1CET

CHLOROQUINE BINDS IN THE COFACTOR BINDING SITE OF PLASMODIUM FALCIPARUM LACTATE DEHYDROGENASE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Chloroquine binds in the cofactor binding site of Plasmodium falciparum lactate dehydrogenase.

Read, J.A.Wilkinson, K.W.Tranter, R.Sessions, R.B.Brady, R.L.

(1999) J.Biol.Chem. 274: 10213-10218

  • Primary Citation of Related Structures:  1CEQ

  • PubMed Abstract: 
  • Although the molecular mechanism by which chloroquine exerts its effects on the malarial parasite Plasmodium falciparum remains unclear, the drug has previously been found to interact specifically with the glycolytic enzyme lactate dehydrogenase from ...

    Although the molecular mechanism by which chloroquine exerts its effects on the malarial parasite Plasmodium falciparum remains unclear, the drug has previously been found to interact specifically with the glycolytic enzyme lactate dehydrogenase from the parasite. In this study we have determined the crystal structure of the complex between chloroquine and P. falciparum lactate dehydrogenase. The bound chloroquine is clearly seen within the NADH binding pocket of the enzyme, occupying a position similar to that of the adenyl ring of the cofactor. Chloroquine hence competes with NADH for binding to the enzyme, acting as a competitive inhibitor for this critical glycolytic enzyme. Specific interactions between the drug and amino acids unique to the malarial form of the enzyme suggest this binding is selective. Inhibition studies confirm that chloroquine acts as a weak inhibitor of lactate dehydrogenase, with mild selectivity for the parasite enzyme. As chloroquine has been shown to accumulate to millimolar concentrations within the food vacuole in the gut of the parasite, even low levels of inhibition may contribute to the biological efficacy of the drug. The structure of this enzyme-inhibitor complex provides a template from which the quinoline moiety might be modified to develop more efficient inhibitors of the enzyme.


    Related Citations: 
    • The Structure of Lactate Dehydrogenase from Plasmodium Falciparum Reveals a New Target for Anti-Malarial Design
      Dunn, C.R.,Banfield, M.J.,Barker, J.J.,Higham, C.W.,Moreton, K.M.,Turgut-Balik, D.,Brady, R.L.,Holbrook, J.J.
      (1996) Nat.Struct.Mol.Biol. 3: 912


    Organizational Affiliation

    Department of Biochemistry and Centre for Molecular Recognition, University of Bristol, Bristol BS8 1TD United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (L-LACTATE DEHYDROGENASE)
A
316Plasmodium falciparumEC: 1.1.1.27
Find proteins for Q27743 (Plasmodium falciparum)
Go to UniProtKB:  Q27743
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLQ
Query on CLQ

Download SDF File 
Download CCD File 
A
N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE
CHLOROQUINE
C18 H26 Cl N3
WHTVZRBIWZFKQO-CQSZACIVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CLQKi: 1300000 nM BINDINGMOAD
CLQKi: 1300000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.154 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.930α = 90.00
b = 85.440β = 90.00
c = 92.190γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-19
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance