Despite extensive study, little is known about the origins of the mutualistic bacterial endosymbionts that inhabit approximately 10% of the world's insects. In this research we focus on the molecular functional regions and 3 dimensional structure predictions on potential protein target in Sitophilus oryzae. Based on the literature information, we identify the Outer membrane component of tripartite multidrug resistance system in Sitophilus oryzae. The insilico techniques would be applied and represents the best inhibitors to future drug docking studies. In this research, we find out that motif and 3 dimensional structures play a major role in structure based drug designing and Computational entomology.