Fmoc-S-3-amino-5-hexynic acid is widely used in peptide synthesis, particularly in solid-phase peptide synthesis (SPPS). Its Fmoc protecting group allows for selective deprotection, enabling the sequential assembly of peptides. The alkyne functional group in the molecule is valuable for click chemistry applications, such as copper-catalyzed azide-alkyne cycloaddition (CuAAC), which is used to conjugate peptides with other biomolecules or functional groups. This compound is also employed in the development of peptide-based drugs, bioconjugation strategies, and the synthesis of peptide-derived materials for biomedical research. Its dual functionality makes it a versatile building block for creating complex peptide architectures.