3AUN

Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR335 and a synthetic peptide containing the NR2 box of DRIP 205


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design, synthesis and X-ray crystallographic study of new nonsecosteroidal vitamin D receptor ligands

Demizu, Y.Takahashi, T.Kaneko, F.Sato, Y.Okuda, H.Ochiai, E.Horie, K.Takagi, K.Kakuda, S.Takimoto-Kamimura, M.Kurihara, M.

(2011) Bioorg.Med.Chem.Lett. 21: 6104-6107

  • DOI: 10.1016/j.bmcl.2011.08.047

  • PubMed Abstract: 
  • We designed and synthesized nonsecosteroidal vitamin D receptor (VDR) ligands that formed H-bonds with six amino acid residues (Tyr143, Ser233, Arg270, Ser274, His301 and His393) of the VDR ligand-binding domain. The ligand YR335 exhibited potent tra ...

    We designed and synthesized nonsecosteroidal vitamin D receptor (VDR) ligands that formed H-bonds with six amino acid residues (Tyr143, Ser233, Arg270, Ser274, His301 and His393) of the VDR ligand-binding domain. The ligand YR335 exhibited potent transcriptional activity, which was comparable to those of 1α,25-dihydroxyvitamin D(3) and YR301. The crystal structure of the complex formed between YR335 and the VDR ligand-binding domain was solved, which revealed that YR335 formed H-bonds with the six amino acid residues mentioned above.


    Organizational Affiliation

    Division of Organic Chemistry, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya, Tokyo 158-8501, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
265Rattus norvegicusMutation(s): 0 
Gene Names: Vdr (Nr1i1)
Find proteins for P13053 (Rattus norvegicus)
Go to UniProtKB:  P13053
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DRIP 205 NR2 box peptide
B
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
YR4
Query on YR4

Download SDF File 
Download CCD File 
A
(2R)-2-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}butane-1,4-diol
C29 H44 O5
DKNLNQKPISQAEP-SQHAQQRYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 44.237α = 90.00
b = 136.521β = 90.00
c = 47.334γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-08-01
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-08-23
    Type: Source and taxonomy