RA Capital Discloses 14.9% Stake in Septerna, Inc.

TL;DR

**RA Capital now owns 14.9% of Septerna! Big move.**

AI Summary

On November 4, 2024, RA Capital Management, L.P. and its affiliates, including Peter Kolchinsky and RA Capital Healthcare Fund, L.P., filed a Schedule 13D. They reported beneficial ownership of 12,000,000 shares of Septerna, Inc. common stock, representing approximately 14.9% of the outstanding shares. This filing indicates a significant stake and potential for influence in the company.

Why It Matters

This filing signals that a major healthcare-focused investment firm has taken a substantial position in Septerna, Inc., potentially leading to strategic changes or increased shareholder activism.

Risk Assessment

Risk Level: medium — The filing indicates a significant ownership stake by an activist investor, which could lead to changes in company strategy or management.

Key Numbers

• 12,000,000 — Shares Owned (Represents a significant stake in Septerna, Inc.)
• 14.9% — Ownership Percentage (Indicates substantial beneficial ownership by RA Capital)

Key Players & Entities

• RA Capital Management, L.P. (company) — Filing entity
• Peter Kolchinsky (person) — Affiliated individual with RA Capital
• RA Capital Healthcare Fund, L.P. (company) — Affiliated entity with RA Capital
• Septerna, Inc. (company) — Subject company
• 12,000,000 (dollar_amount) — Number of shares owned
• 14.9% (dollar_amount) — Percentage of shares owned

FAQ

Key Financial Figures

• $0.001 — Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class o
• $29,999,999.72 — ate purchase price of the foregoing was $29,999,999.72. CUSIP No. 81734D 104 On October 18,
• $18.00 — rwriters of the IPO at the IPO price of $18.00 per share, for an aggregate purchase pr
• $75,060,000 — are, for an aggregate purchase price of $75,060,000. All purchases of the securities descr

Filing Documents

• tm2427408d1_sc13d.htm (SC 13D) — 86KB
• 0001104659-24-113930.txt ( ) — 87KB

Security and Issuer

Item 1. Security and Issuer This Schedule 13D relates to the shares of common stock, par value $0.001 per share (“ Common Stock ”), of Septerna, Inc., a Delaware corporation (the “ Issuer ”), which has its principal executive offices at 250 East Grand Avenue, South San Francisco, CA 94080.

Identity and Background

Item 2. Identity and Background (a) This Schedule 13D is being filed on behalf of RA Capital Management, L.P. (“ RA Capital ”), Peter Kolchinsky, Rajeev Shah, and RA Capital Healthcare Fund, L.P. (the “ Fund ”). RA Capital, Dr. Kolchinsky, Mr. Shah and the Fund are collectively referred to herein as the “ Reporting Persons .” The agreement among the Reporting Persons to file this Schedule 13D jointly in accordance with Rule 13d-1(k) of the Securities Exchange Act of 1934, as amended, (the “ Act ”), is attached hereto as Exhibit 1. The Reporting Persons’ beneficial shares of Common Stock directly held by the RA Capital Nexus Fund III, L.P (the “ Nexus Fund III ”). RA Capital Healthcare Fund GP, LLC is the general partner of the Fund and RA Capital Nexus Fund III GP, LLC is the general partner of the Nexus Fund III. The general partner of RA Capital is RA Capital Management GP, LLC, of which Dr. Kolchinsky and Mr. Shah are the controlling persons. RA Capital serves as investment adviser for each of the Fund and the Nexus Fund III and may be deemed a beneficial owner, for purposes of Section 13(d) of the Act, of any securities of the Issuer held by the Fund or the Nexus Fund III. Each of the Fund and the Nexus Fund III has delegated to RA Capital the sole power to vote and the sole power to dispose of all securities held in its portfolio, including the shares of the Issuer’s Common Stock reported herein. Because each of the Fund and the Nexus Fund III has divested itself of voting and investment power over the reported securities it holds and may not revoke that delegation on less than 61 days’ notice, each of the Fund and the Nexus Fund III disclaims beneficial ownership of the securities it holds for purposes of Section 13(d) of the Act and therefo

