3VHW

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 4-MP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Synthesis of novel C-2 substituted vitamin D derivatives having ringed side chains and their biological evaluation on bone

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

(2013) J Steroid Biochem Mol Biol 136: 3-8

  • DOI: https://doi.org/10.1016/j.jsbmb.2013.02.004
  • Primary Citation of Related Structures:  
    3VHW

  • PubMed Abstract: 

    Up to the present, numerous vitamin D derivatives have been synthesized, but most of them have straight side chains, and there are few publications described about in vitro and in vivo evaluations on bone by vitamin D derivatives. In our previous paper, we reported the synthesis of various C-2 substituted vitamin D derivatives (2b-2i) with a 2,2-dimethylcyclopentanone unit in the CD-ring side chains, and that the derivatives have strong activity for enhancing bone growth. On the basis of results, this time, we report the synthesis of 2α-substituted vitamin D3 derivatives with chiral cyclopentanone (3-6 and 12-16). These derivatives were obtained by Pd-coupling reaction with A-ring precursor and CD-rings precursor. We evaluated novel derivatives in vitro assays, for affinities for VDR and transactivation assays by human osteosarcoma (HOS) cells. In this research, we demonstrated that some novel vitamin D derivatives (12-MP, 13-MP, 15-MP and 16-LP) have strong transactivation activities in spite of lower affinity for VDR than 1. In addition, we also demonstrated that these derivatives have strong activities for enhancing bone growth using OVX therapeutic rats. This article is part of a Special Issue entitled 'Vitamin D Workshop'.


  • Organizational Affiliation

    Teijin Institute for Bio-medical Research, Teijin Pharma Ltd., Tokyo 191-8512, Japan. hi.saitou@teijin.co.jp


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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VHW
Query on VHW

Download Ideal Coordinates CCD File 
B [auth A]methyl (1S,3E)-3-{(2R)-2-[(1R,3aS,4E,7aR)-4-{(2Z)-2-[(3R,4S,5R)-3,5-dihydroxy-4-(3-hydroxypropoxy)-2-methylidenecyclohexylidene]ethylidene}-7a-methyloctahydro-1H-inden-1-yl]propylidene}-1-ethyl-2-oxocyclopentanecarboxylate (non-preferred name)
C34 H50 O7
RRTPTPSZIBNWCN-ZZGOIYGKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.975α = 90
b = 51.47β = 90
c = 131.264γ = 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 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-07-17
    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