4BR3

Determination of potential scaffolds for human choline kinase alpha 1 by chemical deconvolution studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Determination of Potential Scaffolds for Human Choline Kinase Alpha 1 by Chemical Deconvolution Studies

Sahun-Roncero, M.Rubio-Ruiz, B.Conejo-Garcia, A.Velazquez-Campoy, A.Entrena, A.Hurtado-Guerrero, R.

(2013) Chembiochem 14: 1291

  • DOI: https://doi.org/10.1002/cbic.201300195
  • Primary Citation of Related Structures:  
    4BR3

  • PubMed Abstract: 

    Dual binding modes: Combined empirical and computational studies of a series of compounds showed adenine and 1-benzyl-4-(dimethylamino)pyridinium fragments to function most efficiently in binding CHOKα1, and also determined how the latter fragment interacts with the choline binding site through two different binding modes. These data provide a basis for the future design of better and more selective inhibitors.


  • Organizational Affiliation

    Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHOLINE KINASE ALPHA
A, B
383Homo sapiensMutation(s): 0 
EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P35790 (Homo sapiens)
Explore P35790 
Go to UniProtKB:  P35790
PHAROS:  P35790
GTEx:  ENSG00000110721 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35790
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
U85 Binding MOAD:  4BR3 Kd: 1900 (nM) from 1 assay(s)
PDBBind:  4BR3 Kd: 1900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.737α = 90
b = 122.254β = 90
c = 132.173γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-07-31
    Changes: Database references
  • Version 1.3: 2015-03-25
    Changes: Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description