Hirudin
 
Hirudin is a protein inhibitor of thrombin in the saliva of the medicinal leech Hirudo medicinalis. The target enzyme here seems obvious. It is a single polypeptide chain of 65 amino acid residues crosslinked by three disulfide bridges. It combines extremely tightly (K_I10–¹⁴M) with thrombin. The crystal structure of a thrombin-hirudin complex reveals that hirudin is not a standard-mechanism canonical inhibitor. The active site of thrombin is embedded in a canyon restricting the entry of many substrates and of most trypsin inhibitors that do not inhibit thrombin. Hirudin blocks the active site, but none of its residues embeds into the S₁ cavity, a hallmark of standard-mechanism canonical inhibition. The highly flexible COOH terminus of hirudin (residues 50–65) binds to the fibrinogen-binding exosite of thrombin. Many hirudin-based drugs block this fibrinogen-binding exosite rather than the active site of thrombin.