endo-BCN-PEG3-mal
CAS No.: 2141976-33-0
Cat No.: BP-501696
Purity: >90%
4.5 
Endo-BCN-PEG3-maleimide is a heterobifunctional PEG-based linker designed for PROTAC and targeted protein degradation workflows that require orthogonal conjugation. Structurally, it combines an endo-bicyclononyne (BCN) cyclooctyne handle with a short, three-unit polyethylene glycol spacer and a terminal maleimide group, enabling two-step, bioorthogonal coupling to complementary partners. In PROTAC assembly, the BCN moiety can react with tetrazine-modified ligands via strain-promoted inverse-electron-demand Diels–Alder chemistry, providing rapid and selective attachment under mild conditions, while the maleimide enables thiol–maleimide conjugation to cysteine-bearing peptides, antibody fragments, or engineered protein-binding modules. The PEG3 segment improves solubility and spatial presentation, helping to reduce steric interference between the targeting and E3-ligase or recruiting components. This linker is valuable for constructing modular degraders, facilitating systematic optimization of linker length and attachment chemistry, and supporting reproducible synthesis for mechanistic and cellular degradation studies.
Structure of 2141976-33-0
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This endo-BCN-PEG3-mal linker is designed for efficient, bioorthogonal assembly of PROTAC constructs, leveraging the fast and selective reactivity of bicyclononyne (BCN) toward azide-bearing partners under physiological-compatible conditions. Its PEG-based spacer supports favorable solubility and conformational flexibility, while the maleimide handle enables robust coupling to thiol-functionalized ligands. The following sections describe its structure and practical reactivity considerations for PROTAC synthesis.
Structure: The molecule combines an endo-BCN cyclooctyne core with a PEG spacer and a maleimide electrophile. It contains a strained alkyne suitable for click-type cycloaddition, ether linkages within the PEG chain, and a maleimide ring featuring activated alkene functionality for thiol addition.
Reactivity: PROTAC assembly typically uses BCN–azide cycloaddition for selective conjugation, proceeding via strain-promoted alkyne–azide cycloaddition without the need for copper. The maleimide group reacts with thiols through Michael-type addition, forming stable thioether linkages. Suitable conditions generally employ aqueous buffers compatible with maleimide stability and thiol availability; mild temperatures and controlled pH help minimize side reactions such as maleimide hydrolysis and thiol oxidation.
* 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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