title: Metal-ligand interactions: an analysis of zinc binding groups using the Protein Data Bank.
abstract: In the present study, we investigated zinc binding groups (ZBGs) using the coordinates of protein-ligand complex structures obtained from the Protein Data Bank. The distance from the zinc to the nearest ligand atom was measured to determine whether the atom was part of the ZBG. The most frequently found ZBG was carboxylate, followed by sulfonamide, hydroxamate, and phosphonate/phosphate. Because it was found that few heteroatoms, such as nitrogen, oxygen, and sulfur atoms, interacted with zinc, ideal distances between the zinc and these heteroatoms were identified. Whereas carboxylates bound to the zinc via both monodentate and bidentate interactions, the hydroxamates bound dominantly in a bidentate manner. These results will aid in the design of new inhibitors with the potential to interact with zinc in the target protein.
authors.affiliation: Central Research Laboratories, Kaken Pharmaceutical Co., Ltd, 14, Shinomiya Minamikawara-cho, Yamashina, Kyoto 607-8042, Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Kawai
authors.forename: Naoya
authors.initials: N
authors.lastname: Nagata
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D015195:Drug Design; D008024:Ligands; D008667:Metalloproteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D015032:Zinc / Q000378:metabolism*
chemical_list: D008024:Ligands; D008667:Metalloproteins; D015032:Zinc