1J3K

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with WR99210, NADPH, and dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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): 2 
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
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  • 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
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  • 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
WRA
Query on WRA

Download CCD File 
A, B
6,6-DIMETHYL-1-[3-(2,4,5-TRICHLOROPHENOXY)PROPOXY]-1,6-DIHYDRO-1,3,5-TRIAZINE-2,4-DIAMINE
C14 H18 Cl3 N5 O2
MJZJYWCQPMNPRM-UHFFFAOYSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WRAKi:  0.019999999552965164   nM  BindingDB
WRAIC50:  2.299999952316284   nM  BindingDB
WRAKi:  0.03999999910593033   nM  BindingDB
WRAIC50:  90   nM  BindingDB
WRAKi:  0.03700000047683716   nM  Binding MOAD
WRAIC50:  0.5699999928474426   nM  BindingDB
WRAIC50:  18   nM  BindingDB
WRAKi:  0.009999999776482582   nM  BindingDB
WRAIC50:  0.5699999928474426   nM  BindingDB
WRAKi:  0.5   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.679α = 90
b = 158.093β = 90
c = 165.738γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

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