4ITE

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(2H-tetrazol-2-yl)ethyl]vitamin D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis of 2 alpha-heteroarylalkyl active vitamin d3 with therapeutic effect on enhancing bone mineral density in vivo

Matsuo, M.Hasegawa, A.Takano, M.Saito, H.Kakuda, S.Chida, T.Takagi, K.Ochiai, E.Horie, K.Harada, Y.Takimoto-Kamimura, M.Takenouchi, K.Sawada, D.Kittaka, A.

(2013) ACS MED.CHEM.LETT. 4: 671-674

  • DOI: 10.1021/ml400098w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 2α-Heteroarylethyl-1α,25-dihydroxyvitamin D3 analogues, which were designed to form a hydrogen bond between Arg274 of human vitamin D receptor (hVDR) and a nitrogen atom of the heteroaromatic ring at the 2α-position, were synthesized. Among them, 2α- ...

    2α-Heteroarylethyl-1α,25-dihydroxyvitamin D3 analogues, which were designed to form a hydrogen bond between Arg274 of human vitamin D receptor (hVDR) and a nitrogen atom of the heteroaromatic ring at the 2α-position, were synthesized. Among them, 2α-[2-(tetrazol-2-yl)ethyl]-1α,25-dihydroxyvitamin D3 showed higher osteocalcin promoter transactivation activity in human osteosarcoma (HOS) cells and a greater therapeutic effect in ovariectomized (OVX) rats, osteoporosis model animals, on enhancing bone mineral density than those of active vitamin D3. X-ray cocrystallographic analysis of the hVDR-ligand complex confirms that the new hydrogen bond formation stabilized the complex.


    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, Teikyo University , Itabashi-ku, Tokyo 173-8605, Japan.




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
TEY
Query on TEY

Download SDF File 
Download CCD File 
A
(1R,2S,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-2-[2-(1,2,3,4-tetrazol-2-yl)ethyl]cyclohexane-1,3-diol
C30 H48 N4 O3
IFHRQILUGOUOIV-YVUZACRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.760α = 90.00
b = 51.531β = 90.00
c = 131.781γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy