X-ray Structure of Active Site-inhibited Clotting Factor Xa

Abstract

The 3.0-Å resolution x-ray structure of human des-Gla- coagulation factor Xa (fXa) has been determined in com- plex 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 throm- bin 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 at- oms that can accommodate positive charges. This has implications for natural substrate recognition as well as for drug design. Hemostasis