title: Chemocavity: specific concavity in protein reserved for the binding of biologically functional small molecules.
abstract: The idea that there should be a specific site on a protein for a particular functional small molecule is widespread. It is, however, usually not so easy to understand what characteristics of the site determine the binding ability of the functional small molecule. We have focused on the concurrence rate of the 20 standard amino acids at such binding sites. In order to correlate the concurrence rate and the specific binding site, we have analyzed high-quality X-ray structures of complexes between proteins and small molecules. A novel index characterizing the binding site based on the concurrency rate has been introduced. Using this index we have identified that there is a specific concavity designated as a chemocavity where a specific group of small molecules, i.e., canonical molecular group, is highly inclined to be bound. This study has demonstrated that a chemocavity is reserved for a specific canonical molecular group, and the prevalent idea has been confirmed.
authors.affiliation: Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki, Japan. hirayama@is.icc.u-tokai.ac.jp
authors.forename: Shinji
authors.initials: S
authors.lastname: Soga
authors.forename: Hiroki
authors.initials: H
authors.lastname: Shirai
authors.forename: Masato
authors.initials: M
authors.lastname: Kobori
authors.forename: Noriaki
authors.initials: N
authors.lastname: Hirayama
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D008958:Models, Molecular; D004364:Pharmaceutical Preparations / Q000737:chemistry* / Q000378:metabolism*; D011166:Porphyrins / Q000737:chemistry / Q000378:metabolism; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D004364:Pharmaceutical Preparations; D011166:Porphyrins; D011506:Proteins