5E7V

Potent Vitamin D Receptor Agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Carborane-based design of a potent vitamin D receptor agonist.

Otero, R.Seoane, S.Sigueiro, R.Belorusova, A.Y.Maestro, M.A.Perez-Fernandez, R.Rochel, N.Mourino, A.

(2016) Chem Sci 7: 1033-1037

  • DOI: 10.1039/c5sc03084f

  • PubMed Abstract: 
  • The vitamin D nuclear receptor (VDR) is a potential target for cancer therapy. It is expressed in many tumors and its ligand shows anticancer actions. To combine these properties with the application of boron neutron capture therapy (BNCT), we design ...

    The vitamin D nuclear receptor (VDR) is a potential target for cancer therapy. It is expressed in many tumors and its ligand shows anticancer actions. To combine these properties with the application of boron neutron capture therapy (BNCT), we design and synthesize a potent VDR agonist based on the skeleton of the hormone 1α,25-dihydroxyvitamin D 3 (1,25D) and an o -carborane (dicarba- o-closo -1,2-dodecaborane) at the end of its side chain. The present ligand is the first secosteroidal analog with the carborane unit that efficiently binds to VDR and functions as an agonist with 1,25D-like potency in transcriptional assay on vitamin D target genes. Moreover it exhibits similar antiproliferative and pro-differentiating activities but is significantly less hypercalcemic than 1,25D. The crystal structure of its complex with VDR ligand binding domain reveals its binding mechanism involving boron-mediated dihydrogen bonds that mimic vitamin D hydroxyl interactions. In addition to the therapeutic interest, this study establishes the basis for the design of new unconventional vitamin D analogs containing carborane moieties for specific molecular recognition, and drug research and development.


    Organizational Affiliation

    Department of Integrative Structural Biology , IGBMC - CNRS UMR7104 - Inserm U964 , 1, rue Laurent Fries , 67400 Illkirch , France . Email: rochel@igbmc.fr.,Departmento de Química Fundamental , Universidad de A Coruña , Campus da Zapateira s/n , 15071 A Coruña , Spain.,Departamento de Química Orgánica , Laboratorio de Investigación Ignacio Ribas , Universidad de Santiago de Compostela , Avda. Ciencias s/n , 15782 Santiago de Compostela , Spain . Email: antonio.mourino@usc.es.,Departamento de Fisiología-CIMUS , Universidad de Santiago , Avda. Barcelona s/n , 15706 Santiago de Compostela , Spain.




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
M7E
Query on M7E

Download SDF File 
Download CCD File 
A
1-ALPHA-HYDROXY-27-NOR-25-O-CARBONYL-VITAMIN D3
C26 H37 B10 O2
AHSCVXNUZMYYOY-UUSULHAXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M7EIC50: 2.9 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.490α = 90.00
b = 66.490β = 90.00
c = 263.340γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
BUSTERphasing
BUSTERrefinement

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

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence