This research delves into precision medicine for Perivascular epithelioid cell tumors (PEComa), focusing on the repositioning potential of FDA-approved sirolimus similars. Integrating transcriptomic insights and structural analyses, the study identifies analogs with notable similarities to established PEComa treatments. Structural refinement enhances our understanding of drug-target interactions, revealing potential binding sites through cavity detection. Blind docking elucidates interaction patterns and affinities, highlighting sirolimus similars as promising candidates for precision therapy in PEComa. This comprehensive approach contributes crucial knowledge for the effective use of these heliomycins in PEComa treatment, opening avenues for further experimental and clinical exploration.