N-(m-PEG4)-N'-(amino-PEG3)-Cy5
CAS No.: 2107272-96-6
Cat No.: BP-501694
Purity: 97%
4.5 
N-(m-PEG4)-N'-(amino-PEG3)-Cy5 is a heterobifunctional, PEG-based linker conjugated to the near-infrared cyanine dye Cy5. Structurally, it comprises a Cy5 fluorophore attached through a branched polyethylene glycol architecture containing an m-PEG4 segment and an amino-PEG3 segment, providing a flexible, hydrophilic spacer system with an accessible terminal amine for subsequent coupling chemistry. In PROTAC and targeted protein degradation workflows, such PEG spacers are used to tune solubility, reduce nonspecific interactions, and control the effective distance and orientation between the ligand moieties and the degradation-mediating scaffold. The terminal amine enables attachment to activated carboxylates, isothiocyanates, or other electrophiles used to assemble PROTAC constructs, while the Cy5 tag permits fluorescence-based tracking of conjugate synthesis, cellular uptake, and degradation-associated localization. This product is valuable for researchers developing imaging-compatible PROTACs and for mechanistic studies where quantitative monitoring of linker integrity and conjugate behavior is required.
Structure of 2107272-96-6
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This linker is designed to support modular PROTAC assembly by providing orthogonal, bioconjugation-ready functionality alongside a Cy5 reporting handle. Its polyethylene glycol–rich architecture promotes aqueous compatibility and flexible spacing for modular conjugation workflows. The molecule enables efficient attachment of ligands through amine-reactive coupling strategies, and the included fluorophore facilitates tracking of synthesis and degradation workflows. Detailed structural and reactivity considerations are provided below.
Structure: The linker contains an m-PEG4 segment and an amino-PEG3 segment attached to the Cy5 scaffold through cyanine nitrogen substitution, with a terminal primary amine on the amino-PEG3 side chain. The Cy5 chromophore contributes an extended conjugated system for fluorescence, while ether linkages enhance hydrophilicity and conformational mobility.
Reactivity: Suitable PROTAC construction typically employs amide bond formation or amine-reactive coupling routes, depending on the functional groups presented on the partner ligands. Standard conditions use aqueous or mixed aqueous/organic solvents with mild bases to drive acylation, while maintaining PEG integrity and Cy5 fluorescence. Mechanistically, nucleophilic acyl substitution or carbodiimide-mediated coupling can be used, with appropriate coupling reagents and controlled pH to minimize side reactions and preserve labeling efficiency.
* 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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