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


Ligand Structure Quality Assessment 


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 interacts with the choline binding site through two different binding modes ...

    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 ALPHAA, B383Homo sapiensMutation(s): 0 
Gene Names: CHKACHKCKI
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U85 (Subject of Investigation/LOI)
Query on U85

Download Ideal Coordinates CCD File 
C [auth A], E [auth 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 (Subject of Investigation/LOI)
Query on A4V

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

Download Ideal Coordinates CCD File 
G [auth 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



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