We have previously entered into an Open Market Sale AgreementSM(the “sales agreement”) with Jefferies LLC (“Jefferies”) relating to the shares of our common stock,par value $0.001 per share (“common stock”), offered by this prospectus supplement. In accordance with the terms of the sales agreement, we may offer and sell ourcommon stock having an aggregate sales price of up to $75,000,000 from time to time through Jefferies acting as our sales agent. As of the date of this prospectussupplement, no sales have been made by the Company pursuant to the sales agreement. An affiliate (the “Covered Stockholder”) of Invus, L.P., our largest stockholder, has the right, pursuant to our Fifth Amended and Restated Certificate of Incorporation(the “Certificate of Incorporation”), in connection with any sales made pursuant to the sales agreement to concurrently purchase a number of shares of our common stocksufficient to maintain its proportionate ownership interest in us after giving effect to such sales; provided, however, that in any given year, the Covered Stockholder maynot exercise such right unless and until we have otherwise issued, in the aggregate, common stock pursuant to sales under the sales agreement in an amount greater thantwo percent of our issued and outstanding common stock measured as of December31 of the preceding year. Should the Covered Stockholder choose to exercise suchright, we expect that any shares sold to the Covered Stockholder pursuant thereto would occur in a concurrent private placement exempt from the registrationrequirements of the Securities Act of 1933, as amended (the “Securities Act”), at the same price as the price to the public for the corresponding sales made under the salesagreement. Our common stock is listed on the Nasdaq Global Select Market under the symbol “LXRX.” The last reported sale price of our common stock on the Nasdaq GlobalSelect Market on November 5, 2025 was $1.38 per share. Sales of common stock, if any, under this prospectus supplement will be made in sales deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgatedunder the Securities Act. Jefferies is not required to sell any specific amount of securities but will act as our sales agent using commercially reasonable efforts consistentwith its normal trading and sales practices on mutually agreed terms between Jefferies and us. There is no arrangement for funds to be received in any escrow, trust orsimilar arrangement. The compensation to Jefferies for sales of common stock sold pursuant to the sales agreement will be at an amount equal to 3.0% of the gross proceeds of any shares ofcommon stock sold under the sales agreement. The net proceeds from any sales under this prospectus supplement will be used as described under “Use of Proceeds” inthis prospectus supplement. In connection with the sale of the common stock on our behalf, Jefferies will be deemed to be “underwriter” within the meaning of theSecurities Act, and the compensation of Jefferies will be deemed to be underwriting commissions or discounts. We have also agreed to provide indemnification andcontribution to Jefferies with respect to certain liabilities, including liabilities under the Securities Act or the Securities Exchange Act of 1934, as amended (the“Exchange Act”). See “Plan of Distribution” onpageS-9of this prospectus supplement for additional information concerning the compensation to be paid to Jefferies. Investing in our common stock involves risks. You should carefully consider the risks relating to investing in our common stockand each of the risk factors described under “Risk Factors” onpageS-5of this prospectus supplement, as well as those containedin any accompanying prospectus and any related free writing prospectus or prospectus supplement we prepare or authorize inconnection with this offering, and in the other documents that are incorporated by reference into this prospectus supplement oraccompanying prospectus, before you make an investment in our securities. Neither the Securities and Exchange Commission (the “SEC”) nor any state securities commission has approved or disapproved of these securities ordetermined if this prospectus supplement or the accompanying base prospectus is truthful or complete. Any representation to the contrary is a criminal offense. Jefferies The date of this prospectus supplement is November 6, 2025 Table of Contents TABLE OF CONTENTS IMPORTANT NOTICE ABOUT INFORMATION IN THIS PROSPECTUS SUPPLEMENT AND THE ACCOMPANYING BASEPROSPECTUSPROSPECTUS SUPPLEMENT SUMMARYRISK FACTORSCAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTSUSE OF PROCEEDSPLAN OF DISTRIBUTIONLEGAL MATTERSEXPERTSINCORPORATION OF CERTAIN INFORMATION BY REFERENCEWHERE YOU CAN FIND MORE INFORMATION About This ProspectusLexicon Pharmaceuticals, Inc.Risk FactorsDescription of Capital StockDescription of Debt SecuritiesDescription of WarrantsDescription of RightsDescription of UnitsLegal Ownership of Securiti