title: Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domain.
abstract: The ligand binding domain of the human vitamin D receptor (VDR) was modeled based on the crystal structure of the retinoic acid receptor. The ligand binding pocket of our VDR model is spacious at the helix 11 site and confined at the beta-turn site. The ligand 1alpha, 25-dihydroxyvitamin D(3) was assumed to be anchored in the ligand binding pocket with its side chain heading to helix 11 (site 2) and the A-ring toward the beta-turn (site 1). Three residues forming hydrogen bonds with the functionally important 1alpha- and 25-hydroxyl groups of 1alpha,25-dihydroxyvitamin D(3) were identified and confirmed by mutational analysis: the 1alpha-hydroxyl group is forming pincer-type hydrogen bonds with S237 and R274 and the 25-hydroxyl group is interacting with H397. Docking potential for various ligands to the VDR model was examined, and the results are in good agreement with our previous three-dimensional structure-function theory.
authors.affiliation: Institute of Biomaterial, Medical Research Institute, Tokyo Medical and Dental University, 2-3-10, Surugadai Kanda, Chiyoda-ku, Tokyo 101-0062 Japan.
authors.forename: K
authors.initials: K
authors.lastname: Yamamoto
authors.forename: H
authors.initials: H
authors.lastname: Masuno
authors.forename: M
authors.initials: M
authors.lastname: Choi
authors.forename: K
authors.initials: K
authors.lastname: Nakashima
authors.forename: T
authors.initials: T
authors.lastname: Taga
authors.forename: H
authors.initials: H
authors.lastname: Ooizumi
authors.forename: K
authors.initials: K
authors.lastname: Umesono
authors.forename: W
authors.initials: W
authors.lastname: Sicinska
authors.forename: J
authors.initials: J
authors.lastname: VanHooke
authors.forename: H F
authors.initials: HF
authors.lastname: DeLuca
authors.forename: S
authors.initials: S
authors.lastname: Yamada
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019556:COS Cells; D002117:Calcitriol / Q000737:chemistry; D003198:Computer Simulation; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D011485:Protein Binding / Q000235:genetics; D017433:Protein Structure, Secondary; D018167:Receptors, Calcitriol / Q000737:chemistry* / Q000235:genetics; D018168:Receptors, Retinoic Acid / Q000737:chemistry; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D014158:Transcription, Genetic
chemical_list: D008024:Ligands; D018167:Receptors, Calcitriol; D018168:Receptors, Retinoic Acid; D002117:Calcitriol