Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29230.93 
• Atom Count: 2028 
• Residue Count: 253 
• Unique protein chains: 1

3AZ2

Crystal Structure Analysis of Vitamin D receptor

• DOI: 10.2210/pdb3AZ2/pdb

• Classification: HORMONE RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2011-05-20 Released: 2011-11-02 
• Deposition Author(s): Itoh, S., Iijima, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.212 
• R-Value Work: 0.195 

Literature

Novel nonsecosteroidal vitamin D(3) carboxylic acid analogs for osteoporosis, and SAR analysis.

Kashiwagi, H., Ono, Y., Shimizu, K., Haneishi, T., Ito, S., Iijima, S., Kobayashi, T., Ichikawa, F., Harada, S., Sato, H., Sekiguchi, N., Ishigai, M., Takahashi, T.

(2011) Bioorg.Med.Chem. 19: 4721-4729

• PubMed: 21795053 
• DOI: 10.1016/j.bmc.2011.07.001
• Primary Citation of Related Structures:  
  3AZ3, 3AZ1


• PubMed Abstract: 
  

Novel vitamin D(3) analogs with carboxylic acid were explored, focusing on a nonsecosteroidal analog, LG190178, with a bisphenyl skeleton. From X-ray analysis of these analogs with vitamin D receptor (VDR), the carboxyl groups had very unique hydrogen bonding interactions in VDR and mimicked 1α-hydroxy group and/or 3β-hydroxy group of 1α,25-dihydroxyvitamin D(3). A highly potent analog, 6a, with good in vitro activity and pharmacokinetic profiles was identified from an SAR study. Compound 6a showed significant prevention of bone loss in a rat osteoporosis model by oral administration.

---

Organizational Affiliation: 

Research Division, Chugai Pharmaceutical Co. Ltd, 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Vitamin D3 receptor	A	253	Homo sapiens	Mutation(s): 0  Gene Names: VDR (NR1I1)
Find proteins for P11473 (Homo sapiens) Go to Gene View: VDR Go to UniProtKB:  P11473

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DS3	A	5-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}pentanoic acid C30 H44 O5 CWFBRPYCPUENQV-MHZLTWQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.212 
• R-Value Work: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 44.530	α = 90.00
b = 51.840	β = 90.00
c = 132.400	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
BUSTER-TNT	refinement
BUSTER	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-20 
• Released Date: 2011-11-02 
• Deposition Author(s): Itoh, S., Iijima, S.

Revision History 

• Version 1.0: 2011-11-02
  Type: Initial release
• Version 1.1: 2017-08-23
  Type: Refinement description, Source and taxonomy