5TBO

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM421


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.151 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Triazolopyrimidine-Based Dihydroorotate Dehydrogenase Inhibitor with Improved Drug-like Properties for Treatment and Prevention of Malaria.

Phillips, M.A.White, K.L.Kokkonda, S.Deng, X.White, J.El Mazouni, F.Marsh, K.Tomchick, D.R.Manjalanagara, K.Rudra, K.R.Wirjanata, G.Noviyanti, R.Price, R.N.Marfurt, J.Shackleford, D.M.Chiu, F.C.Campbell, M.Jimenez-Diaz, M.B.Bazaga, S.F.Angulo-Barturen, I.Martinez, M.S.Lafuente-Monasterio, M.Kaminsky, W.Silue, K.Zeeman, A.M.Kocken, C.Leroy, D.Blasco, B.Rossignol, E.Rueckle, T.Matthews, D.Burrows, J.N.Waterson, D.Palmer, M.J.Rathod, P.K.Charman, S.A.

(2016) ACS Infect Dis 2: 945-957

  • DOI: 10.1021/acsinfecdis.6b00144

  • PubMed Abstract: 
  • The emergence of drug-resistant malaria parasites continues to hamper efforts to control this lethal disease. Dihydroorotate dehydrogenase has recently been validated as a new target for the treatment of malaria, and a selective inhibitor (DSM265) of ...

    The emergence of drug-resistant malaria parasites continues to hamper efforts to control this lethal disease. Dihydroorotate dehydrogenase has recently been validated as a new target for the treatment of malaria, and a selective inhibitor (DSM265) of the Plasmodium enzyme is currently in clinical development. With the goal of identifying a backup compound to DSM265, we explored replacement of the SF5-aniline moiety of DSM265 with a series of CF3-pyridinyls while maintaining the core triazolopyrimidine scaffold. This effort led to the identification of DSM421, which has improved solubility, lower intrinsic clearance, and increased plasma exposure after oral dosing compared to DSM265, while maintaining a long predicted human half-life. Its improved physical and chemical properties will allow it to be formulated more readily than DSM265. DSM421 showed excellent efficacy in the SCID mouse model of P. falciparum malaria that supports the prediction of a low human dose (<200 mg). Importantly DSM421 showed equal activity against both P. falciparum and P. vivax field isolates, while DSM265 was more active on P. falciparum. DSM421 has the potential to be developed as a single-dose cure or once-weekly chemopreventative for both P. falciparum and P. vivax malaria, leading to its advancement as a preclinical development candidate.


    Organizational Affiliation

    Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia.




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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78Z
Query on 78Z

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Download CCD File 
A
2-(1,1-difluoroethyl)-5-methyl-N-[6-(trifluoromethyl)pyridin-3-yl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine
C14 H11 F5 N6
HDLFZCDEGAWEFX-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

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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
LDA
Query on LDA

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Download CCD File 
A
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.151 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 86.380α = 90.00
b = 86.380β = 90.00
c = 138.608γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-09-12 
  • Released Date: 2016-09-28 
  • Deposition Author(s): Deng, X., Phillips, M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States--

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references
  • Version 1.2: 2016-12-21
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence