Filing Details

Item 3 of Schedule 13D is supplemented and amended, as the case may be, as follows: The Reporting Persons may in the ordinary course of business hold securities in margin accounts maintained for the Funds with prime brokers, which extend margin credit as and when required, subject to applicable margin regulations, stock exchange rules and such firms' credit policies. Positions in securities may be pledged as collateral security for the repayment of debit balances in such accounts.

Item 4 of Schedule 13D is supplemented and amended, as the case may be, as follows: The disclosure in Item 3 and in Item 6 below is incorporated herein by reference. On June 26, 2025, the Issuer entered into an underwriting agreement (the "Underwriting Agreement") with Morgan Stanley & Co. LLC, J.P. Morgan Securities LLC, Jefferies LLC, TD Securities (USA) LLC and Leerink Partners LLC (the "Underwriters"), related to the public offering (the "Offering") of 5,044,500 shares of common stock of the Issuer ("Common Stock") at a price to the public of $44.00 per share and prefunded warrants to purchase 655,500 shares of Common Stock (the "Prefunded Warrants") at a price to the public of $43.9999 per warrant. The Prefunded Warrants are exercisable at any time on a 1-for-1 basis at an exercise price of $0.0001 per share into Common Stock, subject to the limitations discussed below and have no expiration date. In addition, the Issuer granted the Underwriters an option exercisable for 30 days from the date of the Underwriting Agreement to purchase, at the public offering price less any underwriting discounts and commissions, up to an additional 855,000 shares of Common Stock to cover overallotments, if any ("Underwriters Option"). The Offering closed on June 30, 2025. Pursuant to the Offering, 667 and Life Sciences purchased 55,191 and 600,309 shares of Common Stock, respectively, at the offering price of $44.00 per share, totaling 655,500 shares of Common Stock in the aggregate and 55,191 and 600,309 Prefunded Warrants, respectively, at the offering price of $43.9999 per warrant, totaling 655,500 Prefunded Warrants in the aggregate. Each of 667 and Life Sciences purchased the Common Stock and Prefunded Warrants with their working capital. The Funds hold securities of the Issuer for investment purposes. The Reporting Persons or their affiliates may purchase additional securities or dispose of securities in varying amounts and at varying times depending upon the Reporting Persons' continuing assessments of pertinent factors, including the availability of shares of Common Stock or other securities for purchase at particular price levels, the business prospects of the Issuer, other business investment opportunities, economic conditions, stock market conditions, money market conditions, the attitudes and actions of the board of directors of the Issuer (the "Board") and management of the Issuer, the availability and nature of opportunities to dispose of securities of the Issuer and other plans and requirements of the particular entities. The Reporting Persons may discuss items of mutual interest with the Issuer's management, other members of the Board and other investors, which could include items in subparagraphs (a) through (j) of Item 4 Schedule 13D. Depending upon their assessments of the above factors, the Reporting Persons or their affiliates may change their present intentions as stated above and they may assess whether to make suggestions to the management of the Issuer regarding financing, and whether to acquire additional securities of the Issuer, including shares of Common Stock (by means of open market purchases, privately negotiated purchases, exercise of Prefunded Warrants (as defined in Item 4), or otherwise), exercise of some or all of the Stock Options (as defined below) to purchase Common Stock of the Issuer or to dispose of some or all of the securities of the Issuer, including shares of Common Stock, under their control. Except as otherwise disclosed herein, at the present time, the Reporting Persons do not have any plans or proposals with respect to any extraordinary corporate transaction involving the Issuer including, without limitation, those matters described in subparagraphs (a) through (j) of Item 4 of Schedule 13D.

The disclosure in Item 4 is incorporated by reference herein. Item 5 of Schedule 13D is supplemented and amended, as the case may be, as follows: (a) and (b) Items 7 through 11 and 13 of each of the cover pages of this Amendment No. 2 are incorporated herein by reference. The percentage of beneficial ownership for each of the Reporting Persons reported herein is based on 70,157,214 shares of Common Stock outstanding as of June 30, 2025 as reported in the Issuer's Prospectus filed with the Securities and Exchange Commission ("SEC") on June 27, 2025 plus 15,111 vested non-qualified options exercisable for 15,111 shares of Common Stock ("Stock Options") received by Felix J. Baker as compensation for his service on the Board. Set forth below in Exhibit 99.1 is the aggregate number of shares of Common Stock directly held by each of the Funds, which may be deemed to be indirectly beneficially owned by the Reporting Persons, as well as shares of Common Stock that may be acquired upon exercise of Prefunded Warrants, subject to the Beneficial Ownership Limitation (as defined below).

The direct holdings of the Funds are detailed in Exhibit 99.1. The Prefunded Warrants are only exercisable to the extent that after giving effect to such exercise the holders thereof, together with their affiliates and any members of a Section 13(d) group with such holders, would beneficially own, for purposes of Rule 13d-3 under the Securities Exchange Act of 1934, as amended (the "Exchange Act"), no more than 4.99% of the outstanding shares of Common Stock (the "Beneficial Ownership Limitation"). By written notice to the Issuer, the Funds may from time to time increase or decrease the Beneficial Ownership Limitation applicable to that Fund to any other percentage not in excess of 19.99%. Any such increase will not be effective until the 61st day after such notice is delivered to the Issuer. As a result of this restriction, the number of shares that may be issued upon exercise of the Prefunded Warrants by the above holders may change depending upon changes in the number of outstanding shares of Common Stock. The Prefunded Warrants are not currently exercisable due to the effect of the Beneficial Ownership Limitation. The foregoing description of the Prefunded Warrants is qualified in its entirety by reference to the full texts of the Form of Pre-Funded Warrant to Purchase Common Stock, which is incorporated by reference as Exhibit 99.2, and which is incorporated herein by reference. In conjunction with his service on the Board, Felix J. Baker holds 32,000 Stock Options at an exercise price of $40.20 per share which vest in 36 equal monthly installments over a three-year period commencing on March 28, 2024 and expire on March 27, 2034, of which 15,111 are vested as of sixty days following the date of this filing. On June 25, 2025, Felix J. Baker was granted 16,000 Stock Options at an exercise price of $46.47 that vest on the earlier of the first anniversary of the grant date or the date of the 2026 annual meeting of stockholders of the Issuer. Felix J. Baker also serves on the Compensation Committee of the Board. The policies of the Funds and the Adviser do not permit managing members of the Adviser GP to receive compensation for serving as a director of the Issuer, and the Funds are instead entitled to the pecuniary interest in any compensation received for Felix J. Baker's service on the Board. The Adviser GP, and Felix J. Baker and Julian C. Baker as managing members of the Adviser GP, may be deemed to have the power to vote or direct the vote of and the power to dispose or direct the disposition of the Stock Options held by Felix J. Baker disclosed herein and in previous amendments to this Schedule 13D. The Adviser GP, Felix J. Baker and Julian C. Baker as managing members of the Adviser GP, and the Adviser may be deemed to be beneficial owners of securities of the Issuer directly held by the Funds.

(c) Except as disclosed herein the Reporting Persons or their affiliates have not effected any transactions in securities of the Issuer during the past 60 days.

(d) Certain securities of the Issuer are held directly by 667, a limited partnership the sole general partner of which is Baker Biotech Capital, L.P., a limited partnership the sole general partner of which is Baker Biotech Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Biotech Capital (GP), LLC. Certain securities of the Issuer are held directly by Life Sciences, a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital, L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Brothers Life Sciences Capital (GP), LLC.

(e) Not applicable.

