4CG9

Human choline kinase a1 in complex with compound 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Discovery of a New Binding Site on Human Choline Kinase A1: Design, Synthesis, Crystallographic Studies and Biological Evaluation of Asymmetrical Bispyridinium Derivatives

Rubio-Ruiz, B.Figuerola-Conchas, A.Ramos-Torrecillas, J.Capitan-Canadas, F.Rios-Marco, P.Carrasco, M.P.Gallo, M.A.Espinosa, A.Marco, C.Concepcion, C.Entrena-Guadix, A.Hurtado-Guerrero, R.Conejo-Garcia, A.

(2014) J Med Chem 57: 507

  • DOI: https://doi.org/10.1021/jm401665x
  • Primary Citation of Related Structures:  
    4CG8, 4CG9, 4CGA

  • PubMed Abstract: 

    Human choline kinase α (CKα) is a validated drug target for the treatment of cancer. In recent years, a large number of CK inhibitors have been synthesized, and one of them is currently being evaluated in Phase I clinical trials as a treatment for solid tumors. Here we have evaluated a new series of asymmetrical biscationic CK inhibitors by means of enzymatic, crystallographic, and antitumor studies. We demonstrate that one of these structures adopts a completely new binding mode not observed before inducing the aperture of an adjacent binding site. This compound shows antiproliferative and apoptotic effects on cancer cells through activation of caspase-3. Therefore, this study not only provides fruitful insights into the design of more efficient compounds that may target different regions in CKα1 but also explains how these compounds induce apoptosis in cancer cells.


  • Organizational Affiliation

    Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Universidad de Granada , Campus de Cartuja s/n, 18071 Granada, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHOLINE KINASE ALPHA383Homo 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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GQG
Query on GQG

Download Ideal Coordinates CCD File 
B [auth A]N,N-dimethyl-1-[(4-phenylphenyl)methyl]pyridin-1-ium-4-amine
C20 H21 N2
IPMPOJHIUNHPOG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.08α = 90
b = 61.08β = 90
c = 220.56γ = 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: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2014-03-12
    Changes: Source and taxonomy
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description