Fmoc-Orn(ivDde)-OH is widely used in peptide synthesis, particularly in solid-phase peptide synthesis (SPPS) methodologies. The Fmoc (9-fluorenylmethoxycarbonyl) group serves as a temporary protecting group for the amino group, allowing for selective deprotection during the synthesis process. The ivDde (1-(4,4-dimethyl-2,6-dioxocyclohexylidene)-3-methylbutyl) group is a protecting group for the side chain amine of ornithine, providing orthogonality to the Fmoc group. This orthogonality enables the selective deprotection of the side chain without affecting the Fmoc-protected amino groups, which is crucial for the synthesis of complex peptides.

This compound is particularly valuable in the synthesis of peptides that require selective modification or conjugation at specific sites. For example, it is used in the preparation of peptide-based drugs, bioconjugates, and labeled peptides for research and diagnostic purposes. The ivDde group can be removed under mild conditions using hydrazine, allowing for further functionalization or conjugation of the ornithine side chain. This makes Fmoc-Orn(ivDde)-OH a versatile building block in the development of peptide therapeutics, vaccines, and other biologically active peptides.