4DPD

WILD TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE (PfDHFR-TS), DHF COMPLEX, NADP+, dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.USA 109: 16823-16828

  • DOI: 10.1073/pnas.1204556109
  • Primary Citation of Related Structures:  4DDR, 4DP3, 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. ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional dihydrofolate reductase-thymidylate synthase
A, B
608Plasmodium falciparumGene Names: DHFR-TS (dhfr-ts)
Find proteins for A7UD81 (Plasmodium falciparum)
Go to UniProtKB:  A7UD81
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
DHF
Query on DHF

Download SDF File 
Download CCD File 
A
DIHYDROFOLIC ACID
C19 H21 N7 O6
OZRNSSUDZOLUSN-LBPRGKRZSA-N
 Ligand Interaction
UMP
Query on UMP

Download SDF File 
Download CCD File 
A, B
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.057α = 90.00
b = 156.785β = 90.00
c = 165.032γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release