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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.jsbmb.2013.02.004

  • 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 pap ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
263Homo 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
VHW
Query on VHW

Download SDF File 
Download CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.975α = 90.00
b = 51.470β = 90.00
c = 131.264γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy