The crystal structure of alpha-thrombin-hinunorm IV complex reveals a novel specificity site recognition mode

The X-ray crystal structure of the human alpha-thrombin-hirunorm IV complex has been determined at 2.5 Angstrom resolution, and refined to an R-factor of 0.173. The structure reveals an inhibitor binding mode distinctive of a true hirudin mimetic, which justifies the high inhibitory potency and the selectivity of hirunorm IV. This novel inhibitor, composed of 26 amino acid s, interacts through the N-terminal end with the alpha-thrombin active site in a nonsubstrate mode, and binds specifically to the fibrinogen recogniti on exosite through the C-terminal end. The backbone of the N-terminal tripe ptide Chg1 "-Arg2 "-2Nal3 " (Chg, cyclohexyl-glycine; 2Nal, beta-(2-naphthy l)-alanine) forms a parallel beta-strand to the thrombin main-chain segment Ser214-Gly216. The Chg1 " side chain occupies the S2 site, Arg2 " penetrat es into the S1 specificity site, while the 2Na13 " side chain occupies the aryl binding site. The Arg2 " side chain enters the S1 specificity pocket f rom a position quite apart from the canonical P1 site. This notwithstanding , the Arg2 " side chain establishes the typical ion pair with the carboxyla te group of Asp189.