Cy5-PEG4-acid
Cat No.: BP-501982
Purity: 96%
4.5 
Cy5-PEG4-acid is a heterobifunctional PEG-based linker that combines a Cy5 fluorophore with a short, flexible polyethylene glycol spacer terminating in a carboxylic acid. Structurally, it provides a hydrophilic, conformationally mobile chain that can reduce steric interference between a targeting ligand and an E3-recruiting moiety in PROTAC constructs, while the terminal acid enables straightforward conjugation through amide-bond formation or related coupling chemistries. In targeted protein degradation research, such linkers are commonly used to tune effective distance and local presentation of functional groups, improving the likelihood of productive ternary complex formation and facilitating systematic structure–activity studies. The Cy5 label further supports sensitive fluorescence-based tracking of conjugation efficiency, cellular uptake, and subcellular localization of PROTAC intermediates, aiding experimental optimization. Overall, this reagent is valuable for designing and validating linker architectures in degradation workflows where both performance and analytical traceability are required.
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* For research and manufacturing use only. Not for human or clinical use.
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Cy5-PEG4-acid is a PEG-based linker bearing a terminal carboxylic acid functionality and a near-infrared Cy5 fluorophore handle, enabling the construction of well-defined PROTAC conjugates with trackable localization. Its ether-rich PEG segment provides conformational flexibility and improved aqueous compatibility, which can support productive ternary complex formation. The terminal acid enables robust amide coupling to install targeting or E3-ligand motifs, facilitating systematic structure–activity studies. Detailed structural and synthetic considerations are provided below.
Structure: Cy5-PEG4-acid comprises a polymethylene ether (PEG) chain connected to a Cy5 chromophore and terminated with a carboxylic acid. The molecule contains aromatic and polymethoxy ether linkages, with an acid group capable of forming stable amide bonds. Overall, it exhibits amphiphilic character and strong water-phase solubility relative to purely hydrophobic linkers.
Reactivity: The terminal carboxylic acid is suited for standard carboxyl-to-amide coupling used in PROTAC synthesis. Typical approaches employ amine-bearing ligands under activating conditions such as carbodiimide/uroniu m-type reagents, often with base and an inert atmosphere to minimize side reactions. Polar aprotic solvents and controlled pH are commonly used to preserve functional group integrity, while the PEG ether segment generally remains stable under coupling conditions.
* 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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