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The compound ‘3,5,7,3′,5′-pentahydroxy-flavanonol-3-O-α-L-rhamnopyranoside’ reported from Bauhinia strychnifolia Craib (family Fabaceae) possess ten times more cytotoxicity against certain cancer cell line than the anti-cancer drugs, but nontoxic to normal cells. Its stability with the protein ‘cyclin-dependent protein kinase 2/CDK-2′ (-which plays vital role in apoptosis, regulation of the cell cycle, transcription and in the neuronal functions) were performed via molecular docking and molecular dynamics simulation simulations. The molecular dynamics simulation suggests that the protein-ligand complex is stable at least in the time period of 40 ns. This study also shows that after 20 ns of simulation, there is a shift in the ligand position, and it might be due to changes in the binding type. According to the data obtained via MM-PBSA calculations, this shift leads to even stronger binding of ligand. Such binding flexibility can be explained by highly hydrophilic nature of both ligand and binding site. Keywords: Molecular docking, Molecular docking simulation, 3,5,7,3′,5′-pentahydroxy-flavanonol-3-O-α-L-rhamnopyranoside, Bauhinia strychnifolia Craib, Fabaceae, Cyclin-dependent protein kinase 2