9FBF

VDR complex with UG-481


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design, Synthesis, and Biological Evaluation of New Type of Gemini Analogues with a Cyclopropane Moiety in Their Side Chain.

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

(2024) J Med Chem 67: 10386-10400

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00854
  • Primary Citation of Related Structures:  
    9EYR, 9FBF

  • PubMed Abstract: 

    We synthesized two new gemini analogues, UG-480 and UG-481 , that incorporate a modified longer side chain containing a cyclopropane group. The evaluation of the bioactivities of the two gemini analogues indicated that the 17,20 threo (20 S ) compound, UG-480 , is the most active one and is as active as 1,25(OH) 2 D 3 . Docking and molecular dynamics (MD) data showed that the compounds bind efficiently to vitamin D receptor (VDR) with UG-480 to form an energetically more favorable interaction with His397. Structural analysis indicated that whereas the UG-480 compound efficiently stabilizes the active VDR conformation, it induces conformational changes in the H6-H7 VDR region that are greater than those induced by the parental Gemini and that this is due to the occupancy of the secondary channel by its modified side chain.


  • Organizational Affiliation

    Departamento de Química Orgánica and Instituto de Investigación Sanitaría Galicia Sur (IISGS), Campus Lagoas Marcosende, Universidad de Vigo, Vigo 36310, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IBM (Subject of Investigation/LOI)
Query on A1IBM

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-[(1~{S})-5-methyl-1-[(1~{R},2~{R})-2-(3-methyl-3-oxidanyl-butyl)cyclopropyl]-5-oxidanyl-hexyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
C34 H56 O4
IKZQBCYVSWLJFE-OGUMBUAASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.203 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.54α = 90
b = 65.54β = 90
c = 262.95γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-06-19 
  • 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: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Database references