BnO-PEG1-CH2CO2tBu
CAS No.: 1309451-06-6
Cat No.: BP-501403
4.5 
BnO-PEG1-CH2CO2tBu is a short, monofunctional polyethylene glycol–based PROTAC linker fragment featuring a benzyl ether (BnO) at one terminus and a protected carboxylate as a tert-butyl ester at the other, connected through a single ethylene glycol unit and a methylene spacer. In PROTAC architectures, PEG linkers are widely used to provide conformational flexibility and to reduce steric interference between the ligand-binding moieties, thereby improving the effective spatial alignment required for formation of the ternary complex with an E3 ligase and the target protein. The terminal benzyl ether and ester-protected carboxyl group enable synthetic conjugation strategies: the benzyl ether can be selectively removed or functionalized, while the carboxylate can be deprotected to introduce an attachment handle for amide or ester coupling. This reagent is valuable for constructing compact, flexible degraders where controlled linker length and orthogonal functional group manipulation are critical for optimizing degradation potency and selectivity.
Structure of 1309451-06-6
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This PROTAC linker, BnO-PEG1-CH2CO2tBu, is designed to provide a flexible polyethylene glycol spacer that can improve effective proximity between a ligand and the recruited E3 ligase-binding moiety. Its ether-containing, PEG-based architecture supports favorable linker solvation and conformational adaptability, which are commonly leveraged to tune degradation efficiency. The following sections describe its structural features and practical considerations for incorporating the linker into PROTAC constructs.
Structure: The molecule contains a benzyl-protected oxygen functionality and a short PEG segment, linked to a methylene spacer bearing a protected carboxylate. It features ether linkages and an ester (tert-butyl ester) motif, combining hydrophilicity with a stable, masked acid for controlled downstream functionalization.
Reactivity: The tert-butyl ester is typically compatible with mild conditions for ester deprotection, enabling conversion to a carboxylic acid for coupling reactions. For PROTAC assembly, the generated acid can be used in standard amide or ester-forming strategies (e.g., via activated carboxyl intermediates). Deprotection is commonly achieved under acidic conditions, while coupling is generally performed using appropriate coupling reagents and compatible solvents to preserve sensitive functional groups.
* 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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