5NKY

Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.096 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain.

Belorusova, A.Y.Martinez, A.Gandara, Z.Gomez, G.Fall, Y.Rochel, N.

(2017) Eur J Med Chem 134: 86-96

  • DOI: 10.1016/j.ejmech.2017.03.081
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Synthetic analogs of 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) have been developed with the goal of improving the biological profile of the natural hormone for therapeutic applications. Derivatives of 1,25(OH)2D3 with the oxolane moiety branched in the ...

    Synthetic analogs of 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) have been developed with the goal of improving the biological profile of the natural hormone for therapeutic applications. Derivatives of 1,25(OH)2D3 with the oxolane moiety branched in the side chain at carbon C20, act as Vitamin D nuclear Receptor (VDR) superagonists being several orders of magnitude more active than the natural ligand. Here, we describe the synthesis and biological evaluation of three diastereoisomers of (1S, 3R)-Dihydroxy-(20S)-[(2″-hydroxy-2″-propyl)-tetrahydrofuryl]-22,23,24,25,26,27-hexanor-1α-hydroxyvitamin D3, with different stereochemistry at positions C2 and C5 of the oxolane ring branched at carbon C22 (1, C2RC5S; 2, C2SC5R; 3, C2SC5S). These compounds act as weak VDR agonist in transcriptional assays with compound 3 being the most active. X-ray crystallographic analysis of the VDR ligand-binding domain accommodating the three compounds indicates that the oxolane group branched at carbon C22 is not constrained as in case of compound with oxolane group branched at C20 leading to the loss of interactions of the triene group and increased flexibility of the C/D-rings and of the side chain.


    Organizational Affiliation

    Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor A
A
302Danio rerioMutation(s): 0 
Gene Names: vdra (nr1i1a, vdr)
Find proteins for Q9PTN2 (Danio rerio)
Go to UniProtKB:  Q9PTN2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SRC1
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
91W
Query on 91W

Download SDF File 
Download CCD File 
A
(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(1~{S})-1-[(2~{R},5~{S})-5-(2-oxidanylpropan-2-yl)oxolan-2-yl]ethyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
C28 H44 O4
DDIWZQGTNVZJGO-GKBMNYJXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.096 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.226 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.191α = 90.00
b = 66.191β = 90.00
c = 261.698γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-13-BSV8-0024-01
FRMFrance(FRM: FDT20140930978

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence