4ITE | pdb_00004ite

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(2H-tetrazol-2-yl)ethyl]vitamin D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TEYClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Synthesis of 2 alpha-heteroarylalkyl active vitamin d3 with therapeutic effect on enhancing bone mineral density in vivo

Matsuo, M.Hasegawa, A.Takano, M.Saito, H.Kakuda, S.Chida, T.Takagi, K.Ochiai, E.Horie, K.Harada, Y.Takimoto-Kamimura, M.Takenouchi, K.Sawada, D.Kittaka, A.

(2013) ACS Med Chem Lett 4: 671-674

  • DOI: https://doi.org/10.1021/ml400098w
  • Primary Citation of Related Structures:  
    4ITE, 4ITF

  • PubMed Abstract: 

    2α-Heteroarylethyl-1α,25-dihydroxyvitamin D3 analogues, which were designed to form a hydrogen bond between Arg274 of human vitamin D receptor (hVDR) and a nitrogen atom of the heteroaromatic ring at the 2α-position, were synthesized. Among them, 2α-[2-(tetrazol-2-yl)ethyl]-1α,25-dihydroxyvitamin D3 showed higher osteocalcin promoter transactivation activity in human osteosarcoma (HOS) cells and a greater therapeutic effect in ovariectomized (OVX) rats, osteoporosis model animals, on enhancing bone mineral density than those of active vitamin D3. X-ray cocrystallographic analysis of the hVDR-ligand complex confirms that the new hydrogen bond formation stabilized the complex.


  • Organizational Affiliation

    Faculty of Pharmaceutical Sciences, Teikyo University , Itabashi-ku, Tokyo 173-8605, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 receptor263Homo sapiensMutation(s): 0 
Gene Names: VDR
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TEY
Query on TEY

Download Ideal Coordinates CCD File 
B [auth A](1R,2S,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-2-[2-(1,2,3,4-tetrazol-2-yl)ethyl]cyclohexane-1,3-diol
C30 H48 N4 O3
IFHRQILUGOUOIV-YVUZACRZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.76α = 90
b = 51.531β = 90
c = 131.781γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TEYClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description