1-Methanesulfonyl-11-hydroxy-3,6,9-trioxaundecane
CAS No.: 65883-12-7
Cat No.: BP-501335
4.5 
1-Methanesulfonyl-11-hydroxy-3,6,9-trioxaundecane is a heterobifunctional polyethylene glycol–like linker built on a tri-ether (3,6,9-trioxaundecane) scaffold that provides conformational flexibility and aqueous compatibility while presenting a terminal hydroxyl group for further functionalization. The methanesulfonyl substituent acts as an activated sulfonate handle, enabling substitution or coupling reactions under standard organic conditions to install PROTAC “warhead” and “E3 ligase” binding motifs at defined positions. In PROTAC design, such ether-rich linkers help tune the effective distance, relative orientation, and local mobility between the two recruited ligands, which can strongly influence ternary complex formation and degradation efficiency. This linker is therefore valuable for constructing modular targeted protein degradation probes, allowing researchers to systematically vary attachment chemistry while maintaining a hydrophilic, flexible backbone suited to biochemical assays.
Structure of 65883-12-7
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1-Methanesulfonyl-11-hydroxy-3,6,9-trioxaundecane, is a polyethylene-glycol-like, ether-rich chain bearing a terminal hydroxyl and a methanesulfonyl leaving group. Its flexible, hydrophilic architecture supports efficient conjugation chemistry commonly used in PROTAC assembly, enabling controlled attachment of ligands through robust sulfonate-mediated transformations. The following sections describe the structure and practical reactivity considerations for experimental linker incorporation.
Structure: The molecule contains an ether-rich, trioxaundecane backbone with multiple oxygen atoms, providing conformational flexibility and polarity. It features a terminal secondary alcohol and a methanesulfonate (mesylate) functional group, enabling formation of stable covalent linkages via sulfonate chemistry. These features support solubility and predictable coupling behavior.
Reactivity: The methanesulfonate group is designed for nucleophilic substitution under standard sulfonate-activation conditions, where alcohol or amine nucleophiles can displace the mesylate to form new C–O or C–N bonds. Typical approaches use polar aprotic solvents and base or nucleophile systems compatible with ether stability, while maintaining conditions that minimize side reactions such as elimination. The terminal hydroxyl can also serve as a handle for subsequent derivatization in PROTAC linker 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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