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 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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:  
    4RX0, 5BOO

  • 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 to administer drug combinations with broad-ranging activity against all manifestations of the disease ...

    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

    Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia. margaret.phillips@utsouthwestern.edu susan.charman@monash.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrialA401Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: dihydroorotate dehydrogenasePFF0160c
EC: 1.3.5.2
UniProt
Find proteins for Q08210 (Plasmodium falciparum (isolate 3D7))
Explore Q08210 
Go to UniProtKB:  Q08210
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08210
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
D65
Query on D65

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

Download Ideal Coordinates CCD File 
D [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
D65 BindingDB:  4RX0 IC50: min: 10, max: 30 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.179 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.933α = 90
b = 85.933β = 90
c = 138.425γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000data collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Refinement description