MODES OF BINDING SYNTHETIC INHIBITORS TO FACTOR XA : AN AUTOMATED DOCKING APPROACH. Mohan S. Rao and Arthur J. Olson, Department of Molecular Biology, The Scripps Research Institute, La Jolla CA

In order to understand the structural basis of Factor Xa specificity, complexes of synthetic inhibitors are generated using the AutoDock suite of programs (1). The inhibitors docked in the present study are 3-amidino benzyl phenyl ether, 4-amidino benzyl phenyl ether, 3-amidino benzyl pyruvic acid, 4-amidino benzyl pyruvic acid, dibasic amidino aryl propanoic acid,3-amidinoaryl pyrrolidinyl phenyl propanoic acid. These inhibitors are different in size, nature of linkage and properties. Some of the lower energy conformers of these complexes together with their energy and possible hydrogen bond schemes are reported. Our results indicate the possibility of a hydrogen bond between amide hydrogen of amidino aryl moiety of these synthetic inhibitors and the side chain oxygen of Asp-189.

References

1) Goodsell, D.S & Olson, A. J Proteins: Str. Func. Genet., 8 (1990) 195