Isothiazole carboxamidine compounds are potent ATP competitive Chk2 inhibitors. A series of compounds with Chk2 inhibitory activity were taken from literature and different 3D-QSAR models have been generated with Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). In first scheme LB-QSAR models were generated using fully optimized geometries by PM3 approach giving reasonable statistics of CoMFA (q2=0.88, r2=0.96 and r2predictive=0.60) and CoMSIA(q2=0.918 r2=0.99 and r2predictive=0.55). In second and third scheme the ligands 7 docked in to receptor protein (PDB 2CN8). Consequently, two most plausible modes were identified and used as initial templates. The docked conformer based CoMFA model shows good correlation with activity (q2=0.91, r2=0.99 and r2predictive =0.84). Whereas in CoMSIA, the steric and hydrophobic and donor field jointly give a better statistics (q2=0.92 r2=0.99 and r2predictive =0.53). These findings might be helpful to design more potent Chk2 inhibitors.