3JSU | pdb_00003jsu

Quadruple mutant(N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase(PFDHFR-TS) complexed with QN254, NADPH, and dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.206 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3JSU

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Preclinical evaluation of the antifolate QN254, 5-chloro- N'6'-(2,5-dimethoxy-benzyl)-quinazoline-2,4,6-triamine, as an antimalarial drug candidate

Nzila, A.Rottmann, M.Chitnumsub, P.Kiara, S.M.Kamchonwongpaisan, S.Maneeruttanarungroj, C.Taweechai, S.Yeung, B.K.Goh, A.Lakshminarayana, S.B.Zou, B.Wong, J.Ma, N.L.Weaver, M.Keller, T.H.Dartois, V.Wittlin, S.Brun, R.Yuthavong, Y.Diagana, T.T.

(2010) Antimicrob Agents Chemother 54: 2603-2610

  • DOI: https://doi.org/10.1128/AAC.01526-09
  • Primary Citation Related Structures: 
    3JSU

  • PubMed Abstract: 

    Drug resistance against dihydrofolate reductase (DHFR) inhibitors-such as pyrimethamine (PM)-has now spread to almost all regions where malaria is endemic, rendering antifolate-based malaria treatments highly ineffective. We have previously shown that the di-amino quinazoline QN254 [5-chloro-N'6'-(2,5-dimethoxy-benzyl)-quinazoline-2,4,6-triamine] is active against the highly PM-resistant Plasmodium falciparum V1S strain, suggesting that QN254 could be used to treat malaria in regions with a high prevalence of antifolate resistance. Here, we further demonstrate that QN254 is highly active against Plasmodium falciparum clinical isolates, displaying various levels of antifolate drug resistance, and we provide biochemical and structural evidence that QN254 binds and inhibits the function of both the wild-type and the quadruple-mutant (V1S) forms of the DHFR enzyme. In addition, we have assessed QN254 oral bioavailability, efficacy, and safety in vivo. The compound displays favorable pharmacokinetic properties after oral administration in rodents. The drug was remarkably efficacious against Plasmodium berghei and could fully cure infected mice with three daily oral doses of 30 mg/kg. In the course of these efficacy studies, we have uncovered some dose limiting toxicity at higher doses that was confirmed in rats. Thus, despite its relative in vitro selectivity toward the Plasmodium DHFR enzyme, QN254 does not show the adequate therapeutic index to justify its further development as a single agent.


  • Organizational Affiliation
    • Kenya Medical Research Institute/Wellcome Trust Collaborative Research Program, Kilifi, Kenya.

Macromolecule Content 

  • Total Structure Weight: 146.64 kDa 
  • Atom Count: 9,487 
  • Modeled Residue Count: 1,087 
  • Deposited Residue Count: 1,216 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydrofolate reductase-thymidylate synthase
A, B
608Plasmodium falciparumMutation(s): 4 
Gene Names: DHFR-TSV1/S
EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
UniProt
Find proteins for D9N170 (Plasmodium falciparum)
Explore D9N170 
Go to UniProtKB:  D9N170
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9N170
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
KA5

Query on KA5



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
5-chloro-N~6~-(2,5-dimethoxybenzyl)quinazoline-2,4,6-triamine
C17 H18 Cl N5 O2
ZQYDKYDSKVGDJP-UHFFFAOYSA-N
UMP

Query on UMP



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KA5 BindingDB:  3JSU IC50: 0.39 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.991α = 90
b = 157.375β = 90
c = 165.511γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
superguidata collection
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description