Benzyl-PEG2-CH2-Boc
CAS No.: 1643957-26-9
Cat No.: BP-501392
4.5 
Benzyl-PEG2-CH2-Boc is a bifunctional PEG-based linker building block designed for PROTAC and related targeted protein degradation constructs. Structurally, it comprises a benzyl ether-protected hydroxyl terminus connected through a PEG2 spacer to a tert-butyl ester-protected carboxylic acid terminus, providing both solubility-enhancing flexibility and a protected reactive site for subsequent coupling. In PROTAC design, PEG linkers are widely used to tune the spatial relationship between the ligand that recruits the E3 ligase and the substrate-binding moiety, helping to reduce steric clashes and improve productive ternary complex formation. The benzyl ether and tert-butyl ester provide orthogonal protection; hydrogenolysis can reveal the alcohol and acid treatment can reveal the carboxylic acid, while the PEG segment contributes conformational mobility and aqueous compatibility, allowing researchers to introduce the linker into larger degraders under conditions that preserve other reactive functionalities. This makes Benzyl-PEG2-CH2-Boc a practical, modular component for generating and optimizing linker length and geometry in targeted degradation experiments.
Structure of 1643957-26-9
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Benzyl-PEG2-CH2-Boc is a PEG-based, bifunctional PROTAC linker building block designed to connect targeting ligands while providing beneficial chain flexibility and solubility. Its tert-butyl ester-protected carboxyl functionality enables controlled stepwise synthesis, supporting modular assembly of degraders with minimized side reactions. The benzyl group and PEG spacer help tune spatial presentation of the warhead and recruiter moieties, which is critical for efficient ternary complex formation. Detailed structural and reactivity considerations are provided below.
Structure: The linker contains a short ethylene glycol (PEG) segment that imparts hydrophilicity and conformational flexibility, flanked by benzyl and methylene linkages. A tert-butyl ester protects a carboxylic acid, while the benzyl end is a benzyl ether that serves as a protected alcohol.
Reactivity: The tert-butyl ester is typically removed under mild acid conditions to reveal the corresponding carboxylic acid for subsequent coupling. PROTAC construction commonly proceeds via amide or carbamate bond formation using activated carboxylic acid derivatives (such as NHS esters or acid chlorides) or via carbamate-forming reagents, enabling attachment to ligand handles. The benzyl ether can be deprotected separately when a free alcohol is required, with solvent systems chosen to maintain solubility of PEG-containing intermediates.
* 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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