0001193125-11-239145 Sample Contracts

TRIUS THERAPEUTICS, INC., Issuer AND U.S. BANK NATIONAL ASSOCIATION, Trustee INDENTURE Dated as of September 1, 2011 Subordinated Debt Securities
Indenture • September 1st, 2011 • Trius Therapeutics Inc • Pharmaceutical preparations • New York

INDENTURE, dated as of September 1, 2011, among TRIUS THERAPEUTICS, INC., a Delaware corporation (the “Company”), and U.S. BANK NATIONAL ASSOCIATION as trustee (the “Trustee”):

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TRIUS THERAPEUTICS, INC. and , As Warrant Agent FORM OF DEBT SECURITIES WARRANT AGREEMENT Dated As Of
Warrant Agreement • September 1st, 2011 • Trius Therapeutics Inc • Pharmaceutical preparations • New York

DEBT SECURITIES WARRANT AGREEMENT (“Agreement”), dated as of between TRIUS THERAPEUTICS, INC., a Delaware corporation (the “Company”) and , a [corporation] [national banking association] organized and existing under the laws of and having a corporate trust office in , as warrant agent (the “Warrant Agent”).

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TRIUS THERAPEUTICS, INC. and , As Warrant Agent FORM OF PREFERRED STOCK WARRANT AGREEMENT Dated As Of
Preferred Stock Warrant Agreement • September 1st, 2011 • Trius Therapeutics Inc • Pharmaceutical preparations • New York

PREFERRED STOCK WARRANT AGREEMENT (the “Agreement”), dated as of between TRIUS THERAPEUTICS, INC., a Delaware corporation (the “Company”) and , a [corporation] [national banking association] organized and existing under the laws of and having a corporate trust office in , as warrant agent (the “Warrant Agent”).

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TRIUS THERAPEUTICS, INC. and , As Warrant Agent FORM OF COMMON STOCK WARRANT AGREEMENT Dated As Of
Warrant Agreement • September 1st, 2011 • Trius Therapeutics Inc • Pharmaceutical preparations • New York

COMMON STOCK WARRANT AGREEMENT (“Agreement”), dated as of between TRIUS THERAPEUTICS, INC., a Delaware corporation (the “Company”) and , a [corporation] [national banking association] organized and existing under the laws of and having a corporate trust office in , as warrant agent (the “Warrant Agent”).

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