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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 intera ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHOLINE KINASE ALPHA AB383Homo sapiensMutation(s): 0 
Gene Names: CHKACHKCKI
EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (PDB Primary Data)
Find proteins for P35790 (Homo sapiens)
Explore P35790 
Go to UniProtKB:  P35790
NIH Common Fund Data Resources
PHAROS:  P35790
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U85
Query on U85

Download Ideal Coordinates CCD File 
A, B
1-((4'-((6-amino-3H-purin-3-yl)methyl)biphenyl-4-yl)methyl)-4-(dimethylamino)pyridinium
C26 H26 N7
YZNBHTPOBJOYMF-UHFFFAOYSA-N
 Ligand Interaction
A4V
Query on A4V

Download Ideal Coordinates CCD File 
A, B
3-benzyladenine
C12 H12 N5
SNSNPCORSVPUTC-UHFFFAOYSA-O
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
U85Kd:  1900   nM  Binding MOAD
U85Kd :  1900   nM  PDBBind
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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