4RX0

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM265


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A long-duration dihydroorotate dehydrogenase inhibitor (DSM265) for prevention and treatment of malaria.

Phillips, M.A.Lotharius, J.Marsh, K.White, J.Dayan, A.White, K.L.Njoroge, J.W.El Mazouni, F.Lao, Y.Kokkonda, S.Tomchick, D.R.Deng, X.Laird, T.Bhatia, S.N.March, S.Ng, C.L.Fidock, D.A.Wittlin, S.Lafuente-Monasterio, M.Benito, F.J.Alonso, L.M.Martinez, M.S.Jimenez-Diaz, M.B.Bazaga, S.F.Angulo-Barturen, I.Haselden, J.N.Louttit, J.Cui, Y.Sridhar, A.Zeeman, A.M.Kocken, C.Sauerwein, R.Dechering, K.Avery, V.M.Duffy, S.Delves, M.Sinden, R.Ruecker, A.Wickham, K.S.Rochford, R.Gahagen, J.Iyer, L.Riccio, E.Mirsalis, J.Bathhurst, I.Rueckle, T.Ding, X.Campo, B.Leroy, D.Rogers, M.J.Rathod, P.K.Burrows, J.N.Charman, S.A.

(2015) Sci Transl Med 7: 296ra111-296ra111

  • DOI: 10.1126/scitranslmed.aaa6645
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Malaria is one of the most significant causes of childhood mortality, but disease control efforts are threatened by resistance of the Plasmodium parasite to current therapies. Continued progress in combating malaria requires development of new, easy ...

    Malaria is one of the most significant causes of childhood mortality, but disease control efforts are threatened by resistance of the Plasmodium parasite to current therapies. Continued progress in combating malaria requires development of new, easy to administer drug combinations with broad-ranging activity against all manifestations of the disease. DSM265, a triazolopyrimidine-based inhibitor of the pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH), is the first DHODH inhibitor to reach clinical development for treatment of malaria. We describe studies profiling the biological activity, pharmacological and pharmacokinetic properties, and safety of DSM265, which supported its advancement to human trials. DSM265 is highly selective toward DHODH of the malaria parasite Plasmodium, efficacious against both blood and liver stages of P. falciparum, and active against drug-resistant parasite isolates. Favorable pharmacokinetic properties of DSM265 are predicted to provide therapeutic concentrations for more than 8 days after a single oral dose in the range of 200 to 400 mg. DSM265 was well tolerated in repeat-dose and cardiovascular safety studies in mice and dogs, was not mutagenic, and was inactive against panels of human enzymes/receptors. The excellent safety profile, blood- and liver-stage activity, and predicted long half-life in humans position DSM265 as a new potential drug combination partner for either single-dose treatment or once-weekly chemoprevention. DSM265 has advantages over current treatment options that are dosed daily or are inactive against the parasite liver stage.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA. margaret.phillips@utsouthwestern.edu susan.charman@monash.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (quinone), mitochondrial
A
401Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 1.3.5.2
Find proteins for Q08210 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q08210
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
D65
Query on D65

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Download CCD File 
A
2-(1,1-difluoroethyl)-5-methyl-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine
DSM265
C14 H12 F7 N5 S
OIZSVTOIBNSVOS-UHFFFAOYSA-N
 Ligand Interaction
ORO
Query on ORO

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Download CCD File 
A
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D65IC50: 30 nM (92) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.163 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 85.933α = 90.00
b = 85.933β = 90.00
c = 138.425γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXrefinement
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release