Lipopolysaccharide-binding protein is responsible for the natural defense reaction. LBP binds to lipid A moiety of the bacterial lipopolysaccharide (LPS), a glycolipid present in the outer membrane of all Gram-negative microorganisms. Lipopolysaccharide acts as a binding enhancer to CD14, and on cellular surfaces, CD14 behaves as a dissolvable protein and also as an acceptor of LPS in the linked form of phosphatidylinositol. In the present study, we generated a precise 3-Dimensional model of LBP using MODELLER 9.21 and validated its structure using Procheck software. The optimum number of amino acids were found in the core region of the modeled protein. We interpreted the action of natural compounds docking against the modeled LBP protein. Three compounds (Ginkgetin, Linderatone, and Erystagallin A) showed lower binding affinity values towards LBP compared to Diclofenac, Celecoxib, and Indomethacin. Ginkgetin exhibited the lowest binding energy of -11.77 Kcal/mol by interacting with His294 and Lys467. Binding energies of all the twenty compounds manifested exceptionally than the standard drugs for the modeled LBP protein. These computational studies can help discover novel drug candidates.