4G1Z

Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the accommodation of bis- and tris-aromatic derivatives in vitamin d nuclear receptor.

Ciesielski, F.Sato, Y.Chebaro, Y.Moras, D.Dejaegere, A.Rochel, N.

(2012) J.Med.Chem. 55: 8440-8449

  • DOI: 10.1021/jm300858s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Actual use of the active form of vitamin D (calcitriol or 1α,25-dihydroxyvitamin D(3)) to treat hyperproliferative disorders is hampered by calcemic effects, hence the continuous development of chemically modified analogues with dissociated profiles. ...

    Actual use of the active form of vitamin D (calcitriol or 1α,25-dihydroxyvitamin D(3)) to treat hyperproliferative disorders is hampered by calcemic effects, hence the continuous development of chemically modified analogues with dissociated profiles. Structurally distinct nonsecosteroidal analogues have been developed to mimic calcitriol activity profiles with low calcium serum levels. Here, we report the crystallographic study of vitamin D nuclear receptor (VDR) ligand binding domain in complexes with six nonsecosteroidal analogues harboring two or three phenyl rings. These compounds induce a stimulated transcription in the nanomolar range, similar to calcitriol. Examination of the protein-ligand interactions reveals the mode of binding of these nonsecosteroidal compounds and highlights the role of the various chemical modifications of the ligands to VDR binding and activity, notably (de)solvation effects. The structures with the tris-aromatic ligands exhibit a rearrangement of a novel region of the VDR ligand binding pocket, helix H6.


    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor A
A
300Danio rerioMutation(s): 0 
Gene Names: vdra (nr1i1a, vdr)
Find proteins for Q9PTN2 (Danio rerio)
Go to UniProtKB:  Q9PTN2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
B
15Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0VP
Query on 0VP

Download SDF File 
Download CCD File 
A
3-(5'-{[3,4-bis(hydroxymethyl)benzyl]oxy}-2'-ethyl-2-propylbiphenyl-4-yl)pentan-3-ol
C31 H40 O4
SMKNKOCYSYNJHN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.472α = 90.00
b = 66.472β = 90.00
c = 262.336γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement
CNSphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2012-11-21
    Type: Database references