S-Boc-2-mercapto-4,6-dimethylpyrimidine is primarily used in organic synthesis as a key intermediate for the preparation of more complex molecules. It is particularly valuable in the development of pharmaceuticals, where it serves as a building block for the synthesis of active pharmaceutical ingredients (APIs). The compound is often employed in the creation of pyrimidine derivatives, which are essential in drug discovery for their biological activity, including antiviral, anticancer, and anti-inflammatory properties. Additionally, its Boc-protected thiol group allows for selective deprotection and further functionalization, making it a versatile reagent in medicinal chemistry. It is also utilized in the synthesis of peptidomimetics and other biologically relevant compounds, contributing to advancements in therapeutic research.