7ZFX

VDR complex with Aromatic-D-Ring Analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design, Synthesis, Biological Activity, and Structural Analysis of Novel Des-C-Ring and Aromatic-D-Ring Analogues of 1 alpha ,25-Dihydroxyvitamin D 3.

Seoane, S.Gogoi, P.Zarate-Ruiz, A.Peluso-Iltis, C.Peters, S.Guiberteau, T.Maestro, M.A.Perez-Fernandez, R.Rochel, N.Mourino, A.

(2022) J Med Chem 65: 13112-13124

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00900
  • Primary Citation of Related Structures:  
    7ZFG, 7ZFX

  • PubMed Abstract: 

    The toxic calcemic effects of the natural hormone 1α,25-dihydroxyvitamin D 3 (1,25D 3 , 1,25-dihydroxycholecalciferol) in the treatment of hyperproliferative diseases demand the development of highly active and noncalcemic vitamin D analogues. We report the development of two highly active and noncalcemic analogues of 1,25D 3 that lack the C-ring and possess an m -phenylene ring that replaces the natural D-ring. The new analogues ( 3a , 3b ) are characterized by an additional six-carbon hydroxylated side chain attached either to the aromatic nucleus or to the triene system. Both compounds were synthesized by the Pd-catalyzed tandem cyclization/cross coupling approach starting from alkyne 6 and diphenol 8 . Key steps include a stereoselective Cu-assisted addition of a Grignard reagent to an aromatic alkyne and a Takai olefination of an aromatic aldehyde. The new compounds are noncalcemic and show transcriptional and antiproliferative activities similar to 1,25D 3 . Structural analysis revealed that they induce a large conformational rearrangement of the vitamin D receptor around helix 6.


  • Organizational Affiliation

    Department of Physiology-Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, Avda. Barcelona s/n, Santiago de Compostela 15706, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 receptor A302Danio rerioMutation(s): 0 
Gene Names: vdranr1i1avdr
UniProt
Find proteins for Q9PTN2 (Danio rerio)
Explore Q9PTN2 
Go to UniProtKB:  Q9PTN2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PTN2
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 115Homo sapiensMutation(s): 0 
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IV1 (Subject of Investigation/LOI)
Query on IV1

Download Ideal Coordinates CCD File 
D [auth A](1R,3S,5Z)-5-[(E)-3-[3,5-bis(6-methyl-6-oxidanyl-heptyl)phenyl]prop-2-enylidene]-4-methylidene-cyclohexane-1,3-diol
C32 H50 O4
KAXCFKOQLQAHBM-UHLYCMHWSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.723α = 90
b = 65.723β = 90
c = 263.897γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-11-23 
  • Deposition Author(s): Rochel, N.

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-21-CE17-0009-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description