3VJS

Vitamin D receptor complex with a carborane compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Boron Cluster-based Development of Potent Nonsecosteroidal Vitamin D Receptor Ligands: Direct Observation of Hydrophobic Interaction between Protein Surface and Carborane

Fujii, S.Masuno, H.Taoda, Y.Kano, A.Wongmayura, A.Nakabayashi, M.Ito, N.Shimizu, M.Kawachi, E.Hirano, T.Endo, Y.Tanatani, A.Kagechika, H.

(2011) J.Am.Chem.Soc. 133: 20933-20941

  • DOI: 10.1021/ja208797n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report here the design and synthesis of a novel vitamin D receptor (VDR) agonist whose hydrophobic core structure is p-carborane (1,12-dicarba-closo-dodecaborane, an icosahedral carbon-containing boron cluster having remarkable thermal and chemica ...

    We report here the design and synthesis of a novel vitamin D receptor (VDR) agonist whose hydrophobic core structure is p-carborane (1,12-dicarba-closo-dodecaborane, an icosahedral carbon-containing boron cluster having remarkable thermal and chemical stability and a characteristically hydrophobic B-H surface). This carborane-based VDR ligand exhibited moderate vitamin D activity, comparable to that of the natural hormone, despite its simple and flexible structure. X-ray structure analysis provided direct evidence that the carborane cage binds to the hydrophobic surface of the ligand-binding pocket of the receptor, promoting transition to the active conformation. These results indicate that the spherical B-H surface of carborane can function efficiently as a hydrophobic anchor in binding to the receptor surface, thereby allowing induced fitting of the three essential hydroxyl groups on the alkyl chains to the appropriate positions for interaction with the VDR binding site, despite the entropic disadvantage of the flexible structure. We suggest that carborane structure is a promising option in the design of novel drug candidates.


    Organizational Affiliation

    Graduate School of Biomedical Science, Tokyo Medical and Dental University, 2-3-10, Kanda-Surugadai, Tokyo 101-0062, Japan.




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
peptide from 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
10S
Query on 10S

Download SDF File 
Download CCD File 
A
1-(2-[(S)-2,4-Dihydroxybutoxy]ethyl)-12-(5-ethyl-5-hydroxyheptyl)-1,12-dicarba-closo-dodecaborane
C17 H42 B10 O4
CZLKNINFVMBXBM-AWEZNQCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
10SIC50: 640 nM BINDINGMOAD
10SIC50: 640 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.605α = 90.00
b = 43.292β = 95.28
c = 42.085γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release