Fmoc-Orn(Boc)-OPfp is an Fmoc-protected ornithine derivative bearing an additional Boc-protected side-chain amino group and an OPfp ester functionality, classifying it as a protected amino acid building block and activated carboxylate derivative for peptide-related synthesis. The molecule contains an Fmoc carbamate on the α-amino group, a Boc carbamate on the δ-amino side chain of ornithine, and a carboxylate converted to an OPfp ester (pentafluorophenyl ester) that presents a leaving group for acyl transfer while retaining the α-carboxylate functionality in activated form. In synthetic workflows, it is used to support stepwise assembly of protected peptide intermediates or amide-forming couplings where chemoselective deprotection and controlled acyl reactivity are required, and it can also serve as a defined precursor for preparing more complex ornithine-containing amino acid derivatives.
CAT No: CP26258
CAS No:123180-69-8
Synonyms/Alias:Fmoc-Orn(Boc)-OPfp;123180-69-8;00232_FLUKA;ZINC59073288;VA50398;FT-0642996;N|A-Boc-N|A-Fmoc-L-ornithinepentafluorophenylester;N|A-Fmoc-N|A-Boc-L-ornithinepentafluorophenylester;Nalpha-Fmoc-Ndelta-Boc-L-ornithinepentafluorophenylester;Ndelta-Boc-Nalpha-Fmoc-L-ornithinepentafluorophenylester;L-Ornithine,N5-[(1,1-dimethylethoxy)carbonyl]-N2-[(9H-fluoren-9-ylmethoxy)carbonyl]-,pentafluorophenylester(9CI)
Fmoc-Orn(Boc)-OPfp is an orthogonally protected ornithine derivative designed for peptide-building-block workflows, featuring a chiral ornithine backbone with a protected side-chain amine and a carboxyl group converted to an activated pentafluorophenyl ester (OPfp). The molecule combines an Fmoc-protected alpha-amino group with a Boc-protected side-chain amine, enabling controlled deprotection sequences during stepwise solid-phase peptide synthesis and minimizing side reactions from unprotected nucleophiles. The OPfp ester introduces a highly leaving-group-rich acylating handle that can undergo rapid amide-bond formation under peptide-coupling conditions, while the Boc and Fmoc groups provide orthogonal protection compatible with standard base-mediated and nucleophile-mediated transformations. The presence of multiple protecting groups and a stereodefined amino acid framework makes Fmoc-Orn(Boc)-OPfp a practical chiral intermediate for downstream amino acid derivatization, peptide coupling chemistry, and process-oriented synthesis of functionalized ornithine-containing motifs.
1. Peptide Synthesis
Fmoc-Orn(Boc)-OPfp is applied in peptide synthesis to introduce ornithine residues with orthogonally protected N- and side-chain amines, supporting controlled assembly of polycationic or guanidinium-mimetic sequences. The Fmoc group on the alpha-amino function supports standard Fmoc deprotection strategies, while the Boc protection on the side-chain amine helps suppress undesired branching or crosslinking during chain elongation. The OPfp activated ester at the carboxyl position functions as an acylating electrophile that can be coupled to incoming amino components to form peptide bonds with the stereochemical integrity of the ornithine center. Resulting ornithine-containing peptide intermediates can be carried forward to generate protected peptide fragments for library synthesis, sequence optimization, and downstream functionalization of the side-chain. The compound's orthogonal protection pattern aligns with amino acid chemistry approaches that require selective unmasking for later conjugation or cyclization steps.
2. Protected Amino Acid Chemistry
Fmoc-Orn(Boc)-OPfp is used in protected amino acid chemistry as a chiral, activated carboxyl derivative that supports targeted derivatization of ornithine side chains while maintaining orthogonality of protecting groups. The Fmoc-protected alpha-amino group and Boc-protected side-chain amine provide a two-site protection scheme that can be selectively removed or transformed depending on the synthetic stage. The OPfp ester enables conversion into amide-linked products without exposing the free carboxylic acid, which can improve handling and coupling reproducibility in fine chemical synthesis. Downstream derivatives may include peptide-like amides, resin-bound intermediates, or protected ornithine building blocks for subsequent deprotections and functional group interconversions. This structure-function design supports chiral amino acid intermediate preparation where controlled reactivity and selective unmasking are required.
3. Peptidomimetics And SAR Studies
Fmoc-Orn(Boc)-OPfp is suitable for peptidomimetic construction and structure-activity relationship studies where ornithine analogs are incorporated to probe binding modes involving cationic side chains. The protected side-chain amine and activated ester functionality enable rapid incorporation of ornithine units into analog scaffolds, supporting systematic variation of spacing, charge distribution, and linker identity. The orthogonal Fmoc/Boc protection strategy supports sequential modification, such as later conversion of the side-chain functionality into more constrained or chemically distinct motifs used in SAR workflows. The stereodefined ornithine backbone supports reproducible scaffold generation for comparative studies across closely related analogs. The compound therefore functions as a synthetic handle for generating amino acid-based libraries and peptide-mimetic intermediates that feed into medicinal chemistry and molecular design programs.
4. Bioconjugation Chemistry
Fmoc-Orn(Boc)-OPfp can be employed in bioconjugation chemistry to prepare ornithine-containing amide linkers and protected conjugation-ready intermediates for subsequent coupling to biomolecular targets. The OPfp activated ester provides an acylation route to form stable amide bonds with amine-bearing partners, while the Fmoc and Boc groups can be managed to control when the free amines become available for conjugation or crosslinking. The ornithine scaffold contributes a defined, stereochemically consistent cationic side-chain precursor that can be transformed after deprotection into functional motifs compatible with labeling or surface attachment chemistries. Resulting conjugation intermediates can be used to build defined biomolecule constructs, including peptide-based tags, linker modules, and protected spacer units for multistep assembly. This approach leverages amino acid derivatization principles to connect peptide science with applied biomolecule modification.
5. Process Chemistry Intermediate
Fmoc-Orn(Boc)-OPfp is relevant to process chemistry as an activated, protected amino acid intermediate that can be integrated into scalable manufacturing routes for ornithine-containing peptide building blocks. The OPfp ester provides a controlled electrophilic acylating functionality that can reduce reliance on free-acid activation steps, while the orthogonal Fmoc/Boc protection scheme supports predictable deprotection sequencing during downstream processing. The presence of multiple protecting groups helps manage chemoselectivity in multistep synthesis, which is valuable when producing peptide fragments or protected amino acid derivatives on manufacturing timelines. The compound can serve as a standardized input for producing protected peptide coupling units, enabling consistent batch-to-batch synthesis of ornithine-bearing intermediates. This makes Fmoc-Orn(Boc)-OPfp aligned with industrial chemical manufacturing needs for chiral, protected amino acid derivatives that support reliable coupling and controlled downstream transformations.
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