Crystal Structure Analysis of Vitamin D receptor

Experimental Data Snapshot

  • Resolution: 1.36 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

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This is version 1.2 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

    Research Division, Chugai Pharmaceutical Co. Ltd, 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan. kashiwagihrt@chugai-pharm.co.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 receptor253Homo sapiensMutation(s): 0 
Gene Names: NR1I1VDR
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens)
Explore P11473 
Go to UniProtKB:  P11473
PHAROS:  P11473
GTEx:  ENSG00000111424 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11473
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DS6

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • 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 = 44.32α = 90
b = 52.222β = 90
c = 131.946γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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