or requests for registration made
by any Holder after October 25, 2013.” 
  

	5.	Section 14(h) of the Agreement is hereby deleted in its entirety and the following is inserted in lieu thereof: 

“(h) Notwithstanding anything to the contrary set forth in this Agreement, a Holder shall cease to be a Holder for purposes of this
Agreement when such Holder no longer holds Restricted Stock.” 

	6.	Any references to Sections 4 or 5 of the IRA are hereby deleted from the IRA. 

 

	7.	The Company represents and warrants to each Holder as follows: 

(i) The execution, delivery and performance of this Amendment by the Company have been duly authorized by all requisite corporate action
and will not violate any provision of law, any order of any court or other agency of government, the Charter or By-laws of the Company or any provision of any indenture, agreement or other instrument to which it or any of its properties or assets is
bound, conflict with, result in a breach of or constitute (with due notice or lapse of time or both) a default under any such indenture, agreement or other instrument or result in the creation or imposition of any lien, charge or encumbrance of any
nature whatsoever upon any of the properties or assets of the Company. 
 (ii) This Amendment has been duly executed and
delivered by the Company and constitutes the legal, valid and binding obligation of the Company, enforceable in accordance with its terms, subject to (A) laws of general application relating to bankruptcy, insolvency and the relief of debtors
and (B) rules of law governing specific performance, injunctive relief or other equitable remedies. 
  

	8.	Except as amended hereby, the IRA shall remain in full force and effect. 

  

	9.	This Amendment shall be governed by, and construed in accordance with, the laws of the State of Delaware, without regard to principles of conflicts of laws.

  

	10.	This Amendment may be executed in one or more counterparts, each of which shall be deemed to be an original and all of which shall constitute the same document.

 [Remainder of page intentionally left blank] 

 

 - 2 - 

 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the day and year
first above written. 
  

							
	ACHILLION PHARMACEUTICALS, INC.	 		 	
				
	By:	 	 /s/ Michael D. Kishbauch
	 		 	
	Name:	 	Michael D. Kishbauch	 		 	
	Title:	 	President and Chief Executive Officer	 		 	

  

			
	 Address:
	    	300 George Street
		    	New Haven, CT 06511

  

							
	HOLDERS:	 	
		
	 ADVENT HEALTH CARE & LIFE

SCIENCES II LIMITED PARTNERSHIP
	 	
				
	By:	 	 Advent International Limited Partnership,

General Partner
	 		 	
				
	By:	 	Advent International Corporation,	 		 	
		 	General Partner	 		 	
				
	By:	 	 /s/ Jason Fisherman
	 		 	
	Name:	 	Jason Fisherman	 		 	Dated: August 20, 2010
	Title:	 	Attorney-in-Fact	 		 	
			
	 ADVENT HEALTH CARE AND LIFE

SCIENCES II BETEILIGUNG GMBH & CO. KG
	 		 	
				
	By:	 	 Advent International Limited Partnership,

General Partner
	 		 	
				
	By:	 	Advent International Corporation,	 		 	
		 	General Partner	 		 	
				
	By:	 	 /s/ Jason Fisherman
	 		 	
	Name:	 	Jason Fisherman	 		 	
	Title:	 	Attorney-in-Fact	 		 	
		 		 		 	Dated: August 20, 2010

							
	ADVENT PARTNERS HLS II LIMITED PARTNERSHIP	 		 	
				
	By:	 	Advent International Corporation, General Partner	 		 	
				
	By:	 	 /s/ Jason Fisherman
	 		 	Dated: August 20, 2010
	Name:	 	Jason Fisherman	 		 	
	Title:	 	Attorney-in-Fact	 		 	
			
	ADVENT PARTNERS LIMITED PARTNERSHIP	 		 	
				
	By:	 	 Advent International Corporation,

General Partner
	 		 	
				
	By:	 	 /s/ Jason Fisherman
	 		 	Dated: August 20, 2010
	Name:	 	Jason Fisherman	 		 	
	Title:	 	Attorney-in-fact	 		 	
			
	  
	 		 	Dated: August    , 2010
	Jonas V. Alsenas	 		 	
			
	ATLAS VENTURE ENTREPRENEURS’ FUND V, L.P.	 		 	
	ATLAS VENTURE FUND V, L.P.	 		 	
	ATLAS VENTURE PARALLEL FUND V-A, C.V.	 		 	
				
	By:	 	 Atlas Venture Associates V, L.P., their

General Partner
	 		 	
				
	By:	 	 Atlas Venture Associates V, Inc., its

General Partner
	 		 	
				
	By:	 	 /s/ Jean-Francois Formela
	 		 	
	Name:	 	Jean-Francois Formela	 		 	
	Title:	 	Vice President	 		 	
		 		 		 	Dated: August 20, 2010
			
	 BEAR STEARNS HEALTH

INNOVENTURES EMPLOYEE FUND, L.P.
	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	

							
	 BEAR STEARNS HEALTH INNOVENTURES

OFFSHORE, L.P.
	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	
			
	BEAR STEARNS HEALTH INNOVENTURES, L.P.	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	
			
	 BSHI MEMBERS, L.L.C.
	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	
			
	 BX, L.P.
	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	
			
	 CAPITAL VENTURES INTERNATIONAL
	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	 COMMUNITY INVESTMENT PARTNERS IV L.P., LLLP
	 		 	
				
	By:	 	 CIP Management L.P., LLLP, its managing

general partner
	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	

							
	CONNECTICUT EMERGING ENTERPRISES, L.P.	 		 	
				
