4DPH

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with P65 and NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target

Yuthavong, Y.Tarnchompoo, B.Vilaivan, T.Chitnumsub, P.Kamchonwongpaisan, S.Charman, S.A.McLennan, D.N.White, K.L.Vivas, L.Bongard, E.Thongphanchang, C.Taweechai, S.Vanichtanankul, J.Rattanajak, R.Arwon, U.Fantauzzi, P.Yuvaniyama, J.Charman, W.N.Matthews, D.

(2012) Proc Natl Acad Sci U S A 109: 16823-16828

  • DOI: https://doi.org/10.1073/pnas.1204556109
  • Primary Citation of Related Structures:  
    4DDR, 4DP3, 4DPD, 4DPH

  • PubMed Abstract: 

    Malarial dihydrofolate reductase (DHFR) is the target of antifolate antimalarial drugs such as pyrimethamine and cycloguanil, the clinical efficacy of which have been compromised by resistance arising through mutations at various sites on the enzyme. Here, we describe the use of cocrystal structures with inhibitors and substrates, along with efficacy and pharmacokinetic profiling for the design, characterization, and preclinical development of a selective, highly efficacious, and orally available antimalarial drug candidate that potently inhibits both wild-type and clinically relevant mutated forms of Plasmodium falciparum (Pf) DHFR. Important structural characteristics of P218 include pyrimidine side-chain flexibility and a carboxylate group that makes charge-mediated hydrogen bonds with conserved Arg122 (PfDHFR-TS amino acid numbering). An analogous interaction of P218 with human DHFR is disfavored because of three species-dependent amino acid substitutions in the vicinity of the conserved Arg. Thus, P218 binds to the active site of PfDHFR in a substantially different fashion from the human enzyme, which is the basis for its high selectivity. Unlike pyrimethamine, P218 binds both wild-type and mutant PfDHFR in a slow-on/slow-off tight-binding mode, which prolongs the target residence time. P218, when bound to PfDHFR-TS, resides almost entirely within the envelope mapped out by the dihydrofolate substrate, which may make it less susceptible to resistance mutations. The high in vivo efficacy in a SCID mouse model of P. falciparum malaria, good oral bioavailability, favorable enzyme selectivity, and good safety characteristics of P218 make it a potential candidate for further development.


  • Organizational Affiliation

    BIOTEC, National Science and Technology Development Agency, Thailand Science Park, Pathumthani 12120, Thailand. yongyuth@biotec.or.th


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthase
A, B
608Plasmodium falciparum VS/1Mutation(s): 0 
Gene Names: DHFR-TS
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
P65
Query on P65

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
2,4-diamino-6-methyl-5-[3-(2,4,5-trichlorophenoxy)propyloxy]pyrimidine
C14 H15 Cl3 N4 O2
KNUBCZHIBGZRJT-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
BME
Query on BME

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
L [auth B]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
P65 BindingDB:  4DPH IC50: 229 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.951α = 90
b = 156.447β = 90
c = 164.653γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description