The three-dimensional structure of the ternary complex consisting of human α-thrombin, hirugen and the active-site inhibitor RWJ-51438 has been determined at 1.7 Å resolution. The crystals of the complex belong to the orthorhombic space group P21212, with unit-cell parameters a = 62.98, b = 117.52, c = 47.99 Å. The refined R and R(free) values are 0.196 and 0.232, respectively. The ketone carbonyl group of the inhibitor is covalently linked to the hydroxyl O atom of Ser195, forming a tetrahedral intermediate hemiketal structure; the benzothiazole ring N atom of RWJ-51438 forms a hydrogen bond with His57. Surprisingly, the carboxylate substituent on the benzothiazole group forms salt bridges with Lys60F NZ and the NZ of the symmetry-related residues Lys236 and Lys240, which introduces steric effects that perturb the 60A-60I insertion loop, especially at residues Trp60D and Phe60H.