The 3.0-Å resolution x-ray structure of human des-Glacoagulation factor Xa (fXa) has been determined in complex with the synthetic inhibitor DX-9065a. The binding geometry is characterized primarily by two interaction sites: the naphthamidine group is fixed in the S1 pocket by a typical salt bridge to Asp-189, while the pyrrolidine ring binds in the unique aryl-binding site (S4) of fXa. Unlike the large majority of inhibitor complexes with serine proteinases, Gly-216 (S3) does not contribute to hydrogen bond formation. In contrast to typical thrombin binding modes, the S2 site of fXa cannot be used by DX-9065a since it is blocked by Tyr-99, and the arylbinding site (S4) of fXa is lined by carbonyl oxygen atoms that can accommodate positive charges. This has implications for natural substrate recognition as well as for drug design.Hemostasis is the blood clotting process that, when functioning properly, occurs when an injury to the vasculature leads to a series of vasculomotor and cellular reactions and the activation of the blood coagulation cascade. The latter process is initiated via the extrinsic pathway, leading first to thrombin activation and then massively amplified thrombin activation due to the positive feedback of the intrinsic pathway (1). Both extrinsic and intrinsic pathways merge at the factor X activation step. An imbalance between these clotting processes, clotting inactivation processes (protein C inactivation of hemostasis cofactors), and thrombolytic processes (tissue plasminogen activator, plasminogen) can lead to thrombotic or bleeding disorders. Antithrombotics include inhibitors of thrombin, factor Xa and factor IXa, factors involved in both the extrinsic and intrinsic pathways (2). As evidence accumulates that thrombin has other important functions in cellular (3, 4) and neurological (5-10) processes, new synthetic anticoagulants increasingly target factor Xa. Daiichi published the first tight binding (K i ϭ 41 nM), specific inhibitor of fXa, 1 DX-9065a (11-13). We present here the crystal structure of the factor Xa⅐DX-9065a complex. The inhibitor binds in the active site in an extended conformation, which was expected from earlier studies (14, 15). Both hydrophobic and electrostatic interactions characterize the complex formation, which is also accompanied by local rearrangements in the active site of fXa. Considering these subtle interactions and the unpredictable ligand-induced motions involved in binding, there is clearly a need for a series of fXa-ligand complex structures to provide adequate information for structure-based drug design and an understanding of how fXa recognizes physiological substrates.EXPERIMENTAL PROCEDURES fX was isolated from human plasma; des-Gla-fX was produced via chymotryptic cleavage (removing amino acids L1-L44; chymotrypsinogen numbering is used for the catalytic domain; the sequential fX numbering, which is used for the light chain, will be indicated by the prefix "L"). Subsequently, fX was activated with the purified factor X activator from Russell's vip...