C-NH-Boc-C-Bis-(C1-PEG1-PFP)
C-NH-Boc-C-Bis-(C1-PEG1-PFP) is a branched trifunctional PROTAC linker building block featuring one Boc-protected amine and two short arms terminating in pentafluorophenyl (PFP) activated esters. The PEG spacers provide aqueous solubility and conformational flexibility, while the PFP groups enable efficient, chemoselective acylation of primary amines on target-binding ligands (e.g., lysine-containing peptides or amine-functionalized small molecules) to form stable amide linkages. In PROTAC design, this scaffold is used to conjugate two components in a controlled geometry, allowing the degrader to position a ligase-recruiting moiety and a target-binding moiety for productive ternary complex formation. Its practical value lies in simplifying linker synthesis, improving handling due to PEG-based solubility, and supporting systematic optimization of spacing and linker chemistry to enhance targeted protein degradation performance.
Structure of 1807521-01-2
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* For research and manufacturing use only. Not for human or clinical use.
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This PROTAC linker is designed to enable efficient, modular assembly of targeted protein degraders by providing a protected amine handle and two PFP-activated ester electrophiles for controlled conjugation. Its architecture supports flexible spacing and improved solubility, while the reactive functional group enables reliable formation of the key covalent linkage to partner ligands. The points below describe the structure and practical reactivity considerations for PROTAC construction.
Structure: The linker contains a Boc-protected amine and a PEG-containing bis-functional motif, incorporating ether linkages that confer conformational flexibility and hydrophilicity. Two pentafluorophenyl (PFP) activated esters support nucleophile-driven acyl substitution. The molecule features amide and carbamate functionalities alongside ether oxygen atoms.
Reactivity: PROTAC synthesis using this linker typically involves deprotection of the Boc group under standard acid-mediated conditions to reveal a nucleophilic amine, followed by coupling to activated electrophiles. Each PFP activated ester reacts with amine-containing ligands by nucleophilic acyl substitution at the ester carbonyl, with pentafluorophenoxide serving as the leaving group. Common approaches use polar aprotic solvents and base or scavenger systems to maintain nucleophile availability and minimize side reactions.
* 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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