Benzyloxy carbonyl-PEG3-C2-acid

Name: Benzyloxy carbonyl-PEG3-C2-acid
Brand: BOC Sciences
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CAS No.: 2100306-73-6

Cat No.: BP-501295 4.5

Benzyloxy carbonyl-PEG3-C2-acid is a polyethylene glycol (PEG)–based PROTAC linker featuring a benzyl ester-protected carboxylic acid terminus and a free carboxylic acid at the opposite end. The PEG3 segment provides a hydrophilic, flexible spacer that can reduce steric interference between the target-binding ligand and the E3 ligase–recruiting moiety, while the free carboxylic acid enables straightforward coupling and the benzyl ester can be removed by hydrogenolysis to reveal a second acid to attach the linker to activated functional groups on partner components. In PROTAC design, such linkers are used to tune the effective distance and relative orientation of the two binding domains, thereby supporting formation of a productive ternary complex and efficient ubiquitination-driven degradation. This linker is valuable for constructing modular degraders where controlled linker chemistry and solubility properties are critical for systematic structure–activity studies, optimization of cellular activity, and improving experimental handling in aqueous assay conditions.

Structure of 2100306-73-6

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PROTAC Linker

Molecular Formula

C₁₇H₂₄O₇

Molecular Weight

340.37

* For research and manufacturing use only. Not for human or clinical use.

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Please store the product under the recommended conditions in the Certificate of Analysis.

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IUPACName

3-[2-[2-(3-oxo-3-phenylmethoxypropoxy)ethoxy]ethoxy]propanoic acid

InChI Key

XTVQHJQMAHLFTN-UHFFFAOYSA-N

InChI

InChI=1S/C17H24O7/c18-16(19)6-8-21-10-12-23-13-11-22-9-7-17(20)24-14-15-4-2-1-3-5-15/h1-5H,6-14H2,(H,18,19)

SMILES

C1=CC=C(C=C1)COC(=O)CCOCCOCCOCCC(=O)O

1. 1,5-ethano-2,3,4,5-tetrahydro-1H-3-benzazepines

L A Walter, W K Chang J Med Chem. 1975 Feb;18(2):206-8.doi: 10.1021/jm00236a022.

1,5-Ethano-2,3,4,5-tetrahydro-1H-3-benzazepine, from the LiA1H4 reduction of 2-benzyloxy-1,5-ethano-4-oxo-2,3,4,5-tetrahydro-1H-3-benzazepine, was converted to N-alkyl, aralkyl, cycloalkyl, and alkenyl derivatives which were inactive as morphine type analgetics in mice. The LiA1H4 reduction of 2-benzyloxy-1,5-etheno-4-oxo-2,3,4,5-tetrahydro-1H-3-benzazepine gave unstable products from which only the skeletally rearranged dihydro- and tetrahydrobenzo[e]isoindolines, were isolated.

2. Enzymes responsible for the conversion of N alpha-[(Benzyloxy)carbonyl]-D-lysine to N alpha-[(Benzyloxy)carbonyl]-D-aminoadipic acid by Rhodococcus sp. AIU Z-35-1

Kimiyasu Isobe, Nahoko Fukuda, Shouko Nagasawa, Kaoru Saitou Chem Biodivers. 2010 Jun;7(6):1549-54.doi: 10.1002/cbdv.200900251.

The enzymes responsible for the conversion of N(alpha)-[(benzyloxy)carbonyl]-D-lysine (N(alpha)-Z-D-lysine) to N(alpha)-Z-D-aminoadipic acid (N(alpha)-Z-D-AAA) by Rhodococcus sp. AIU Z-35-1 were identified. N(alpha)-Z-D-Lysine was first converted to N(alpha)-Z-D-aminoadipic delta-semialdehyde (N(alpha)-Z-D-AASA) by D-specific amino acid deaminase, whereas N(alpha)-Z-L-lysine was converted to N(alpha)-Z-L-AASA by L-specific amino acid oxidase. The resulting N(alpha)-Z-D-AASA was then converted to N(alpha)-Z-D-AAA by the same aldehyde dehydrogenase that is responsible for N(alpha)-Z-L-AASA oxidation. The product amount of the D-specific amino acid deaminase reached the maximum at one day of cultivation in the L-lysine medium. The aldehyde dehydrogenase reached the maximum at three days of cultivation.

This Benzyloxy carbonyl-PEG3-C2-acid linker is designed for modular assembly of PROTACs, providing a flexible polyethylene glycol spacer that can tune linker length, solubility, and the spatial presentation of binding warheads. Its protected carboxylic acid functionality supports reliable conjugation strategies, enabling systematic optimization of targeted protein degradation constructs. Detailed structural and synthetic considerations are provided below to guide experimental PROTAC preparation.

Structure: The linker incorporates an ether-containing PEG segment that imparts conformational flexibility and improved aqueous compatibility. A benzyloxy carbonyl protecting group and a terminal carboxylic acid are present, enabling orthogonal functional-group handling. Key features include ester/amide-reactive carbonyl functionality and stable C–O and C–C connectivity.

Reactivity: Suitable PROTAC synthesis commonly uses carboxylic-acid activation followed by coupling to an amine or other nucleophile-bearing warhead, typically via carbodiimide or related activation chemistries under mild base conditions. The benzyloxy carbonyl group can be removed under hydrogenolysis to reveal the acid when orthogonal steps are required. Solvent systems such as polar aprotic media are frequently employed to support efficient coupling and minimize side reactions.

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* 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