9FW8 | pdb_00009fw8

VDR complex with UG-650

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.261 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Design, synthesis and biological evaluation of a novel non-Gemini analog of UVB1 and crystal structure of its complex with the vitamin D receptor.

Gomez-Bouzo, U., Peluso-Iltis, C., Santalla, H., Verlinden, L., Verstuyf, A., Rochel, N., Gomez, G., Fall, Y.

(2025) Bioorg Chem 157: 108239-108239

  • DOI: https://doi.org/10.1016/j.bioorg.2025.108239
  • Primary Citation of Related Structures:  
    9FW8

  • PubMed Abstract: 

    We synthesized UG-650, a novel non-Gemini analog of UVB1 that combines structural features of UVB1 and MC 1288. The evaluation of the bioactivities indicates that UG-650 dose-dependently inhibited MCF-7 cell proliferation. In comparison to calcitriol, slightly lower concentrations of UG-650 were needed to achieve equivalent levels of proliferation inhibition. Structural analysis revealed that the analog forms additional interactions stabilizing VDR active form.

    • Organizational Affiliation: 
    • Departamento de Química Orgánica and Instituto de Investigación Sanitaria Galicia Sur (IISGS), Campus Lagoas Marcosende, Universidad de Vigo 36310 Vigo, Spain.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 receptor A302Danio rerioMutation(s): 0 
Gene Names: vdra, nr1i1a, vdr
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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 213Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IGV (Subject of Investigation/LOI)
Query on A1IGV
Download Ideal Coordinates CCD File 
C [auth A](1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{S})-7-methyl-4-methylidene-7-oxidanyl-octan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
C29 H46 O3
LVXRHQNFZLEICU-LIOGGTHJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.261 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.01α = 90
b = 66.01β = 90
c = 264.2γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-05-07 
    • Deposition Author(s): Rochel, N.
Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release