N-PEG3-N'-(propargyl-PEG4)-Cy5 is a multifunctional PEG-based linker conjugated to a Cy5 fluorophore and bearing two orthogonal reactive handles: a PEG3 segment terminating in a Cy5-linked amide region and a propargyl group that enables copper-free or copper-catalyzed azide–alkyne cycloaddition for subsequent bioconjugation. The extended PEG chains provide aqueous solubility and conformational flexibility, while the Cy5 label allows sensitive fluorescence tracking of PROTAC-related intermediates, cellular uptake, and degradation kinetics when paired with appropriate target engagement reagents. In targeted protein degradation workflows, such linkers are used to connect or tag other PROTAC components without significantly perturbing binding pharmacophores, thereby facilitating mechanistic studies of ternary complex formation, intracellular trafficking, and linker stability. Its modular PEG architecture and fluorogenic readout make it valuable for optimizing linker length and attachment chemistry in PROTAC design and for validating conjugation efficiency in experimental assays.
Structure of 2107273-06-1
* For research and manufacturing use only. Not for human or clinical use.
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This N-PEG3-N'-(propargyl-PEG4)-Cy5 linker is a PEG-based, bifunctional handle designed to support targeted protein degradation workflows by enabling efficient conjugation between a ligand and a reactive partner. Its flexible, hydrophilic PEG architecture can improve solubility and reduce nonspecific interactions, while the terminal propargyl functionality provides a practical site for click-type coupling. The Cy5 label facilitates tracking and characterization of PROTAC intermediates and final constructs. The structure and reactivity considerations are described in detail below.
Structure: The molecule comprises a PEG-rich, flexible linker framework bearing a propargyl group and a Cy5 chromophore. It contains ether linkages typical of PEG segments, a carbon–carbon triple bond within the propargyl moiety, and stable amide/ether connectivity that supports aqueous compatibility and controlled conjugation.
Reactivity: The propargyl terminus is suitable for copper-catalyzed azide–alkyne cycloaddition or related alkyne–azide coupling strategies commonly used in PROTAC assembly. Conjugation is typically performed under conditions that preserve PEG solubility and minimize side reactions, using appropriate Cu(I) sources and stabilizing ligands, in polar solvents compatible with both partners. Reaction progress can be monitored via Cy5 fluorescence for intermediate verification and purification guidance.
* 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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