6FO8

Vitamin D nuclear receptor complex 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor A
1
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
DZT
Query on DZT

Download SDF File 
Download CCD File 
1
(1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]non-2-enylidene]cyclohexane-1,3-diol
C30 H46 O3
ISCBFPXNVUJFJI-HSDCXWRNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.690α = 90.00
b = 66.690β = 90.00
c = 264.520γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-06 
  • 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