Thrombin is a Na+ -activated allosteric serine protease that catalyzes the formation of thrombus as well as a series of flux-regulating reactions through the coagulation cascade. In response to vascular injury, thrombin is produced through the activation of its inactive precursor, prothrobin, catalyzed by Factor Xa (a trypsin-like proteinase). As a serine protease characterized by the presence of a catalytic triad, thrombin possess a triad of S195-H57-D189 in its active center, which is required for the nucleophilic attack of the target peptide bond. Located “south-west” of the active center is a Na+ -binding site, through which the binding of a sodium ion allosterically modulates the activity of the serine proteinase.