5-endo-BCN-pentanoic acid
CAS No.: 2364591-80-8
Cat No.: BP-501543
Purity: 98%
4.5 
5-endo-BCN-pentanoic acid is a bicyclononyne (BCN)–derived strained alkyne linker bearing a pentanoic acid handle, featuring a defined endo cyclooctyne-like geometry that promotes fast, bioorthogonal reactivity. In PROTAC and targeted protein degradation workflows, BCN linkers are commonly used to enable site-specific conjugation to azide-functionalized ligands (e.g., E3 ligase recruiters or targeting moieties) via strain-promoted azide–alkyne cycloaddition, avoiding copper catalysts that can interfere with sensitive biomolecules. The pentanoic acid functionality provides a chemically versatile attachment point for coupling strategies and can be used to tune solubility and linker presentation, which are critical determinants of ternary complex formation and degradation potency. This product is valuable for researchers seeking robust, catalyst-free assembly of PROTAC constructs, enabling modular synthesis and rapid optimization of linker length and connectivity to improve controlled proximity between the recruited protein and the E3 ligase.
Structure of 2364591-80-8
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5-endo-BCN-pentanoic acid is a strained bicyclic cyclooctyne-derived linker designed to enable efficient bioorthogonal conjugation in PROTAC workflows. Its key advantage is the ability to form rapid, selective covalent bonds with appropriate azide or cyclooctyne-compatible partners under mild conditions, supporting modular assembly of targeted protein degraders. The structure and reactivity considerations for constructing PROTACs using this linker are described in detail below.
Structure: The linker contains a strained bicyclo[6.1.0] motif characteristic of BCN derivatives, coupled to a pentanoic acid side chain. It includes an aliphatic carboxylic acid functionality for handle-based coupling, along with rigid, conformationally biased bonds that promote fast cycloaddition.
Reactivity: BCN-based linkers typically participate in strain-promoted azide–alkyne cycloaddition without the need for copper catalysis, following a mechanism driven by ring strain. For PROTAC assembly, the carboxylic acid can be activated for amide or ester bond formation using standard coupling chemistries, then paired with azide-bearing ligands. Suitable solvents are commonly polar aprotic media or buffered aqueous systems, with reaction progress monitored by chromatographic or spectroscopic methods.
* 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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