8CK5

VDR LBD complex with 25-nitro derivative of 1,25D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Structural analysis and biological activities of C25-amino and C25-nitro vitamin D analogs.

Gomez-Bouzo, U.Belorusova, A.Y.Rivadulla, M.L.Santalla, H.Verlinden, L.Verstuyf, A.Ferronato, M.J.Curino, A.C.Facchinetti, M.M.Fall, Y.Gomez, G.Rochel, N.

(2023) Bioorg Chem 136: 106528-106528

  • DOI: https://doi.org/10.1016/j.bioorg.2023.106528
  • Primary Citation of Related Structures:  
    8CK5, 8CKC

  • PubMed Abstract: 

    Intense synthetic efforts have been directed towards the development of noncalcemic analogs of 1,25-dihydroxyvitamin D 3 . We describe here the structural analysis and biological evaluation of two derivatives of 1,25-dihydroxyvitamin D 3 with modifications limited to the replacement of the 25-hydroxyl group by a 25-amino or 25-nitro groups. Both compounds are agonists of the vitamin D receptor. They mediate biological effects similar to 1,25-dihydroxyvitamin D 3 , the 25-amino derivative being the most potent one while being less calcemic than 1,25-dihydroxyvitamin D 3 . The in vivo properties of the compounds make them of potential therapeutic value.


  • Organizational Affiliation

    Departamento de Química Orgánica and Instituto de Investigación Sanitaria Galicia Sur (IISGS), Campus Lagoas Marcosende, Universidad de Vigo, 36310 Vigo, 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
UYO (Subject of Investigation/LOI)
Query on UYO

Download Ideal Coordinates CCD File 
D [auth A](1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-nitro-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
C27 H43 N O4
SSROHWHVGDBOBJ-NKMMMXOESA-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: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.701α = 90
b = 65.701β = 90
c = 262.106γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UYOClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2023-04-26 
  • Deposition Author(s): Rochel, N.

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-13-BSV8-0024-01
Agence Nationale de la Recherche (ANR)FranceANR-21-CE17-0009-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection