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X-ray Structure of Active Site-inhibited Clotting Factor Xa
Open accessAbstract
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.
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Cited by
Intrinsic Disorder and Protein Function
Dunker, A. K., Brown, C. J., Lawson, J. D., Iakoucheva, L. M., & Obradović, Z. (2002) · Biochemistry · doi:10.1021/bi012159+ · Cited by 1,731
Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding
Abel, R., Young, T., Farid, R., Berne, B. J., & Friesner, R. A. (2008) · Journal of the American Chemical Society · doi:10.1021/ja0771033 · Cited by 668
Molecular Docking Screens Using Comparative Models of Proteins
Fan, H., Irwin, J. J., Webb, B. M., Klebe, G., Shoichet, B. K., & Sali, A. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci9003706 · Cited by 135
Recruiting Zn2+to Mediate Potent, Specific Inhibition of Serine Proteases
Katz, B. A., & Luong, C. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3071 · Cited by 34
Metadata
- Authors
- Brandstetter, H., Kühne, A., Bode, W., Huber, R., von der Saal, W., Wirthensohn, K., & Engh, R. A.
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 1996-11
- Volume
- 271
- Issue
- 47
- Pages
- 29988-29992
- ISSN
- 0021-9258 (ISSN-L)
- OpenAlex
- W1964069747
- Cited by
- 279
- References
- 0
- FWCI
- 12.80
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- CoChat. (2026). Citation check: X-ray Structure of Active Site-inhibited Clotting Factor Xa. https://app.cochat.ai/papers/10.1074/jbc.271.47.29988
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- Brandstetter, H., Kühne, A., Bode, W., Huber, R., von der Saal, W., Wirthensohn, K., & Engh, R. A. (1996). X-ray Structure of Active Site-inhibited Clotting Factor Xa. Journal of Biological Chemistry. https://doi.org/10.1074/jbc.271.47.29988
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