Source and Amount of Funds or Other Consideration

Item 3. Source and Amount of Funds or Other Consideration Prior to the Issuer’s initial public offering (the “ IPO ”), the Fund purchased 14,598,896 shares of Series B Convertible Preferred Stock and the Nexus Fund III purchased 9,732,596 shares of Series B Convertible Preferred Stock. The aggregate purchase price of the foregoing was $29,999,999.72. CUSIP No. 81734D 104 On October 18, 2024, the Issuer effected a one-for-8.6103 reverse stock split of its common stock and a corresponding adjustment to the conversion ratio of its convertible preferred stock (the “ Reverse Stock Split ”). In connection with the closing of the IPO, on October 28, 2024, the Preferred Stock discussed above automatically converted into shares of Common Stock. The Fund and the Nexus Fund III also purchased 3,828,400 and 341,600 shares of Common Stock, respectively, from the underwriters of the IPO at the IPO price of $18.00 per share, for an aggregate purchase price of $75,060,000. All purchases of the securities described herein were for cash and were funded by working capital of the Fund and the Nexus Fund III, as applicable.

Purpose of Transaction

Item 4. Purpose of Transaction The Reporting Persons acquired the Common Stock reported herein for investment purposes and not with an intent, purpose or effect of changing control of the Issuer. Although the Reporting Persons currently have no plan or proposal to acquire any additional Issuer securities or to dispose of any of the Issuer securities reported herein, the Reporting Persons may, from time to time, acquire additional equity securities or debt securities of the Issuer, which debt securities may be convertible or non-convertible, secured or unsecured, and could involve the monetization of potential revenue streams deriving from development-stage or commercial programs of the Issuer, or dispose of Issuer securities they beneficially own, on the open market or in private transactions or otherwise (including by means of 10b5-1 programs), consistent with their investment purposes and in amounts, on such terms and at such times as to be determined by the Reporting Persons based upon a number of factors, including, without limitation, their ongoing assessment of the Issuer’s business prospects, the availability of Issuer securities at prices that would make the purchase or sale of such securities desirable, prevailing market conditions, the availability of other investment opportunities, and/or other considerations. In addition, consistent with their investment purpose, the Reporting Persons may engage in communications with persons associated with the Issuer, including stockholders of the Issuer, officers of the Issuer, members of the board of directors of the Issuer, and/or or other third parties, to discuss matters regarding the Issuer, including but not limited to its operations, strategic direction, governance or capitalization, and potential business combinations or dispositions involving the Issuer or certain of its businesses. Jake Simson, a Partner at RA Capital, currently serves as a director of the Issuer and therefore will engage in regular

Interest in Securities of the Issuer

Item 5. Interest in Securities of the Issuer (a) The information set forth in rows 11 and 13 of the cover pages to this Schedule 13D is incorporated by reference. The percentage set forth in row 13 is based upon 44,402,794 shares of Common Stock outstanding as of October 30, 2024 upon the closing of the Issuer’s public offering, as reported in the prospectus, dated October 24, 2024, filed with the SEC on October 25, 2024, after giving effect to an additional 2,400,000 shares issued and sold pursuant to the underwriters’ option. (b) The information set forth in rows 7 through 10 of the cover pages to this Schedule 13D and Item 2 above is incorporated by reference. (c) Except as described herein, the Reporting Persons have not effected any transactions in the Common Stock during the past sixty days. CUSIP No. 81734D 104 (d) No person (other than the Reporting Persons) is known to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, the shares of Common Stock subject to this Schedule 13D. (e) Not applicable.

Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer

Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer Lock-up Agreements The holders of substantially all of the Issuer’s pre-IPO capital stock, including the Fund and the Nexus Fund III, and each of the Issuer’s directors, entered into lock-up agreements (the “ Lock-Up Agreements ”) with the representatives of the underwriters of the Issuer’s IPO. Pursuant to the Lock-Up Agreements, none of the Fund and the Nexus Fund III is permitted, with limited exceptions, for a period of 180 days from October 24, 2024, to offer, sell, or otherwise transfer or dispose of any of the Issuer’s securities, without the written consent of J.P. Morgan Securities LLC. The description of the Lock-Up Agreements contained in this Item 6 is qualified in its entirety by reference to the full text of the form of Lock-up Agreement filed as Exhibit 2 to this Schedule 13D and incorporated by reference herein. Investors’ Rights Agreement On June 28, 2023, the Issuer, the Fund, the Nexus Fund III and certain other parties entered into an amended and restated investors’ rights agreement (the “ Investors’ Rights Agreement ”). The Investors’ Rights Agreement provides the Fund, the Nexus Fund III and other parties thereto with certain demand registration rights, including shelf registration rights, in respect of the shares of Common Stock issued to it upon conversion of the convertible preferred stock, subject to certain conditions. In addition, in the event that the Issuer registers additional shares of Common Stock for its own account or for the account of other holders of its securities, the Fund, the Nexus Fund III and certain other parties are entitled to include their shares in the registration, subject to certain limitations. The registration rights will terminate on the earliest to occur of (a) the closing of certain liquidation events, (b) the fifth anniversary

Material to be Filed as Exhibits

Item 7. Material to be Filed as Exhibits Exhibit 1 Joint Filing Agreement Exhibit 2 Form of Lock-up Agreement (incorporated by reference to Exhibit A to the Form of Underwriting Agreement filed as Exhibit 1.1 to the Issuer’s Registration Statement on Form S-1, as amended (Registration No. 333 282469), filed with the SEC on October 21, 2024). Exhibit 3 Amended and Restated Investors’ Rights Agreement among the Registrant and certain of its stockholders, dated June 28, 2023 (incorporated by reference to Exhibit 4.1 to the Issuer’s Registration Statement on Form S-1, as amended (Registration No. 333 282469), filed with the SEC on October 10, 2024). CUSIP No. 81734D 104

SIGNATURES

SIGNATURES After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct. Dated: November 4, 2024 RA CAPITAL MANAGEMENT, L.P. By: /s/ Peter Kolchinsky Name: Peter Kolchinsky Title: Authorized Signatory PETER KOLCHINSKY /s/ Peter Kolchinsky RAJEEV SHAH /s/ Rajeev Shah RA CAPITAL HEALTHCARE FUND, L.P. By: RA Capital Healthcare Fund GP, LLC Its: General Partner By: /s/ Peter Kolchinsky Name: Peter Kolchinsky Title: Manager CUSIP No. 81734D 104 EXHIBIT 1 JOINT FILING AGREEMENT This Joint Filing Agreement, dated as of November 4, 2024, is by and among RA Capital Management, L.P., Peter Kolchinsky, Rajeev Shah, and RA Capital Healthcare Fund, L.P. (the foregoing are collectively referred to herein as the “ Filers ”). Each of the Filers may be required to file with the United States Securities and Exchange Commission a statement on Schedule 13G and/or 13D with respect to Common Stock, par value $0.001 per share of Septerna, Inc. beneficially owned by them from time to time. Pursuant to and in accordance with Rule 13(d)(1)(k) promulgated under the Securities Exchange Act of 1934, as amended, the Filers hereby agree to file a single statement on Schedule 13G and/or 13D (and any amendments thereto) on behalf of each of such parties, and hereby further agree to file this Joint Filing Agreement as an exhibit to such statement, as required by such rule. This Joint Filing Agreement may be terminated by any of the Filers upon one week’s prior written notice or such lesser period of notice as the Filers may mutually agree. Executed and delivered as of the date first above written. RA CAPITAL MANAGEMENT, L.P. By: /s/ Peter Kolchinsky Name: Peter Kolchinsky Title: Authorized Signatory PETER KOLCHINSKY /s/ Peter Kolchinsky RAJEEV SHAH /s/ Rajeev Shah RA CAPITAL HEALTHCARE FUND, L.P. By: RA Capital Heal

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View this SC 13D filing on SEC EDGAR