5YT2

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor.

Sawada, D.Kakuda, S.Takeuchi, A.Kawagoe, F.Takimoto-Kamimura, M.Kittaka, A.

(2018) Org. Biomol. Chem. 16: 2448-2455

  • DOI: 10.1039/C8OB00158H
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Both 2α- and 2β-hydroxypropyl substituted 14-epi-1α,25-dihydroxy-19-nortachysterols were synthesized to study the human vitamin D receptor (hVDR) binding affinity, binding configurations, and interactions with amino acid residues in the ligand bindin ...

    Both 2α- and 2β-hydroxypropyl substituted 14-epi-1α,25-dihydroxy-19-nortachysterols were synthesized to study the human vitamin D receptor (hVDR) binding affinity, binding configurations, and interactions with amino acid residues in the ligand binding domain of hVDR by X-ray co-crystallographic analysis. In conjunction with our previous results on 14-epi-19-nortachysterol, 2-methylidene-, 2α-methyl-, 2β-methyl, and 2α-hydroxypropoxy-14-epi-19-nortachysterol, we propose a variety of effects of substitution at the C2 position in the 14-epi-19-nortachysterol skeleton on biological activities.


    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, Teikyo University, Kaga, Itabashi, Tokyo 173-8605, Japan. akittaka@pharm.teikyo-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
255Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
90O
Query on 90O

Download SDF File 
Download CCD File 
A
(1R,2S,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]ethenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol
(1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol
C29 H48 O4
FSKKMLBYNCANGG-IATMLIOWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.565α = 90.00
b = 51.565β = 90.00
c = 132.490γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
SCALAdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references