6FOD

Vitamin D nuclear receptor complex 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Aromatic-Based Design of Highly Active and Noncalcemic Vitamin D Receptor Agonists.

Gogoi, P.Seoane, S.Sigueiro, R.Guiberteau, T.Maestro, M.A.Perez-Fernandez, R.Rochel, N.Mourino, A.

(2018) J. Med. Chem. 61: 4928-4937

  • DOI: 10.1021/acs.jmedchem.8b00337
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the design, synthesis, biological evaluation, and structural analysis of a new class of vitamin D analogues that possess an aromatic m-phenylene D-ring and an alkyl chain replacing the C-ring. A key feature of the synthetic strategy is a st ...

    We report the design, synthesis, biological evaluation, and structural analysis of a new class of vitamin D analogues that possess an aromatic m-phenylene D-ring and an alkyl chain replacing the C-ring. A key feature of the synthetic strategy is a stereoselective Pd-catalyzed construction of the triene system in aqueous medium that allows the rapid preparation of small amounts of VDR ligands for biological screening. Analogues with the shorter (2a) and longer (2d, 2e) side chains attached to the triene system have no calcemic activity. Compound 2a binds to VDR with the same order of magnitude than calcipotriol and oxacalcitriol. It also reduces proliferation in normal and tumor cells similarly to the natural hormone 1α,25-dihydroxyvitamin D 3 , calcipotriol, and oxacalcitriol, suggesting preclinical studies related to hyperproliferative disorders such as psoriasis and cancer.


    Organizational Affiliation

    Department of Organic Chemistry, Research Laboratory Ignacio Ribas , University of Santiago de Compostela , Avenida das Ciencias s/n , 15782 Santiago de Compostela , Spain.,Department of Integrative Structural Biology , IGBMC-Université de Strasbourg, CNRS UMR 7104, INSERM U1258 , 67400 Illkirch , France.,Laboratoire ICube , Université de Strasbourg, CNRS UMR 7357 , 67000 Strasbourg , France.,Department of Chemistry-CICA , University of A Coruña , Campus da Zapateira s/n , 15071 A Coruña , Spain.,Department of Physiology-Center for Research in Molecular Medicine and Chronic Diseases (CIMUS) , University of Santiago de Compostela , Avenida 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
E05
Query on E05

Download SDF File 
Download CCD File 
A
(1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]pent-2-enylidene]cyclohexane-1,3-diol
C26 H38 O3
BQVXPWDQMUNMLU-FIKMVKLPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
E05IC50: 10 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.187 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 65.930α = 90.00
b = 65.930β = 90.00
c = 264.200γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-07 
  • Released Date: 2018-05-16 
  • Deposition Author(s): Rochel, N.

Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-13-BSV8-0024-01
Spanish Ministry of Economy and CompetitivenessSpainSAF2015-69221-R

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references