3AZ3

Crystal Structure Analysis of Vitamin D receptor

• PDB DOI: https://doi.org/10.2210/pdb3AZ3/pdb

• Classification: HORMONE RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.243 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 

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: https://doi.org/10.1016/j.bmc.2011.07.001
• Primary Citation of Related Structures:  
  3AZ1, 3AZ2, 3AZ3


• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 29.24 kDa 
• Atom Count: 2,177 
• Modelled Residue Count: 250 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	253	Homo sapiens	Mutation(s): 0  Gene Names: NR1I1, VDR
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens) Explore P11473  Go to UniProtKB:  P11473
PHAROS:  P11473 GTEx:  ENSG00000111424

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DS6	B [auth A]	(4S)-4-hydroxy-5-[4-(3-{4-[(3S)-3-hydroxy-4,4-dimethylpentyl]-3-methylphenyl}pentan-3-yl)-2-methylphenoxy]pentanoic acid C31 H46 O5 YAAVVZVAZRPBGF-XCZPVHLTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.243 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.32	α = 90
b = 52.222	β = 90
c = 131.946	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations