3WWR

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1-((((1S,2R,6R,Z)-2,6-dihydroxy-4-((E)-2-((1R,3aS,7aR)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methylhexahydro-1H-inden-4(2H)-ylidene)ethylidene)-3-methylenecyclohexyl)oxy)methyl)cyclopropanecarbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis and biological activities of vitamin D3 derivatives with cyanoalkyl side chain at C-2 position

Saitoh, H.Watanabe, H.Kakuda, S.Takimoto-Kamimura, M.Takagi, K.Takeuchi, A.Takenouchi, K.

(2014) J.Steroid Biochem.Mol.Biol. --: --

  • DOI: 10.1016/j.jsbmb.2014.12.004

  • PubMed Abstract: 
  • We synthesized and evaluated novel vitamin D3 derivatives with cyanoalkyl side chain at C-2 position on the basis of our previous research for 2α side chain which bears nitrogen atom-containing functional group. Through a study of X-ray co-crystal st ...

    We synthesized and evaluated novel vitamin D3 derivatives with cyanoalkyl side chain at C-2 position on the basis of our previous research for 2α side chain which bears nitrogen atom-containing functional group. Through a study of X-ray co-crystal structures of human VDR and compound 3, we demonstrated that the 2α alkyl side chain in compound 3 shows a novel interaction in the complex of hVDR-LBD and ligand. This article is part of a Special Issue entitled '17th Vitamin D Workshop'.


    Organizational Affiliation

    Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan. Electronic address: hi.saitou@teijin.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
263Homo sapiensMutation(s): 0 
Gene Names: VDR (NR1I1)
Find proteins for P11473 (Homo sapiens)
Go to Gene View: VDR
Go to UniProtKB:  P11473
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3AJ
Query on 3AJ

Download SDF File 
Download CCD File 
A
1-({[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}methyl)cyclopropanecarbonitrile
C32 H49 N O4
XRVHRGHHDVJYGR-IPBGMLIISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.167α = 90.00
b = 51.826β = 90.00
c = 132.384γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2017-08-16
    Type: Refinement description, Source and taxonomy