X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition

• Published in: The Journal of biological chemistry Vol. 271; no. 47; pp. 29988 - 29992
• Main Authors: Brandstetter, H, Kühne, A, Bode, W, Huber, R, von der Saal, W, Wirthensohn, K, Engh, R A
• Format: Journal Article
• Language: English
• Published: United States 22.11.1996
• Subjects: Anticoagulants - metabolism; Binding Sites; Calcium - metabolism; Crystallography, X-Ray; Drug Design; Factor Xa - chemistry; Factor Xa - metabolism; Factor Xa Inhibitors; Humans; Naphthalenes - metabolism; Propionates - metabolism; Substrate Specificity
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.271.47.29988

The 3.0-A resolution x-ray structure of human des-Gla-coagulation 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 aryl-binding 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.