A novel 3,4-dimethyl-N-((thiophen-2-yl)methylene)isoxazol-5-amine (DMTMIA) Schiff base has been synthesized by condensation of 3,4-dimethyl-5-amine isoxazole with thiophene-2-carboxaldehyde and characterized by using elemental analysis, H-1 NMR, C-13 NMR, Mass, IR and UV-Visible spectroscopic techniques. The structure of DMTMIA has also been determined crystallographically. It crystallizes in the orthorhombic crystal system with Pbca space group. The unit cell dimensions of the Schiff base are a = 11.326(4), b = 12.198(4), c = 14.954(5) . The Schiff base was designed and energy minimization was carried out with the help of HyperChem software and subsequently structure activity study was employed to investigate the ability to stabilize DNA-Topoisomerase I. Docking results revealed that the Schiff base involved in van der Waals interactions.