Crystal structure of the human α-thrombin-haemadin complex:: an exosite II-binding inhibitor

The serine proteinase alpha -thrombin plays a pivotal role in the regulation of blood fluidity, and therefore constitutes a primary target in the treatment of various haemostatic disorders. Haemadin is a slow tight-binding thrombin inhibitor from the land-living leech Haemadipsa sylvestris. Here we present the 3.1 Angstrom crystal structure of the human alpha -thrombin-haemadin 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 another leech-derived inhibitor, hirudin. In contrast to hirudin, however, the markedly acidic C-terminal peptide of haemadin does not bind the fibrinogen-recognition exosite, but interacts with the heparin-binding exosite of thrombin, Thus, haemadin binds to thrombin according to a novel mechanism, despite an overall structural similarity with hirudin. Haemadin inhibits both free and thrombomodulin-bound alpha -thrombin, but not intermediate activation forms such as meizothrombin, This specific anticoagulant ability of haemadin makes it an ideal candidate for an antithrombotic agent, as well as a starting point for the design of novel antithrombotics.