CONFORMATIONAL CHANGES OF SMALL MOLECULES BINDING TO PROTEINS -- COMPARISON OF CSD AND PDB STRUCTURES. Marc C. Nicklaus, Shaomeng Wang, John S. Driscoll, and George W. A. Milne; Laboratory of Medicinal Chemistry, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bldg. 37, Rm. 5B29, 37 Convent Drive, Bethesda, MD 20892-4255, USA.

Flexible molecules change their conformation upon binding to a protein. This was shown by the analysis of small molecules whose structures have been determined by x-ray crystallography of both the pure compound and the compound bound to a protein. Thirty-three compounds present both in the Cambridge Structural Database and the Brookhaven Protein Data Bank were analyzed, and both were compared with the global energy minimum conformation in vacuum, computed by molecular mechanics force fields calculations. It was found that the conformation bound to the protein differs from that in the crystal structure and also from that of the global energy minimum, and the degree of deformation depends upon the number of freely rotatable bonds in the molecule. Four rotatable bonds appeared to be a limit beyond which no great similarities can generally be expected between the crystal, protein-bound, and vacuum conformations. Analysis of the conformational energies of the flexible molecules showed that, for most of those compounds, both the crystal and the protein-bound conformations are energetically well above the vacuum global minimum, and, in many cases, not even in any local energy minimum. Semi-empirical calculations performed for a select number of structures, using both the AM1 and PM3 hamiltonians, confirmed these results. The number of ligand atoms forming hydrogen bonds was found to be correlated with the energy available for deformation of the ligand. The accuracy of the determination of the conformation of protein-bound small molecules is discussed in the context of the resolution of the crystallographic structures. These findings are discussed as to their impact upon contemporary methods of drug design.