5XUQ

Crystal structure of VDR-LBD complexed with an antagonist, 2-methylidene-19,26,27-trinor-22-(S)-butyl-1-hydroxy-25-oxo-25-(1H-pyrrol-2-yl)- vitamin D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of Potent Vitamin D Receptor Antagonist

Kato, A.Tabei, M.Itoh, T.Yamamoto, K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
271Rattus norvegicusMutation(s): 0 
Gene Names: Vdr (Nr1i1)
Find proteins for P13053 (Rattus norvegicus)
Go to UniProtKB:  P13053
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 1
C
13Homo sapiensMutation(s): 0 
Gene Names: MED1 (ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2)
Find proteins for Q15648 (Homo sapiens)
Go to Gene View: MED1
Go to UniProtKB:  Q15648
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8FF
Query on 8FF

Download SDF File 
Download CCD File 
A
(4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(1~{H}-pyrrol-2-yl)octan-1-one
C33 H49 N O3
LSFVNCITLLLHBJ-LTRSXRPOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 151.800α = 90.00
b = 41.490β = 96.97
c = 42.020γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release