5FTG

Human choline kinase a1 in complex with compound 1-[[4-[2-[4-[[4-(dimethylamino)pyridin-1- yl]methyl]phenoxy]ethoxy]phenyl]methyl]-N,N- dimethyl-pyridin-4-amine (compound 10a)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.174 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Design, Synthesis, Crystallization and Biological Evaluation of New Symmetrical Biscationic Compounds as Selective Inhibitors of Human Choline Kinase Alpha1 (Chokalpha1)

Schiaffino-Ortega, S.Baglioni, E.Mariotto, E.Bortolozzi, R.Serran-Aguilera, L.Rios-Marco, P.Carrasco-Jimenez, M.P.Gallo, M.A.Hurtado-Guerrero, R.Marco, C.Basso, G.Viola, G.Entrena, A.Lopez-Cara, L.C.

(2016) Sci Rep 6: 23793

  • DOI: https://doi.org/10.1038/srep23793
  • Primary Citation of Related Structures:  
    5FTG

  • PubMed Abstract: 

    A novel family of compounds derivative of 1,1'-(((ethane-1,2-diylbis(oxy))bis(4,1-phenylene))bis(methylene))-bispyridinium or -bisquinolinium bromide (10a-l) containing a pair of oxygen atoms in the spacer of the linker between the biscationic moieties, were synthesized and evaluated as inhibitors of choline kinase against a panel of cancer-cell lines. The most promising compounds in this series were 1,1'-(((ethane-1,2-diylbis(oxy))bis(4,1-phenylene))bis(methylene))bis(4-(dimethylamino)pyridinium) bromide (10a) and 1,1'-(((ethane-1,2-diylbis(oxy))bis(4,1-phenylene))bis(methylene))-bis(7-chloro-4-(pyrrolidin-1-yl)quinolinium) bromide (10l), which inhibit human choline kinase (ChoKα1) with IC50 of 1.0 and 0.92 μM, respectively, in a range similar to that of the previously reported biscationic compounds MN58b and RSM932A. Our compounds show greater antiproliferative activities than do the reference compounds, with unprecedented values of GI50 in the nanomolar range for several of the cancer-cell lines assayed, and more importantly they present low toxicity in non-tumoral cell lines, suggesting a cancer-cell-selective antiproliferative activity. Docking studies predict that the compounds interact with the choline-binding site in agreement with the binding mode of most previously reported biscationic compounds. Moreover, the crystal structure of ChoKα1 with compound 10a reveals that this compound binds to the choline-binding site and mimics HC-3 binding mode as never before.


  • Organizational Affiliation

    Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Campus de Cartuja, 18071 Granada (Spain).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHOLINE KINASE ALPHA378Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NBR
Query on NBR

Download Ideal Coordinates CCD File 
B [auth A]1-[[4-[2-[4-[[4-(dimethylamino)pyridin-1-yl]methyl]phenoxy]ethoxy]phenyl]methyl]-N,N-dimethyl-pyridin-4-amine
C30 H36 N4 O2
SBSYTSUJNSFXCL-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.174 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.65α = 90
b = 60.65β = 90
c = 220.404γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-13
    Changes: Database references
  • Version 1.2: 2016-12-07
    Changes: Structure summary
  • Version 2.0: 2019-10-23
    Changes: Data collection, Non-polymer description, Other
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description