Background: Natural resources are often sought for potential molecules which are pharmacologically active. Carica papaya is a well-known plant, studied for its constituent secondary metabolites and their benefits. Methods: This study focuses on identifying low molecular weight secondary metabolites form Carica papaya as potential pharmacophores, based on their structure. We determined their similarity with pharmaceutically active anti-clotting molecules using clustering method. Cheminformatic and Statistical analysis was done with data on molecular characteristics. Results: We have identified Carica papaya compounds to be pharmacologically active. In this study, we have differentiated Carica papaya compounds, through statistical analysis using clustering method, on the basis of significant molecular properties. Conclusion: Molecular similarity of secondary metabolites revealed through this study identifies, Carica papaya metabolites as a possible substitute drug and a preventive medicine against thrombosis.