3,6,9,12,15,18,21,24,27-Nonaoxatriacont-29-yn-1-ol
3,6,9,12,15,18,21,24,27-Nonaoxatriacont-29-yn-1-ol is a long, poly(ethylene glycol)-like ether linker built from nine repeating oxygen units, bearing a terminal hydroxyl group at one end and a terminal alkyne at the other. Structurally, it provides a flexible, hydrophilic spacer with an alkyne handle that is well suited for orthogonal conjugation chemistries, including copper-catalyzed azide–alkyne cycloaddition or related click-based coupling strategies. In PROTAC design, such linkers are used to tune the effective distance and relative orientation between the ligand that binds the target protein and the ligand that recruits an E3 ubiquitin ligase, thereby improving productive ternary complex formation. The terminal hydroxyl and alkyne provide two distinct handles for modular assembly of degraders, facilitating systematic optimization of linker length and attachment points while minimizing steric interference. As a research-grade spacer, it supports rapid generation of PROTAC analogs for structure–activity relationship studies, helping map how linker flexibility and geometry influence degradation potency and selectivity.
Structure of 2055022-35-8
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* For research and manufacturing use only. Not for human or clinical use.
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This PROTAC linker, 3,6,9,12,15,18,21,24,27-Nonaoxatriacont-29-yn-1-ol, is designed to provide a flexible, ether-rich spacer that can spatially tune ternary complex formation while maintaining a terminal functional handle for conjugation. Its alkyne-bearing terminus enables chemoselective installation of target-binding ligands in PROTAC architectures. The following sections describe the linker’s structure and the practical considerations for its use in PROTAC synthesis.
Structure: The linker is a long-chain polyether featuring repeating ether oxygen atoms that confer conformational flexibility and hydrophilicity. A terminal propargyl alcohol motif provides an alkyne and a primary alcohol. Ether linkages, an alkyne, and an alcohol define its key functional groups and reactivity profile.
Reactivity: PROTAC construction typically uses the terminal alcohol for derivatization (e.g., activation to form esters or carbonates, or conversion to leaving groups) followed by coupling to complementary amine or carboxylate functionalities on ligand fragments. The alkyne can also be exploited for orthogonal conjugation strategies, including copper-catalyzed azide–alkyne cycloaddition under standard click conditions. Mild bases and polar aprotic solvents are commonly used to preserve sensitive ligand groups.
* 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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