endo-BCN-PEG3-NH2
CAS No.: 1883512-27-3
Cat No.: BP-501695
Purity: >90%
4.5 
Endo-BCN-PEG3-NH2 is a BCN (bicyclononyne)–functionalized, three-unit polyethylene glycol linker bearing a terminal primary amine. Structurally, it combines the strained BCN cyclooctyne core, which reacts rapidly and selectively with azide groups via strain-promoted azide–alkyne cycloaddition, with a short PEG spacer that improves solubility and reduces steric hindrance at the conjugation site. In PROTAC and targeted degradation workflows, this linker serves as a modular “click” handle to connect two molecular components—typically an azide-bearing ligand (e.g., a warhead or targeting moiety) and a BCN-bearing partner—under catalyst-free conditions, enabling efficient assembly of heterobifunctional degraders. The PEG3 length provides a flexible tether that can help maintain productive binding geometries for both target engagement and E3 ligase recruitment. This makes endo-BCN-PEG3-NH2 a practical reagent for constructing and optimizing PROTAC linkages, facilitating rapid synthesis and iterative structure–activity studies.
Structure of 1883512-27-3
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This PROTAC linker, endo-BCN-PEG3-NH2, is designed to provide a bioorthogonal handle for efficient conjugation in targeted protein degradation workflows. Its endo-BCN motif supports rapid strain-promoted cycloaddition chemistry, while the PEG-based spacer improves solubility and presentation of reactive groups. These features can help researchers build stable PROTAC architectures and optimize linker-mediated geometry for productive ternary complex formation. The detailed structure and reactivity considerations are provided below.
Structure: The linker contains an endo-bicyclononyne (BCN) strained-alkyne moiety connected to a short polyethylene glycol (PEG) spacer terminating in a primary amine. It comprises aromatic/alkyne functionalities and ether linkages within the PEG chain, yielding a polar, flexible, and water-compatible scaffold suitable for bioconjugation.
Reactivity: BCN reacts with azide-bearing partners via strain-promoted azide–alkyne cycloaddition (SPAAC) under catalyst-free, mild conditions, typically using aqueous or mixed aqueous buffers compatible with biomolecules. The primary amine enables further coupling to activated carboxylic acids or isothiocyanates through standard amide- or urea-forming chemistries. Reaction progress can be monitored by analytical chromatography or mass spectrometry, following established SPAAC and amine-coupling protocols.
* 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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