Helicobacter pylori is a bacterium that infects half of the world’s population and causes gastric disorders and severe diseases, including active chronic gastritis and gastric or duodenal ulcers. Peptidoglycan biosynthesis of H.pyroli reveals that protein with the entry HP0648 could be potential drug target. In this present study, we used different In silico tools and technique to analyze the protein sequence of HP0648 retrieved from the E.C 2.5.1.7. We predicted the 3-Dimenstional structure of protein sequence, its physiochemical properties and binding site port. 3D structure predicted by using the Swiss Model server and validated by Ramachandran plot analysis. We suggest that protein with the entry HP0648 could be a potential drug target for the H.pyroli.