C-NH-Boc-C-Bis-(C1-PEG1-PFP)

 CAS No.: 1807521-01-2  Cat No.: BP-501339 4.5  

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.

C-NH-Boc-C-Bis-(C1-PEG1-PFP)

Structure of 1807521-01-2

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PROTAC Linker
Molecular Formula
C₂₆H₂₃F₁₀NO₈
Molecular Weight
667.45

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

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Please store the product under the recommended conditions in the Certificate of Analysis.
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IUPACName
(2,3,4,5,6-pentafluorophenyl) 3-[2-[(2-methylpropan-2-yl)oxycarbonylamino]-3-[3-oxo-3-(2,3,4,5,6-pentafluorophenoxy)propoxy]propoxy]propanoate
InChI Key
IBFNCENUPUCYOT-UHFFFAOYSA-N
InChI
InChI=1S/C26H23F10NO8/c1-26(2,3)45-25(40)37-10(8-41-6-4-11(38)43-23-19(33)15(29)13(27)16(30)20(23)34)9-42-7-5-12(39)44-24-21(35)17(31)14(28)18(32)22(24)36/h10H,4-9H2,1-3H3,(H,37,40)
SMILES
CC(C)(C)OC(=O)NC(COCCC(=O)OC1=C(C(=C(C(=C1F)F)F)F)F)COCCC(=O)OC2=C(C(=C(C(=C2F)F)F)F)F
1. Stroke genetics informs drug discovery and risk prediction across ancestries
Aniket Mishra, Rainer Malik, Tsuyoshi Hachiya, et al. Meta-AnalysisNature. 2022 Nov;611(7934):115-123.doi: 10.1038/s41586-022-05165-3.Epub 2022 Sep 30.
Previous genome-wide association studies (GWASs) of stroke - the second leading cause of death worldwide - were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries.
2. Ionic Liquids and Water: Hydrophobicity vs. Hydrophilicity
Rita F Rodrigues, Adilson A Freitas, José N Canongia Lopes, Karina Shimizu Molecules. 2021 Nov 26;26(23):7159.doi: 10.3390/molecules26237159.
Many chemical processes rely extensively on organic solvents posing safety and environmental concerns. For a successful transfer of some of those chemical processes and reactions to aqueous media, agents acting as solubilizers, or phase-modifiers, are of central importance. In the present work, the structure of aqueous solutions of several ionic liquid systems capable of forming multiple solubilizing environments were modeled by molecular dynamics simulations. The effect of small aliphatic chains on solutions of hydrophobic 1-alkyl-3-methylimidazolium bis(trifluoromethyl)sulfonylimide ionic liquids (with alkyl = propyl [C3C1im][NTf2], butyl [C4C1im][NTf2] and isobutyl [iC4C1im][NTf2]) are covered first. Next, we focus on the interactions of sulphonate- and carboxylate-based anions with different hydrogenated and perfluorinated alkyl side chains in solutions of [C2C1im][CnF2n+1SO3], [C2C1im][CnH2n+1SO3], [C2C1im][CF3CO2] and [C2C1im][CH3CO2] (n = 1, 4, 8). The last system considered is an ionic liquid completely miscible with water that combines the cation N-methyl-N,N,N-tris(2-hydroxyethyl)ammonium [N1 2OH 2OH 2OH]+, with high hydrogen-bonding capability, and the hydrophobic anion [NTf2]-. The interplay between short- and long-range interactions, clustering of alkyl and perfluoroalkyl tails, and hydrogen bonding enables a wealth of possibilities in tailoring an ionic liquid solution according to the needs.
3. Extraction, chemical characterization and biological activity determination of broccoli health promoting compounds
Ana M Ares, María J Nozal, José Bernal J Chromatogr A. 2013 Oct 25;1313:78-95.doi: 10.1016/j.chroma.2013.07.051.Epub 2013 Jul 16.
Broccoli (Brassica oleracea L. var. Italica) contains substantial amount of health-promoting compounds such as vitamins, glucosinolates, phenolic compounds, and dietary essential minerals; thus, it benefits health beyond providing just basic nutrition, and consumption of broccoli has been increasing over the years. This review gives an overview on the extraction and separation techniques, as well as the biological activity of some of the above mentioned compounds which have been published in the period January 2008 to January 2013. The work has been distributed according to the different families of health promoting compounds discussing the extraction procedures and the analytical techniques employed for their characterization. Finally, information about the different biological activities of these compounds has been also provided.

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.

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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

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Tip: Chemical formula is case sensitive. C22H30N4O c22h30n40
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