Azido-PEG6-MS
CAS No.: 352439-38-4
Cat No.: BP-500768
4.5 
Azido-PEG6-MS is a heterobifunctional polyethylene glycol linker featuring a terminal azide group and a methanesulfonate (mesylate) leaving group, connected through an approximately six-unit PEG chain. The azide enables bioorthogonal conjugation via copper-catalyzed or strain-promoted azide–alkyne cycloaddition, allowing attachment to alkyne-bearing ligands such as PROTAC warheads or targeting moieties under conditions compatible with many biomolecule formats. The mesylate provides an electrophilic handle for substitution reactions with nucleophiles (e.g., amines or thiols), facilitating the formation of stable covalent bonds to complementary functional groups during PROTAC assembly. In targeted protein degradation workflows, this linker serves as a modular “build-and-connect” element that helps tune linker length, solubility, and effective spatial orientation between the E3 ligase ligand and the recruited target-binding ligand. Its use can improve synthetic flexibility and support systematic structure–activity relationship studies in PROTAC development.
Structure of 352439-38-4
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Azido-PEG6-MS is a PEG-based, azide-functional linker designed for modular PROTAC synthesis, enabling efficient conjugation of targeting ligands to E3-recruiting modules through bioorthogonal azide chemistry. Its flexible polyethylene glycol scaffold supports favorable linker solvation and conformational adaptability, which can improve productive ternary complex formation. The azide handle facilitates reliable attachment strategies under mild conditions, and the subsequent sections below describe the structure and practical reactivity considerations in detail.
Structure: The linker contains an azide functional group attached to a polyethylene glycol chain, providing a flexible, hydrophilic scaffold. Ether linkages within the PEG backbone confer conformational mobility, while the terminal azide enables selective coupling. Overall, it is typically characterized by good solubility in polar organic and aqueous-compatible media.
Reactivity: The azide group is commonly used in PROTAC linker assembly via azide–alkyne cycloaddition or azide-to-amine conversion workflows, depending on the chosen coupling partner. For click-type conjugations, copper(I) catalysis or copper-free strain-promoted approaches are used to minimize side reactions, with polar solvents such as DMF or aqueous buffers. Reaction progress is monitored by standard analytical methods, and purification typically follows established PROTAC intermediate handling practices.
* 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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