2BL9

X-ray crystal structure of Plasmodium vivax dihydrofolate reductase in complex with pyrimethamine and its derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Dihydrofolate Reductase from Plasmodium Vivax: Pyrimethamine Displacement Linked with Mutation-Induced Resistance.

Kongsaeree, P.Khongsuk, P.Leartsakulpanich, U.Chitnumsub, P.Tarnchompoo, B.Walkinshaw, M.D.Yuthavong, Y.

(2005) Proc.Natl.Acad.Sci.USA 102: 13046

  • DOI: 10.1073/pnas.0501747102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyrimethamine (Pyr) targets dihydrofolate reductase of Plasmodium vivax (PvDHFR) as well as other malarial parasites, but its use as antimalarial is hampered by the widespread high resistance. Comparison of the crystal structures of PvDHFR from wild- ...

    Pyrimethamine (Pyr) targets dihydrofolate reductase of Plasmodium vivax (PvDHFR) as well as other malarial parasites, but its use as antimalarial is hampered by the widespread high resistance. Comparison of the crystal structures of PvDHFR from wild-type and the Pyr-resistant (SP21, Ser-58 --> Arg + Ser-117 --> Asn) strain as complexes with NADPH and Pyr or its analog lacking p-Cl (Pyr20) clearly shows that the steric conflict arising from the side chain of Asn-117 in the mutant enzyme, accompanied by the loss of binding to Ser-120, is mainly responsible for the reduction in binding of Pyr. Pyr20 still effectively inhibits both the wild-type and SP21 proteins, and the x-ray structures of these complexes show how Pyr20 fits into both active sites without steric strain. These structural insights suggest a general approach for developing new generations of antimalarial DHFR inhibitors that, by only occupying substrate space of the active site, would retain binding affinity with the mutant enzymes.


    Organizational Affiliation

    Department of Chemistry and Center for Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
A
238Plasmodium vivaxMutation(s): 0 
Find proteins for O02604 (Plasmodium vivax)
Go to UniProtKB:  O02604
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CP6
Query on CP6

Download SDF File 
Download CCD File 
A
5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
PYRIMETHAMINE
C12 H13 Cl N4
WKSAUQYGYAYLPV-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CP6Ki: 0.2 - 3 nM (98) BINDINGDB
CP6IC50: 180 - 20010 nM (98) BINDINGDB
CP6Ki: 0.16 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.280α = 90.00
b = 55.740β = 107.09
c = 45.720γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance