N-PEG3-N'-(propargyl-PEG4)-Cy5

 CAS No.: 2107273-06-1  Cat No.: BP-501258  Purity: 97% 4.5  

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.

N-PEG3-N'-(propargyl-PEG4)-Cy5

Structure of 2107273-06-1

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Category
PROTAC Linker
Molecular Formula
C₄₂H₅₇ClN₂O₇
Molecular Weight
737.36

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

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Popular Publications Citing BOC Sciences Products
Purity
97%
Solubility
Water, DMSO, DMF, DCM
Storage
Please store the product under the recommended conditions in the Certificate of Analysis.
Shipping
Room temperature in continental US; may vary elsewhere.
IUPACName
2-[2-[2-[2-[(1E,3E)-5-[3,3-dimethyl-1-[2-[2-[2-(2-prop-2-ynoxyethoxy)ethoxy]ethoxy]ethyl]indol-2-ylidene]penta-1,3-dienyl]-3,3-dimethylindol-1-ium-1-yl]ethoxy]ethoxy]ethanol;chloride
Synonyms
N-(hydroxy-PEG2)-N'-(propargyl-PEG4)-Cy5
Excitation
649
Emission
667
InChI Key
MXPPWWDNHJQAKX-UHFFFAOYSA-M
InChI
InChI=1S/C42H57N2O7.ClH/c1-6-23-46-27-31-50-33-34-51-32-29-48-25-21-44-38-17-13-11-15-36(38)42(4,5)40(44)19-9-7-8-18-39-41(2,3)35-14-10-12-16-37(35)43(39)20-24-47-28-30-49-26-22-45;/h1,7-19,45H,20-34H2,2-5H3;1H/q+1;/p-1
SMILES
CC1(C2=CC=CC=C2[N+](=C1C=CC=CC=C3C(C4=CC=CC=C4N3CCOCCOCCOCCOCC#C)(C)C)CCOCCOCCO)C.[Cl-]
1. A Fluorescent Peptide Toxin for Selective Visualization of the Voltage-Gated Potassium Channel KV1.3
Dorothy C C Wai, Muhammad Umair Naseem, Gábor Mocsár, Sanjeevini Babu Reddiar, Yijun Pan, Agota Csoti, Peter Hajdu, Cameron Nowell, Joseph A Nicolazzo, Gyorgy Panyi, Raymond S Norton Bioconjug Chem. 2022 Nov 16;33(11):2197-2212.doi: 10.1021/acs.bioconjchem.2c00436.Epub 2022 Nov 4.
Upregulation of the voltage-gated potassium channel KV1.3 is implicated in a range of autoimmune and neuroinflammatory diseases, including rheumatoid arthritis, psoriasis, multiple sclerosis, and type I diabetes. Understanding the expression, localization, and trafficking of KV1.3 in normal and disease states is key to developing targeted immunomodulatory therapies. HsTX1[R14A], an analogue of a 34-residue peptide toxin from the scorpion Heterometrus spinifer, binds KV1.3 with high affinity (IC50 of 45 pM) and selectivity (2000-fold for KV1.3 over KV1.1). We have synthesized a fluorescent analogue of HsTX1[R14A] by N-terminal conjugation of a Cy5 tag. Electrophysiology assays show that Cy5-HsTX1[R14A] retains activity against KV1.3 (IC50 ~ 0.9 nM) and selectivity over a range of other potassium channels (KV1.2, KV1.4, KV1.5, KV1.6, KCa1.1 and KCa3.1), as well as selectivity against heteromeric channels assembled from KV1.3/KV1.5 tandem dimers. Live imaging of CHO cells expressing green fluorescent protein-tagged KV1.3 shows co-localization of Cy5-HsTX1[R14A] and KV1.3 fluorescence signals at the cell membrane. Moreover, flow cytometry demonstrated that Cy5-HsTX1[R14A] can detect KV1.3-expressing CHO cells. Stimulation of mouse microglia by lipopolysaccharide, which enhances membrane expression of KV1.3, was associated with increased staining by Cy5-HsTX1[R14A], demonstrating that it can be used to identify KV1.3 in disease-relevant models of inflammation. Furthermore, the biodistribution of Cy5-HsTX1[R14A] could be monitored using ex vivo fluorescence imaging of organs in mice dosed subcutaneously with the peptide. These results illustrate the utility of Cy5-HsTX1[R14A] as a tool for visualizing KV1.3, with broad applicability in fundamental investigations of KV1.3 biology, and the validation of novel disease indications where KV1.3 inhibition may be of therapeutic value.

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.

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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

* Total Molecular Weight:
g/mol
Tip: Chemical formula is case sensitive. C22H30N4O c22h30n40
g/mol
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