endo-BCN-PEG12-acid
Cat No.: BP-501847
4.5 
endo-BCN-PEG12-acid is a BCN (bicyclononyne)–functionalized, carboxy-terminated polyethylene glycol linker designed for bioorthogonal conjugation in targeted protein degradation workflows. Structurally, it comprises a strained cyclooctyne (BCN) handle connected to a PEG chain of defined length and terminated with a terminal carboxylic acid, enabling both aqueous solubility and straightforward coupling to PROTAC-building blocks via amide or ester-forming chemistries. In PROTAC design, the BCN moiety can react selectively with azide-bearing partners through strain-promoted azide–alkyne cycloaddition, providing a robust way to assemble or diversify degraders without requiring copper catalysis. The PEG spacer helps tune effective molarity, reduce steric congestion, and improve the accessibility of the conjugation site, which can be critical when linking warheads and ligands. As a modular linker, it supports systematic structure–activity studies and efficient synthesis of BCN-enabled PROTACs for researchers investigating targeted protein degradation.
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* For research and manufacturing use only. Not for human or clinical use.
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This PROTAC linker, endo-BCN-PEG12-acid, is designed to enable efficient conjugation between targeting ligands and E3-recruiting modules through a PEG-based spacer terminating in a carboxylic acid handle. Its flexible, hydrophilic architecture supports favorable solubility and reduced steric constraints, which can improve productive ternary complex formation. The BCN (bicyclononyne) functionality supports strain-promoted cycloaddition chemistry widely used in PROTAC assembly. Detailed structural and reaction considerations are provided below.
Structure: endo-BCN-PEG12-acid comprises a bicyclononyne core linked to a polyethylene glycol chain, ending with a carboxylic acid. The molecule contains an alkyne-containing strained ring system for bioorthogonal reactivity and ether linkages that impart flexibility, hydrophilicity, and improved aqueous compatibility.
Reactivity: The BCN group undergoes strain-promoted azide–alkyne cycloaddition with azide-bearing partners under mild, catalyst-free conditions typical of bioorthogonal click chemistry. The carboxylic acid terminus enables standard amide or ester coupling to complement ligands using coupling reagents and base in suitable organic solvents or mixed aqueous systems. Reaction performance is generally optimized by maintaining neutral-to-slightly basic pH and minimizing competing nucleophiles.
* 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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