3O1D

Structure-function study of Gemini derivatives with two different side chains at C-20, Gemini-0072 and Gemini-0097.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4007 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-function study of gemini derivatives with two different side chains at C-20, Gemini-0072 and Gemini-0097.

Huet, T.Maehr, H.Lee, H.J.Uskokovic, M.R.Suh, N.Moras, D.Rochel, N.

(2011) Medchemcomm 2: 424-429

  • DOI: 10.1039/C1MD00059D
  • Primary Citation of Related Structures:  3O1E

  • PubMed Abstract: 
  • Derivatives of vitamin D(3) containing a second side-chain emanating at C-20 are known as gemini and act as vitamin D receptor agonists. Recently, two of these, namely Gemini-0072 and the epimeric Gemini-0097, were selected for further studies in vie ...

    Derivatives of vitamin D(3) containing a second side-chain emanating at C-20 are known as gemini and act as vitamin D receptor agonists. Recently, two of these, namely Gemini-0072 and the epimeric Gemini-0097, were selected for further studies in view of their high biological activities and lack of hypercalcemic effects. We now show that the two analogs recruit coactivator SRC-1 better than the parental gemini and act as VDR superagonists. The crystal structures of complexes of zVDR with Gemini-0072 and Gemini-0097 indicate that these ligands induce an extra cavity within the ligand-binding pocket similar to gemini and that their superagonistic activity is due to an increased stabilization of helix H12.


    Organizational Affiliation

    Département de Biologie et de Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Centre National de la Recherche Scientifique, Institut National de la Santé de la Recherche Méedicale, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor A
A
302Danio rerioGene Names: vdra (nr1i1a, vdr)
Find proteins for Q9PTN2 (Danio rerio)
Go to UniProtKB:  Q9PTN2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
B
13Homo sapiensGene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G72
Query on G72

Download SDF File 
Download CCD File 
A
(1R,3R,7E,17beta)-17-[(1S)-6,6,6-trifluoro-5-hydroxy-1-(4-hydroxy-4-methylpentyl)-5-(trifluoromethyl)hex-3-yn-1-yl]-9,10-secoestra-5,7-diene-1,3-diol
1,25-dihydroxy-20S-21(3-trideuteromethyl-3-hydroxy-4,4,4-trideuterobutyl)-23-yne-26,27-hexafluoro-19-nor-cholecalciferol (Gemini-0072)
C31 H44 F6 O4
RAYDHJNMFBHXHA-KPUKIUDSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4007 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.209 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.108α = 90.00
b = 66.108β = 90.00
c = 264.640γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MxCuBEdata collection
PHENIXphasing
PHENIXmodel building
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references