1J3J

Double mutant (C59R+S108N) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with pyrimethamine, NADPH, and dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into antifolate resistance from malarial DHFR-TS structures.

Yuvaniyama, J.Chitnumsub, P.Kamchonwongpaisan, S.Vanichtanankul, J.Sirawaraporn, W.Taylor, P.Walkinshaw, M.D.Yuthavong, Y.

(2003) Nat Struct Biol 10: 357-365

  • DOI: 10.1038/nsb921
  • Primary Citation of Related Structures:  
    1J3K, 1J3J, 1J3I

  • PubMed Abstract: 
  • Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) is an important target of antimalarial drugs. The efficacy of this class of DHFR-inhibitor drugs is now compromised because of mutations that prevent drug binding yet reta ...

    Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) is an important target of antimalarial drugs. The efficacy of this class of DHFR-inhibitor drugs is now compromised because of mutations that prevent drug binding yet retain enzyme activity. The crystal structures of PfDHFR-TS from the wild type (TM4/8.2) and the quadruple drug-resistant mutant (V1/S) strains, in complex with a potent inhibitor WR99210, as well as the resistant double mutant (K1 CB1) with the antimalarial pyrimethamine, reveal features for overcoming resistance. In contrast to pyrimethamine, the flexible side chain of WR99210 can adopt a conformation that fits well in the active site, thereby contributing to binding. The single-chain bifunctional PfDHFR-TS has a helical insert between the DHFR and TS domains that is involved in dimerization and domain organization. Moreover, positively charged grooves on the surface of the dimer suggest a function in channeling of substrate from TS to DHFR active sites. These features provide possible approaches for the design of new drugs to overcome antifolate resistance.


    Organizational Affiliation

    Department of Biochemistry, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthaseAB280Plasmodium falciparumMutation(s): 0 
EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
Find proteins for P13922 (Plasmodium falciparum (isolate K1 / Thailand))
Explore P13922 
Go to UniProtKB:  P13922
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthaseCD328Plasmodium falciparumMutation(s): 0 
EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
Find proteins for P13922 (Plasmodium falciparum (isolate K1 / Thailand))
Explore P13922 
Go to UniProtKB:  P13922
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
UMP
Query on UMP

Download CCD File 
C, D
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
CP6
Query on CP6

Download CCD File 
A, B
5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
C12 H13 Cl N4
WKSAUQYGYAYLPV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CP6Ki:  0.1899999976158142   nM  BindingDB
CP6IC50:  80   nM  BindingDB
CP6IC50:  2480   nM  BindingDB
CP6Ki:  0.20000000298023224   nM  BindingDB
CP6Ki:  112   nM  BindingDB
CP6Ki:  53.900001525878906   nM  BindingDB
CP6IC50:  30900   nM  BindingDB
CP6IC50:  100000   nM  BindingDB
CP6Ki:  0.8500000238418579   nM  BindingDB
CP6IC50:  41700   nM  BindingDB
CP6Ki:  9.800000190734863   nM  BindingDB
CP6Ki:  1.5   nM  BindingDB
CP6Ki:  380   nM  BindingDB
CP6Ki:  385   nM  BindingDB
CP6IC50:  180   nM  BindingDB
CP6Ki:  283   nM  BindingDB
CP6Ki:  67.0999984741211   nM  BindingDB
CP6IC50:  73500   nM  BindingDB
CP6Ki:  2   nM  BindingDB
CP6Ki:  3.5999999046325684   nM  BindingDB
CP6IC50:  26   nM  BindingDB
CP6IC50:  100000   nM  BindingDB
CP6Ki:  9.800000190734863   nM  Binding MOAD
CP6IC50:  80   nM  BindingDB
CP6Ki:  0.20999999344348907   nM  BindingDB
CP6Ki:  72   nM  BindingDB
CP6Ki:  860   nM  BindingDB
CP6Ki:  1.399999976158142   nM  BindingDB
CP6Ki:  6   nM  BindingDB
CP6IC50:  58   nM  BindingDB
CP6Ki:  0.6000000238418579   nM  BindingDB
CP6Ki:  28.600000381469727   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.343α = 90
b = 154.999β = 90
c = 164.001γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance