3O1E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.3 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, 3O1D

  • 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 view of their high biological activities and lack of hypercalcemic effects ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vitamin D3 receptor AA302Danio rerioMutation(s): 0 
Gene Names: vdranr1i1avdr
UniProt
Find proteins for Q9PTN2 (Danio rerio)
Explore Q9PTN2 
Go to UniProtKB:  Q9PTN2
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2B13Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H97 (Subject of Investigation/LOI)
Query on H97

Download Ideal Coordinates CCD File 
C [auth A](1R,3R,7E,17beta)-17-[(1R)-6,6,6-trifluoro-5-hydroxy-1-(4-hydroxy-4-methylpentyl)-5-(trifluoromethyl)hex-3-yn-1-yl]-9,1 0-secoestra-5,7-diene-1,3-diol
C31 H44 F6 O4
RAYDHJNMFBHXHA-DUSBBPLISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.842α = 90
b = 65.842β = 90
c = 263.718γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2021-03-10
    Changes: Advisory, Database references, Derived calculations, Structure summary