X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition.
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.
Brandstetter
H
H
Max-Planck-Institut für Biochemie, Strukturforschung, D-82125 Martinsried, Federal Republic of Germany. engh@biochem.mpg.de
Kühne
A
A
Bode
W
W
Huber
R
R
von der Saal
W
W
Wirthensohn
K
K
Engh
R A
RA
D000925:Anticoagulants / Q000378:metabolism; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D018360:Crystallography, X-Ray; D015195:Drug Design; D015951:Factor Xa / Q000737:chemistry* / Q000378:metabolism; D065427:Factor Xa Inhibitors; D006801:Humans; D009281:Naphthalenes / Q000378:metabolism; D011422:Propionates / Q000378:metabolism; D013379:Substrate Specificity
C086910:(2S)-2-(4-(((3S)-1-acetimidoyl-3-pyrrolidinyl)oxy)phenyl)-3-(7-amidino-2-naphtyl)propanoic acid; D000925:Anticoagulants; D065427:Factor Xa Inhibitors; D009281:Naphthalenes; D011422:Propionates; D015951:Factor Xa; D002118:Calcium