Biotin-PEG4-amino-t-Bu-DADPS-C3-alykne

 CAS No.: 2241685-22-1  Cat No.: BP-501184 4.5  

Biotin-PEG4-amino-t-Bu-DADPS-C3-alkyne is a bifunctional PROTAC linker building block that combines a biotin handle for affinity capture with a polyethylene glycol (PEG) spacer to enhance solubility and reduce steric interference. The molecule contains a branched, tert-butyl-substituted DADPS-derived segment that provides a defined hydrophobic scaffold, connected through a short carbon linker to an alkyne terminus suitable for orthogonal conjugation chemistry. In PROTAC design, this linker can mediate controlled spatial presentation between a biotin-tagged component (e.g., for pull-down, enrichment, or assay readouts) and a second PROTAC module bearing a complementary reactive group, enabling modular assembly and consistent linker length across analog series. The PEG4 segment helps maintain effective productive geometry for ternary complex formation, while the alkyne enables further functionalization for attaching warheads, E3 ligase binders, or reporter groups. Overall, it is valuable for constructing biotin-enabled targeted degradation probes and for systematic structure–activity studies where linker identity and conjugation position are critical.

Biotin-PEG4-amino-t-Bu-DADPS-C3-alykne

Structure of 2241685-22-1

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PROTAC Linker
Molecular Formula
C₄₂H₆₂N₄O₉SSi
Molecular Weight
827.11

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

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IUPACName
5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]-N-[2-[2-[2-[2-[3-[[2-methyl-2-[pent-4-ynoxy(diphenyl)silyl]oxypropyl]amino]-3-oxopropoxy]ethoxy]ethoxy]ethoxy]ethyl]pentanamide
InChI Key
DJUQDDBYPFLTPN-HKGQQODZSA-N
InChI
InChI=1S/C42H62N4O9SSi/c1-4-5-14-23-54-57(34-15-8-6-9-16-34,35-17-10-7-11-18-35)55-42(2,3)33-44-39(48)21-24-50-26-28-52-30-31-53-29-27-51-25-22-43-38(47)20-13-12-19-37-40-36(32-56-37)45-41(49)46-40/h1,6-11,15-18,36-37,40H,5,12-14,19-33H2,2-3H3,(H,43,47)(H,44,48)(H2,45,46,49)/t36-,37-,40-/m0/s1
SMILES
CC(C)(CNC(=O)CCOCCOCCOCCOCCNC(=O)CCCCC1C2C(CS1)NC(=O)N2)O[Si](C3=CC=CC=C3)(C4=CC=CC=C4)OCCCC#C

This PROTAC linker is designed to enable efficient conjugation of a biotin-based handle to a PEG spacer and a bioorthogonal alkyne functionality, supporting modular assembly of targeted protein degradation constructs. Its flexible polyethylene glycol segment can help tune solubility and spatial presentation of the binding and recruitment elements, while the terminal alkyne provides the principal reactive attachment point for subsequent coupling steps. The molecule will be described in detail below, including its structural and reactivity features for PROTAC synthesis.

Structure: The linker contains a PEG-based hydrophilic spacer and a DADPS-derived core bearing a tert-butyl substituent; the nitrogens are incorporated in amide/biotin-derived connectivity rather than a free amino group. A terminal alkyne (alkyne handle) enables click-type conjugation, while ether and amide-related connectivity supports chemical stability under typical coupling conditions.

Reactivity: The alkyne functionality is suitable for copper-catalyzed azide–alkyne cycloaddition or related click chemistries to form stable triazole linkages with azide-bearing partners. PROTAC assembly commonly proceeds through the terminal alkyne using CuAAC or another appropriate alkyne coupling strategy; no free amino site is available for routine acylation. Mild bases and polar aprotic solvents are often used to maintain linker integrity, with copper catalysts and appropriate ligands for controlled click kinetics.

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Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C1V1 = C2V2

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g/mol
Tip: Chemical formula is case sensitive. C22H30N4O √ c22h30n40 ╳
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