3,6,9,12,15,18,21,24,27,30,33,36-Dodecaoxanonatriacont-38-yn-1-ol
3,6,9,12,15,18,21,24,27,30,33,36-Dodecaoxanonatriacont-38-yn-1-ol is a long, poly(ether)–type PROTAC linker featuring a terminal propargyl alcohol motif and an internal alkyne handle, consistent with a flexible, oxygen-rich chain that can span the distance between a ligand-derived “warhead” and an E3-recruiting module. The repeated ether units provide conformational adaptability and improved solvation, which can help maintain productive geometry for ternary-complex formation by reducing steric mismatch between binding domains. The terminal alkyne enables orthogonal chemical conjugation strategies (e.g., click-type coupling or subsequent derivatization after functional-group interconversion), allowing researchers to install this linker between targeting ligands and to tune linker length and polarity. In targeted protein degradation research, such linkers are valuable for systematically optimizing degradation potency and selectivity by balancing flexibility, hydrophilicity, and effective reach while preserving the binding pharmacophores of each recruited component.
Structure of 1036204-61-1
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* For research and manufacturing use only. Not for human or clinical use.
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This PROTAC linker is designed to provide a chemically stable, functional handle for assembling bifunctional degraders that connect a target-binding ligand to an E3-ligase recruiter. Its extended polyether architecture supports conformational flexibility and can help maintain productive spatial orientation for ternary complex formation. The subsequent sections describe the linker’s structural features and practical considerations for PROTAC construction and coupling chemistry.
Structure: The molecule is a long-chain polyether alcohol featuring multiple ether linkages and a terminal propargyl alcohol motif. Its framework contains repeating C–O–C bonds that impart flexibility, while the terminal alkyne enables controlled orthogonal functionalization. Overall, it is an oxygen-rich, hydrogen-bonding scaffold with ether-dominated polarity.
Reactivity: The terminal alkyne and hydroxyl functionality support common PROTAC assembly strategies, including alkyne-based coupling and orthogonal derivatization routes. Typical approaches rely on activating the alcohol for ester/ether formation or using alkyne-compatible chemistries to attach complementary warheads under mild, anhydrous conditions. Solvents such as polar aprotic media are often used to promote solubility, while base or coupling reagents facilitate nucleophilic substitution or esterification; copper-free or copper-assisted click-type transformations can be considered when compatible with the remaining functional 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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