5AFV

Pharmacophore-based virtual screening to discover new active compounds for human choline kinase alpha1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pharmacophore-Based Virtual Screening to Discover New Active Compounds for Human Choline Kinase Alpha1

Serran-Aguilera, L.Nuti, R.Lopez-Cara, L.C.Gallo Mezo, M.A.Macchiarulo, A.Entrena, A.Hurtado-Guerrero, R.

(2015) Mol Inform 34: 458

  • DOI: 10.1002/minf.201400140

  • PubMed Abstract: 
  • Choline kinase (CK) catalyses the transfer of the ATP γ-phosphate to choline to generate phosphocholine and ADP in the presence of magnesium leading to the synthesis of phosphatidylcholine. Of the three isoforms of CK described in humans, only the α ...

    Choline kinase (CK) catalyses the transfer of the ATP γ-phosphate to choline to generate phosphocholine and ADP in the presence of magnesium leading to the synthesis of phosphatidylcholine. Of the three isoforms of CK described in humans, only the α isoforms (HsCKα) are strongly associated with cancer and have been validated as drug targets to treat this disease. Over the years, a large number of Hemicholinium-3 (HC-3)-based HsCKα biscationic inhibitors have been developed though the relevant common features important for the biological function have not been defined. Here, selecting a large number of previous HC-3-based inhibitors, we discover through computational studies a pharmacophore model formed by five moieties that are included in the 1-benzyl-4-(N-methylaniline)pyridinium fragment. Using a pharmacophore-guided virtual screening, we then identified 6 molecules that showed binding affinities in the low μM range to HsCKα1. Finally, protein crystallization studies suggested that one of these molecules is bound to the choline and ATP-binding sites. In conclusion, we have developed a pharmacophore model that not only allowed us to dissect the structural important features of the previous HC-3 derivatives, but also enabled the identification of novel chemical tools with good ligand efficiencies to investigate the biological functions of HsCKα1.


    Organizational Affiliation

    Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, Granada 18071, Spain phone: +34 958 243848.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHOLINE KINASE ALPHA
A, B
378Homo sapiensMutation(s): 0 
Gene Names: CHKA (CHK, CKI)
EC: 2.7.1.32
Find proteins for P35790 (Homo sapiens)
Go to Gene View: CHKA
Go to UniProtKB:  P35790
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JH5
Query on JH5

Download SDF File 
Download CCD File 
A, B
1-benzyl-4-(benzylamino)-1H-1,2,4-triazol-4-ium
C16 H17 N4
FPCLJFAEMFICTP-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.129α = 90.00
b = 120.180β = 90.00
c = 132.393γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Data collection