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In this study, interaction of small molecular weight drug compounds with proteins has been characterized. The binding constants of interactions were first theoretically calculated using molecular docking simulations. Next, these interactions were experimentally investigated via Surface Plasmon Resonance (SPR). The theoretical binding constants, KD, predicted from theoretical calculations have been compared with the experimental values obtained from SPR. As a model protein, Escherichia coli (E.coli) DNA photolyase was used due to its known crystal structure. Among the eight drugs analyzed, theoretical and experimental values have shown similar binding affinities between selected drug and protein pairs. The results obtained in this study may be significant to characterize the unknown interactions of existing drugs with various proteins.