5FUT

Human choline kinase a1 in complex with compound 4-(dimethylamino)-1-{4-[4-(4-{[4-(pyrrolidin- 1-yl)pyridinium-1-yl]methyl}phenyl)butyl]benzyl}pyridinium (compound BR25)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Plasmodium Falciparum Choline Kinase Inhibition Leads to a Major Decrease in Phosphatidylethanolamine Causing Parasite Death.

Serran-Aguilera, L.Denton, H.Rubio-Ruiz, B.Lopez-Gutierrez, B.Entrena, A.Izquierdo, L.Smith, T.K.Conejo-Garcia, A.Hurtado-Guerrero, R.

(2016) Sci Rep 6: 33189

  • DOI: https://doi.org/10.1038/srep33189
  • Primary Citation of Related Structures:  
    5FUT

  • PubMed Abstract: 

    Malaria is a life-threatening disease caused by different species of the protozoan parasite Plasmodium, with P. falciparum being the deadliest. Increasing parasitic resistance to existing antimalarials makes the necessity of novel avenues to treat this disease an urgent priority. The enzymes responsible for the synthesis of phosphatidylcholine and phosphatidylethanolamine are attractive drug targets to treat malaria as their selective inhibition leads to an arrest of the parasite's growth and cures malaria in a mouse model. We present here a detailed study that reveals a mode of action for two P. falciparum choline kinase inhibitors both in vitro and in vivo. The compounds present distinct binding modes to the choline/ethanolamine-binding site of P. falciparum choline kinase, reflecting different types of inhibition. Strikingly, these compounds primarily inhibit the ethanolamine kinase activity of the P. falciparum choline kinase, leading to a severe decrease in the phosphatidylethanolamine levels within P. falciparum, which explains the resulting growth phenotype and the parasites death. These studies provide an understanding of the mode of action, and act as a springboard for continued antimalarial development efforts selectively targeting P. falciparum choline kinase.


  • Organizational Affiliation

    Department of Pharmaceutical and Organic Chemistry, c/ Campus de Cartuja, Faculty of Pharmacy, University of Granada, 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
PQ7
Query on PQ7

Download Ideal Coordinates CCD File 
K [auth A]4-(dimethylamino)-1-{4-[4-(4-{[4-(pyrrolidin-1-yl)pyridinium-1-yl]methyl}phenyl)butyl]benzyl}pyridinium
C34 H42 N4
OXXBKOUHROTSGV-UHFFFAOYSA-N
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.364α = 90
b = 61.364β = 90
c = 219.705γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
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: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Data collection, Structure summary
  • Version 1.2: 2017-08-23
    Changes: Data collection
  • Version 1.3: 2019-05-29
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description