APN-C3-NH-Boc
CAS No.: 1539292-60-8
Cat No.: BP-501389
4.5 
APN-C3-NH-Boc is a PROTAC linker building block containing an APN (arylpropiolonitrile) electrophilic alkyne motif and a three-carbon spacer terminated with a Boc-protected amine. Structurally, it contains an aliphatic C3 chain that serves as a defined length element to tune the geometry and distance between the target-binding ligand and the E3-ligase recruiter when constructing bifunctional degraders. The APN motif can undergo thiol/cysteine addition, while the Boc group masks the amine until deprotection for subsequent coupling. In PROTAC design, such linkers are critical for optimizing productive ternary complex formation, improving cooperativity, and reducing off-target or non-productive binding by adjusting linker flexibility and reach. As a modular intermediate, APN-C3-NH-Boc supports systematic linker optimization workflows in targeted protein degradation research, facilitating reproducible synthesis of degraders for structure–activity relationship studies.
Structure of 1539292-60-8
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APN-C3-NH-Boc is a protected, functionalized PROTAC linker building block designed to enable controlled assembly of targeted protein degraders. Its Boc-protected amine functionality supports stepwise synthesis, helping researchers optimize coupling efficiency and manage reactivity during linker elaboration. In PROTAC workflows, such linkers are used to connect a ligand for an E3 ligase to a target-binding moiety, facilitating formation of productive ternary complexes upon degradation trigger. Detailed structural and reactivity considerations are provided below.
Structure: APN-C3-NH-Boc features a Boc-protected amine and a 3-arylpropiolonitrile (APN) group containing an electron-deficient alkyne adjacent to a nitrile. The molecule contains a carbamate carbonyl within the Boc group and a flexible linker segment, while the APN alkyne/nitrile motif provides an additional electrophilic reaction site.
Reactivity: The Boc group can be removed under standard acid-mediated deprotection conditions to reveal a primary amine for subsequent amide or urea-forming couplings. After Boc deprotection, the amine can be coupled by standard acylation chemistry, while the electron-deficient APN alkyne can undergo thiol-selective conjugate addition under appropriate conditions. Reaction design should account for carbamate stability during earlier steps and compatibility with PROTAC ligand chemistries.
* 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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