“Hepatotoxicity is the capacity of a drug or chemical to produce injury to the liver diseases. The liver plays a central role in transforming and clearing chemicals which is susceptible to the toxicity from agents. Agents with recognized hepatotoxicity include carbon tetrachloride, alcohol”. In the present study the functional properties of target proteins which are responsible for liver cancer were studied and comparative modeling of target proteins was done for high percent sequence identity for structural homology. The protein structure was modeled using Swiss-PDB as its corresponding structure not available in Protein Data Bank. Docking study of the modeled protein was done with natural compounds Beta sitosterol (Justicia adhatoda), Mimosine (Mimosa pudica), Berberine (Vitex negundo) and synthetic compounds Tiagabine, Vigabatrin, Zolpidem, Chloramphenicol, Gentamicin, Linezolid to treat Liver disease to find the preferred orientation and binding affinity of drug with target protein using scoring functions. Berberine was found to be effective drug selected on the basis of its binding affinity with the target protein and that can be potential target for Liver cancer.