3ZM9

The mechanism of allosteric coupling in choline kinase a1 revealed by a rationally designed inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The Mechanism of Allosteric Coupling in Choline Kinase A1 Revealed by a Rationally Designed Inhibitor

Sahun-Roncero, M.Rubio-Ruiz, B.Saladino, G.Conejo-Garcia, A.Espinosa, A.Velazquez-Campoy, A.Gervasio, F.L.Entrena, A.Hurtado-Guerrero, R.

(2013) Angew Chem Int Ed Engl 52: 4582

  • DOI: https://doi.org/10.1002/anie.201209660
  • Primary Citation of Related Structures:  
    3ZM9

  • PubMed Abstract: 

    Applying a CHOK hold: Combined experimental and computational studies of the binding mode of a rationally designed inhibitor of the dimeric choline kinase α1 (CHOKα1) explain the molecular mechanism of negative cooperativity (see scheme) and how the monomers are connected. The results give insight into how the symmetry of the dimer can be partially conserved despite a lack of conservation in the static crystal structures.


  • 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; Fundacion ARAID, Edificio Pignatelli 36, 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
GTEx:  ENSG00000110721 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35790
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QMQ
Query on QMQ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
1-(4-(4-(4-((6-amino-9H-purin-9-yl)methyl)phenyl)butyl)benzyl)-4- (dimethylamino)pyridinium
C30 H34 N7
NKYSQEHAAOKBTL-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
QMQ PDBBind:  3ZM9 Kd: 38 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.746α = 90
b = 121.214β = 90
c = 131.861γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2013-04-17
    Changes: Refinement description
  • Version 1.3: 2013-05-01
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description