Fmoc-Orn(pyrazinylcarbonyl)-OH is an Fmoc-protected ornithine derivative in which the side-chain amine of ornithine is acylated with a pyrazinylcarbonyl group, yielding a non-proteinogenic, structurally modified amino acid building block for peptide chemistry. The molecule contains an Fmoc carbamate on the α-amino group and a free carboxylic acid at the α-position, while the side chain bears a pyrazinylcarbonyl amide that introduces a heteroaromatic pyrazine functionality and reduces side-chain basicity. In synthesis and chemical biology workflows, it is employed as a protected amino acid component to incorporate an ornithine-based residue bearing a heteroaryl amide handle into peptides or peptide-related intermediates, supporting structure-activity studies, conjugation strategies, or analytical labeling where a pyrazine-containing motif is required.
CAT No: CP26686
CAS No:201046-61-9
Synonyms/Alias:Fmoc-Orn(Pyrazic)-OH;201046-61-9;Fmoc-Orn(pyrazinylcarbonyl)-OH;ZINC2567628;6977AH;KB-301262;FT-0643874;N~2~-[(9H-Fluoren-9-ylmethoxy)carbonyl]-N~5~-(2-pyrazinylcarbonyl)-L-ornithine
Fmoc-Orn(pyrazinylcarbonyl)-OH is an Fmoc-protected ornithine derivative bearing a pyrazinylcarbonyl acyl group on the side-chain, providing a chiral amino acid framework with an N-fluorenylmethoxycarbonyl (Fmoc) protecting group and a free carboxylic acid for coupling chemistry. The molecule contains an orthogonally masked α-amino functionality suitable for solid-phase peptide synthesis, while the pyrazine-containing carbonyl introduces a heteroaromatic, electron-deficient handle that can participate in hydrogen-bonding and coordination-relevant interactions. The side-chain amine is acylated as a carbonylated pyrazinylcarbonyl substituent, shaping reactivity by reducing unprotected nucleophilicity and directing subsequent transformations toward amide-level functionalization or deprotection/reacylation strategies. The combination of protected amine, carboxylic acid, and heteroaromatic carbonyl makes the compound a practical intermediate for chiral building block assembly and downstream derivatization in peptide and peptidomimetic workflows.
1. Peptide Synthesis
Fmoc-Orn(pyrazinylcarbonyl)-OH supports peptide building block preparation in solid-phase and solution-phase peptide synthesis by pairing an Fmoc-protected α-amino group with a free C-terminal carboxylic acid for amide bond formation. The ornithine backbone contributes an extended, flexible side-chain topology that can be incorporated into peptide sequences to position the pyrazinylcarbonyl heteroaromatic motif at defined internal or terminal positions. The acylated side-chain carbonyl moderates side-chain reactivity during coupling and can be retained through iterative deprotection cycles, enabling controlled construction of heteroaryl-containing peptide analogs. The resulting peptides can be used as research-grade scaffolds for studying sequence-dependent binding features and for generating peptidomimetics with heteroaromatic recognition elements.
2. Peptidomimetics And SAR
Fmoc-Orn(pyrazinylcarbonyl)-OH enables medicinal chemistry-oriented peptidomimetic construction by introducing a pyrazinylcarbonyl group that can act as a polar, heteroaromatic pharmacophore within constrained peptide-like frameworks. The Fmoc-protected amino acid derivative can be incorporated into analog libraries where stereochemically defined ornithine geometry and the heteroaryl carbonyl influence conformational preferences and intermolecular interactions. The protected α-amino functionality supports systematic variation of neighboring residues while maintaining the heteroaryl motif for structure-activity relationship studies. Downstream derivatives generated from the same scaffold can be used to probe how heteroaromatic placement and amide chemistry affect binding patterns in biochemical screening campaigns and SAR mapping workflows.
3. Chemical Biology Probes
Fmoc-Orn(pyrazinylcarbonyl)-OH is suitable for chemical biology workflows that require heteroaromatic, amide-bearing peptide conjugation handles for molecular recognition and labeling strategies. The pyrazine-containing carbonyl provides a defined polar surface element that can participate in noncovalent interactions, supporting the design of probes that target specific binding pockets or modulate biomolecular association through sequence context. The Fmoc group allows controlled incorporation into peptide carriers, while the carboxylic acid enables conversion to activated ester or coupling-ready forms for attachment to linkers used in probe synthesis. The resulting labeled or conjugatable constructs can serve as research intermediates for studying biomolecule binding, trafficking, or interaction networks using amino acid chemistry-compatible assembly routes.
4. Protected Amino Acid Chemistry
Fmoc-Orn(pyrazinylcarbonyl)-OH functions as a protected amino acid derivative for orthogonal protection and staged deprotection strategies in synthetic organic chemistry. The Fmoc group provides an established base-labile protecting group for iterative peptide assembly, while the side-chain pyrazinylcarbonyl amide reduces competing side-chain nucleophilicity during coupling steps. The free carboxylic acid supports activation-based transformations to generate peptide coupling intermediates, enabling downstream synthesis of longer sequences or conversion into alternative C-terminal formats. The compound's defined stereochemistry at the ornithine center supports reproducible chiral building block incorporation, making it a practical reagent for manufacturing-oriented fine chemical synthesis of heteroaryl-containing amino acid derivatives.
5. Analytical Standards
Fmoc-Orn(pyrazinylcarbonyl)-OH can be employed in analytical research and method development as a structurally defined reference material for mass spectrometry and chromatography-based characterization of Fmoc-amino acid derivatives and peptide fragments. The combination of the Fmoc chromophore and the pyrazinylcarbonyl heteroaromatic moiety yields distinctive ionization and fragmentation patterns that can assist in verifying incorporation of the ornithine-derived residue in peptide synthesis. The presence of a free carboxylic acid and an amide-linked heteroaryl group supports targeted derivatization or calibration workflows when monitoring coupling completeness, identity, or stability under deprotection conditions. The compound thereby serves as a useful chemical benchmark for quality-oriented characterization of amino acid building block preparations and heteroaryl-containing peptide intermediates.
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