A quantitative structure activity relationship study was performed on a series of uracil based hydroxamide Inhibitors of maize deacetylases HD2 and histone deacetylase (Mouse HDAC1) activity for establishing quantitative relationship between biological activity and their physicochemical properties. The two dimensional and k-nearest neighbor studies were performed using partial least square methodology coupled with genetic algorithm (GA) and simulated annealing (SA) was applied to derive models. The 2D model developed gave good correlation coefficient (r 2 ) of 0.8498, and r 2 for external test set (pred_r 2 ) 0.7932 was developed by GA-PLS with the descriptors such as Hydrogen count, SsssCHcount, and SdsCHE-index. k-nearest neighbor method was applied for the generation of steric and electrostatic descriptors based on aligned structures. 3D QSAR studies produced reasonably good predictive models with high cross-validated q 2 value of 0.679 and pred_r 2 = 0.733 values using the model GA kNN-MFA method. The best pharmacophore shows that the four features used were one AroC feature (Aromatic), one AlaC (aliphatic) and two HAc (Hydrogen bond acceptor) features. The average RMSD of the pharmacophore alignment of each two molecules is 0.0754 Å . The QSAR result gives relationship between structural Uracil-based hydroxamic acids derivatives and their activities which should be useful to design newer histone deacetylase inhibitors. ª 2015 The Authors. Production and hosting by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).