In this study, docking panobinostat into the active zone of the HDAC2 (pdb: 4LXZ) and HDAC8 (pdb: 1W22) using AutoDock Tools. The calculations were conducted on AutoDock Vina and AutoDock4 and used automatic docking method of Lamarckian genetic algorithm. According to the pharmacophore model, panobinostat structure was established typically consisting of a zinc binding group (ZBG), a linker and a capping group, which interact with the active sites of HDAC2 (pdb: 4LXZ) and HDAC8 (pdb: 1W22). Panobinostat interacts with HDAC2 more strongly than HDAC8 which may contribute to slightly better binding affinity of phenyl rings parallel displaced pi-pi stacking interaction at linker. The interaction between panobinostat and the active sites of two enzymes closely resembles the vorinostat HDAC2 (pdb: 4LXZ) and MS27-275-HDAC8 complex (pdb: 1W22) published in the Protein Data Bank database. This molecular docking model, can be used to compare the inhibitory potential of panobinostat with HDACs, assist future design of more potent and selective inhibitors for HDAC2 and HDAC8.