Crystal structure of the human alpha-thrombin-haemadin complex: an exositeII-binding inhibitor

The serine proteinase alpha -thrombin plays a pivotal role in the regulatio n of blood fluidity, and therefore constitutes a primary target in the trea tment of various haemostatic disorders. Haemadin is a slow tight-binding th rombin inhibitor from the land-living leech Haemadipsa sylvestris. Here we present the 3.1 Angstrom crystal structure of the human alpha -thrombin-hae madin complex. The N-terminal segment of haemadin binds to the active site of thrombin, forming a parallel beta -strand with residues Ser214-Gly216 of the proteinase, This mode of binding is similar to that observed in anothe r leech-derived inhibitor, hirudin. In contrast to hirudin, however, the ma rkedly acidic C-terminal peptide of haemadin does not bind the fibrinogen-r ecognition exosite, but interacts with the heparin-binding exosite of throm bin, Thus, haemadin binds to thrombin according to a novel mechanism, despi te an overall structural similarity with hirudin. Haemadin inhibits both fr ee and thrombomodulin-bound alpha -thrombin, but not intermediate activatio n forms such as meizothrombin, This specific anticoagulant ability of haema din makes it an ideal candidate for an antithrombotic agent, as well as a s tarting point for the design of novel antithrombotics.