	By:	 	Emerging Enterprises Management LLC, its General Partner	 		 	
				
	By:	 	Connecticut Innovations, Incorporated, its Sole Member	 		 	
				
	By:	 	 /s/ Peter Longo
	 		 	Dated: August 20, 2010
	Name:	 	Peter Longo	 		 	
	Title:	 	President & Executive Director	 		 	
			
	CONNECTICUT INNOVATIONS, INCORPORATED	 		 	
				
	By:	 	 /s/ Peter Longo
	 		 	Dated: August 20, 2010
	Name:	 	Peter Longo	 		 	
	Title:	 	President & Executive Director	 		 	
			
	CRESTWOOD CAPITAL MASTER FUND LTD.	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	CRESTWOOD CAPITAL PARTNERS II, L.P.	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	  
	 		 	Dated: August    , 2010
	Kim Fennebresque	 		 	
			
	GE CAPITAL CORPORATION	 		 	
				
	By:	 	 /s/ Scott R. Towers
	 		 	Dated: August 20, 2010
	Name:	 	Scott R. Towers	 		 	
	Title:	 	Duly Authorized Signatory	 		 	

							
	GILEAD SCIENCES, INC.	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	H&D INVESTMENTS 2001	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	INTERNATIONAL BIOTECHNOLOGY TRUST PLC.	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	KBL HEALTHCARE, L.P.	 		 	
				
	By:	 	 /s/ Marlene Krauss
	 		 	Dated: August 20, 2010
	Name:	 	Marlene Krauss	 		 	
	Title:	 	Managing Director	 		 	
			
	KBL PARTNERSHIP, L.P.	 		 	
				
	By:	 	 /s/ Marlene Krauss
	 		 	Dated: August 20, 2010
	Name:	 	Marlene Krauss	 		 	
	Title:	 	Managing Director	 		 	
			
	  
	 		 	Dated: August    , 2010
	David M. Malcolm	 		 	
			
	OAK INVESTMENT PARTNERS VIII, LIMITED PARTNERSHIP	 		 	
				
	By:	 	Oak Associates VIII, LLC, its General Partner	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
		 	            A Member	 		 	

							
	OAK VIII AFFILIATES FUND , LIMITED PARTNERSHIP	 		 	
				
	By:	 	Oak Associates VIII, LLC, its General Partner	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
		 	        A Member	 		 	
			
	OAKWOOD MEDICAL INVESTORS III (QP), L.L.C.	 		 	
				
	By:	 	 Oakwood Medical Management III, L.L.C.,

its Manager
	 		 	
				
	By:	 	 /s/ Raul E. Perez
	 		 	Dated: August 20, 2010
	Name:	 	Raul E. Perez, M.D.	 		 	
	Title:	 	President	 		 	
			
	OAKWOOD MEDICAL INVESTORS III, L.L.C.	 		 	
				
	By:	 	 Oakwood Medical Management III, L.L.C.,

its Manager
	 		 	
				
	By:	 	 /s/ Raul E. Perez
	 		 	Dated: August 20, 2010
	Name:	 	Raul E. Perez, M.D.	 		 	
	Title:	 	President	 		 	
			
	  
	 		 	Dated: August    , 2010
	Stelios Papadopoulos	 		 	
			
	PGE INVESTMENTS 2002, LLC	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	  
	 		 	Dated: August    , 2010
	Barbara A. Piette	 		 	
			
	POUND CAPITAL CORPORATION	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	

  

							
	  
	 		 	Dated: August    , 2010
	Peter Reikes	 		 	
			
	SCHEER INVESTMENT HOLDINGS III, LLC	 		 	
				
	By:	 	 /s/ David I. Scheer
	 		 	Dated: August 20, 2010
	Name:	 	David I. Scheer	 		 	
	Title:	 	Managing Member	 		 	
			
	 SCHRODER VENTURES INTERNATIONAL LIFE

SCIENCES FUND II GROUP CO-INVESTMENT SCHEME
	 		 	
				
	By:	 	SITCO Nominees Ltd. – VC 01903, its Nominee	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	
			
	 SCHRODER VENTURES INTERNATIONAL LIFE

SCIENCES FUND II LP1
	 		 	
				
	By:	 	Schroder Venture Managers Inc., its General Partner	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	
			
	SCHRODER VENTURES INTERNATIONAL LIFE SCIENCES FUND II LP2	 		 	
				
	By:	 	Schroder Venture Managers Inc., its General Partner	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	

  

							
	 SCHRODER VENTURES INTERNATIONAL LIFE

SCIENCES FUND II LP3
	 		 	
				
	By:	 	Schroder Venture Managers Inc., its General Partner	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	
			
	 SCHRODER VENTURES INTERNATIONAL LIFE

SCIENCES FUND II STRATEGIC PARTNERS L.P.
	 		 	
				
	By:	 	Schroder Venture Managers Inc., its General Partner	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	
			
	SCHRODER VENTURES INVESTMENTS LIMITED	 		 	
				
	By:	 	SV (Nominees) Limited, its Nominee	 		 	
				
	By:	 	 /s/ John Marren
	 		 	Dated: August 20, 2010
	Name:	 	John Marren	 		 	
	Title:	 	Director	 		 	
			
	SG VENTURES I, L.P.	 		 	
				
	By:	 	 Société Générale Investment Corporation,

its General Partner
	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	TRINITY EQUITY INVESTMENTS I, LLC	 		 	
				
	By:	 	 /s/ Sengal Selassie
	 		 	Dated: August 20, 2010
	Name:	 	Sengal Selassie	 		 	
	Title:	 	President	 		 	

							
	WEBSTER FINANCIAL CORPORATION	 		 	
				
	By:	 	 /s/ Joseph Savage
	 		 	Dated: August 20, 2010
	Name:	 	Joseph Savage	 		 	
	Title:	 	EVP – Commercial Banking	 		 	
			
	  
	 		 	Dated: August    , 2010
	Christopher White	 		 	
			
	YALE UNIVERSITY	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:

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