Histone deacetylases (HDACs) enzyme is a promising target for the development of anticancer drugs. The enzyme-bound conformation of Trichostatin A (TSA) in complex with the protein Histone deacetylase was used for a detailed study of the binding site of the protein. Hydroxamic acid analogues, the class to which TSA belongs were used for docking and the docked ligands obtained after refinement of docking result were used to build the pharmacophore model. The best 3D QSAR model was obtained by plotting the Experimental IC50 (Expt. IC50) and the Predicted IC50 (Pred. IC50) and calculating the regression coefficient (R2) value for the hypotheses. The value of the regression coefficient for both the training sets (R2 = 0.7098) and the test set (R2 = 0.9592) were satisfactory. Graphical interpretation and the 3D QSAR model built revealed important structural features of the inhibitors related to the active site of HDACs. The results can therefore be exploited for further design and virtual screening for some novel HDAC inhibitors.