Propargyl-PEG3-OCH2-Boc
CAS No.: 888010-02-4
Cat No.: BP-501387
Purity: >95%
4.5 
Propargyl-PEG3-OCH2-Boc is a PEG-based PROTAC linker featuring a propargyl (alkyne) handle for bioorthogonal conjugation and a tert-butyl ester-protected carboxylic acid at the opposite end. Structurally, it comprises a short, flexible polyethylene glycol chain that provides aqueous solubility and spatial separation between the warhead/ligand and the E3-recruiting module, while the ether linkage supports conformational freedom to favor productive ternary-complex formation. In PROTAC design, the alkyne enables reliable attachment to azide-bearing partners via copper-catalyzed azide–alkyne cycloaddition (CuAAC), allowing modular assembly of degraders with defined linker length and attachment geometry. The PEG3 segment helps reduce steric hindrance and can improve the effective presentation of binding motifs, which is critical for efficient ubiquitin–proteasome pathway engagement. This linker is therefore valuable for constructing and optimizing targeted protein degradation probes and for systematically evaluating linker effects on degradation potency and selectivity.
Structure of 888010-02-4
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Propargyl-PEG3-OCH2-Boc is a PEG-based PROTAC linker building block designed to provide controlled spacing and solubility between a warhead and an E3 ligase ligand. Its propargyl handle enables widely used bioorthogonal conjugation strategies, while the tert-butyl ester-protected carboxyl functionality supports orthogonal synthetic sequences. These features make it suitable for constructing targeted protein degradation (PROTAC) architectures where linker flexibility and modular attachment chemistry are critical; the following sections describe its structure and reactivity in detail below.
Structure: The molecule contains a PEG-derived polyether segment that imparts conformational flexibility and improved aqueous compatibility. It also features an alkyne-bearing propargyl group and an ether linkage, along with a tert-butyl ester that masks a carboxylic acid until deprotection. Overall, it behaves as a stable, modular linker suitable for stepwise assembly.
Reactivity: The propargyl group supports alkyne-based conjugation approaches commonly used in PROTAC synthesis, including copper-catalyzed azide–alkyne cycloaddition or related alkyne click chemistries under inert conditions. The tert-butyl ester is typically removed under acid-mediated conditions to reveal the corresponding carboxylic acid for subsequent coupling. Solvent systems are chosen to maintain linker solubility and preserve functional group integrity, and reaction design follows established orthogonal protection/deprotection principles.
* 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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