4,7,10-Trioxa-1,13-tridecanediamine is a flexible, long-chain diamine featuring three ether linkages within a triethylene-oxide–containing segment, yielding a polar yet conformationally adaptable spacer between two terminal primary amines. This structural motif is well suited for PROTAC linker engineering because ether-rich chains can enhance solubility and help maintain productive relative positioning of the two binding partners by reducing unfavorable hydrophobic effects while allowing entropic freedom. In targeted protein degradation constructs, the terminal amines are commonly used as reactive handles for amide or urea bond formation (or other amine-compatible conjugation chemistries), enabling covalent attachment to ligands that recruit an E3 ligase and a target protein. As a result, this linker supports systematic tuning of linker length, polarity, and flexibility—key parameters that influence ternary complex formation, degradation potency, and selectivity—thereby providing a practical building block for experimental PROTAC optimization.
Structure of 4246-51-9
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4,7,10-Trioxa-1,13-tridecanediamine, provides a flexible, polyether-based scaffold that can be used to connect ligands while maintaining an appropriate spatial relationship for ternary complex formation. Its ether-rich backbone supports solubility and conformational adaptability, which are advantageous in targeted protein degradation workflows. The following sections describe the structure and practical reactivity considerations for PROTAC assembly in detail below.
Structure: The linker is a long-chain diamine featuring a trioxa motif that introduces multiple ether linkages along the backbone. It contains primary amine functionalities capable of forming stable amide or urea derivatives. The ether-rich segment contributes polarity and conformational flexibility, supporting linker-mediated distance control between binding elements.
Reactivity: The primary amines enable straightforward coupling to activated carboxylic acids (for amide formation) or to electrophiles used for urea/amide linkages under standard peptide-coupling strategies. Typical approaches employ carbodiimide or related coupling reagents with an appropriate base, using polar aprotic solvents to maintain reactivity. Mechanistically, nucleophilic acyl substitution or condensation reactions proceed from the amine nucleophile to activated carbonyl intermediates, allowing controlled formation of stable linker–ligand conjugates suitable for PROTAC construction.
* Our calculator is based on the following equation:
Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C1V1 = C2V2
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