Azide-PEG2-Ms
CAS No.: 176520-23-3
Cat No.: BP-500814
Purity: 98%
4.5 
Azide-PEG2-Ms is a heterobifunctional PEG-based linker designed for PROTAC and targeted protein degradation workflows, featuring a terminal azide group for bioorthogonal conjugation and a mesylate (Ms) leaving group for efficient nucleophilic substitution. Structurally, it provides a short, flexible ethylene glycol spacer that helps present reactive handles with minimal steric hindrance while maintaining solubility and reducing nonspecific aggregation relative to purely hydrophobic linkers. In PROTAC assembly, the mesylate handle can be displaced by an amine or other nucleophile on a ligand scaffold, enabling rapid attachment to one binding module, while the azide functionality can be retained for subsequent click chemistry to install the second module or to introduce degraders, reporters, or solubilizing groups. This linker is valuable for modular synthesis, allowing researchers to systematically tune connectivity and spatial relationships between the E3 ligase ligand and the target-binding moiety, which can be critical for achieving productive ternary complex formation and degradation potency.
Structure of 176520-23-3
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Azide-PEG2-Ms is a bifunctional PEG-based linker designed for modular PROTAC assembly, enabling efficient conjugation between a ligand bearing an azide handle and a partner that can be functionalized for electrophilic substitution. Its ether-rich PEG segment promotes favorable solubility and linker flexibility, which can improve productive ternary complex formation. The subsequent points describe the structure and the practical reactivity options for constructing PROTACs using this linker.
Structure: The linker contains a short polyethylene glycol backbone with ether linkages, terminating in an azide group and a mesylate leaving group. These heteroatoms provide polarity and conformational flexibility, while the mesylate is an activated sulfonate ester suitable for nucleophilic substitution.
Reactivity: The mesylate reacts under nucleophilic substitution conditions with appropriate nucleophiles to install the linker onto a functionalized ligand or scaffold. Typical approaches use polar aprotic solvents and base-mediated generation of nucleophiles, proceeding via an SN2-type displacement at the mesylate-bearing carbon. The azide handle can be retained for orthogonal “click” conjugation strategies in subsequent PROTAC assembly steps.
* 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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