Item 6 of Schedule 13D is supplemented and amended, as the case may be, as follows: Prefunded Warrants The disclosure in Item 5 regarding the Prefunded Warrants is incorporated herein by reference. The foregoing description of the Prefunded Warrants is qualified in its entirety by reference to the full text of the form of Pre-Funded Warrant to Purchase Common Stock, which is incorporated by reference as Exhibit 99.2 hereto and is incorporated herein by reference. Registration Rights Agreement On June 26, 2025, the Funds and certain other investors entered into a registration rights agreement (the "Registration Rights Agreement") with the Issuer pursuant to which the Funds are entitled to certain resale registration rights with respect to all securities of the Company (whether equity, debt, or otherwise) and any Common Stock issued or issuable upon the exercise or conversion of any such securities that is now owned or hereafter acquired by the Funds or such other investors (collectively, the "Registrable Securities"). Under the Registration Rights Agreement, as promptly as reasonably practicable following a request by the Funds, the Issuer is obligated to file a resale registration statement on Form S-3, or other appropriate form, covering Registrable Securities held by the Funds (the "Resale Registration Shelf") (provided the Company shall not be obligated to make any such filing until February 28, 2026 (the "Demand Effective Date")), and to use reasonable best efforts to keep the Resale Registration Shelf effective until the earlier of such time that (i) all Registrable Securities covered by the Resale Registration Shelf have been sold or may be sold freely without limitations or restrictions as to volume or manner of sale pursuant to Rule 144 of the Securities Act of 1933, as amended, or (ii) all Registrable Securities covered by the Resale Registration Shelf otherwise cease to be considered Registrable Securities pursuant to the terms of the Registration Rights Agreement. Under the Registration Rights Agreement, the Funds have the right to (i) one underwritten public offering per calendar year, but no more than three underwritten public offerings in total, and (ii) no more than two underwritten public offerings or block trades in any twelve-month period, to effect the sale or distribution of Registrable Securities, subject to specified exceptions, conditions and limitations. The rights of the Funds under the Registration Rights Agreement will continue in effect for up to ten years following the Demand Effective Date. The foregoing description of the Registration Rights Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of the Registration Rights Agreement, which is incorporated by reference as Exhibit 99.3 and is incorporated herein by reference. Director Lock-Up Agreement On June 26, 2025, Felix Baker entered into a Lock-Up Agreement (the "Director Lock-Up Agreement") pursuant to which, subject to specified exceptions, Dr. Baker in his personal capacity agreed, without the prior written consent of the representatives of the Underwriters, not to (1) offer, pledge, sell, contract to sell, sell any option or contract to purchase, purchase any option or contract to sell, grant any option, right or warrant to purchase, lend, or otherwise transfer or dispose of, directly or indirectly, any of his Common Stock or any of his other securities convertible into or exercisable or exchangeable for Common Stock or (2) enter into any swap or other arrangement that transfers to another, in whole or in part, any of the economic consequences of ownership of such Common Stock, in each case for a period beginning on June 26, 2025 and continuing until September 24, 2025. The foregoing description of the Director Lock-Up Agreement is qualified in its entirety by reference to the full text of the form of Director Lock-Up Agreement, which is incorporated by reference as Exhibit 99.4 and is incorporated herein by reference

99.1 Holdings by the Funds in Securities of the Issuer 99.2 Form of Pre-Funded Warrant to Purchase Common Stock (incorporated by reference to Exhibit 4.1 to the Issuer's Current Report on Form 8-K, filed with the SEC on June 27, 2025). 99.3 Registration Rights Agreement, by and among Kymera Therapeutics, Inc., 667, L.P., Baker Brothers Life Sciences, L.P., and certain other investors, dated as of June 26, 2025 (incorporated by reference to Exhibit 10.1 to the Issuer's Current Report on Form 8-K, filed with the SEC on June 27, 2025). 99.4 Form of Lock-Up Agreement (incorporated by reference to Exhibit A to Exhibit 1.1 to the Issuer's Current Report on Form 8-K, filed with the SEC on June 27, 2025).