ENTA Enanta Pharmaceuticals Inc

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Form 10-K

(Amendment No. 1)

For the fiscal year ended September 30, 2016

OR

Commission File Number 001-35839

500 Arsenal Street

Watertown, Massachusetts 02472

(617) 607-0800

(Address, including zip code, and telephone number, including area code, of registrant’s principal executive offices)

Securities registered pursuant to Section 12(g) of the Act: None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.    Yes  ☐    No  ☒

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.    Yes  ☐    No  ☒

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days:    Yes  ☒    No  ☐

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files):    Yes  ☒    No  ☐

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.  ☒

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act:

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act):    Yes  ☐    No  ☒

The aggregate market value of the registrant’s common stock held by non-affiliates of the registrant as of the last business day of the registrant’s most recently completed second fiscal quarter, March 31, 2016, based on the last reported sale price of the registrant’s common stock of $29.37 per share was $556,755,420. The number of shares of the registrant’s Common Stock, $0.01 par value, outstanding as of December 27, 2016, was 19,040,267 shares.

DOCUMENTS INCORPORATED BY REFERENCE

Portions of the registrant’s Definitive Proxy Statement for its 2016 Annual Meeting of Stockholders scheduled to be held on February 16, 2017, which Definitive Proxy will be filed with the Securities and Exchange Commission not later than 120 days after the registrant’s fiscal year end of September 30, 2016, are incorporated by reference into Part III of the Original Report (as defined below), as amended by this 10-K/A.

As used in this Form 10-K/A, “Enanta,” “the Company,” “we,” “our,” and “us” refer to Enanta Pharmaceuticals, Inc., except where the context otherwise requires or as otherwise indicated.

EXPLANATORY NOTE

Enanta Pharmaceuticals, Inc. is filing this Amendment No. 1 on Form 10-K/A (“Amendment No. 1”) to the Company’s Annual Report on Form 10-K for the period ended September 30, 2016, which was filed with the Securities and Exchange Commission (the “SEC”) on December 9, 2016 (the “Original Report”). This Amendment No. 1 is being filed to: (i) file Exhibit 10.14, the Company’s 2012 Equity Incentive Plan (As adjusted to reflect the application of the 1-for-4.31 reverse stock split of the Company’s common stock effected on March 1, 2013), because the Company’s 2012 Equity Incentive Plan, as originally filed with the SEC, inadvertently did not reflect the adjustment to the per-participant limitation under Section 162(m) of the Internal Revenue Code that resulted from the application of the 1-for-4.31 reverse stock split of the Company’s common stock effected on March 1, 2013 and (ii) make a corresponding update to Exhibit 10.14 and the required certifications as listed in Item 15(b) of Part IV of the Original Report. As required by Rule 12b-15 under the Securities and Exchange Act of 1934, as amended, new certifications by our principal executive officer and our principal financial officer are filed herewith and listed as exhibits to this Amendment No. 1 under Item 15(b) of Part IV hereof. This Amendment No. 1 does not affect any other items in the Original Report.

Except as otherwise expressly stated in the items contained in this Amendment No. 1, this Amendment No. 1 continues to speak as of the date of the Original Report and the Company has not modified or updated the disclosures contained herein to reflect events that have occurred since the filing of the Original Report. Accordingly, this Amendment No. 1 should be read in conjunction with the Original Report.

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