5FI8

Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bounded with DSM422 (Tetrahydro-2-naphthyl and 2-indanyl triazolopyrimidine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tetrahydro-2-naphthyl and 2-Indanyl Triazolopyrimidines Targeting Plasmodium falciparum Dihydroorotate Dehydrogenase Display Potent and Selective Antimalarial Activity.

Kokkonda, S.Deng, X.White, K.L.Coteron, J.M.Marco, M.de Las Heras, L.White, J.El Mazouni, F.Tomchick, D.R.Manjalanagara, K.Rudra, K.R.Chen, G.Morizzi, J.Ryan, E.Kaminsky, W.Leroy, D.Martinez-Martinez, M.S.Jimenez-Diaz, M.B.Bazaga, S.F.Angulo-Barturen, I.Waterson, D.Burrows, J.N.Matthews, D.Charman, S.A.Phillips, M.A.Rathod, P.K.

(2016) J.Med.Chem. 59: 5416-5431

  • DOI: 10.1021/acs.jmedchem.6b00275

  • PubMed Abstract: 
  • Malaria persists as one of the most devastating global infectious diseases. The pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) has been identified as a new malaria drug target, and a triazolopyrimidine-based DHODH inhibitor 1 (DS ...

    Malaria persists as one of the most devastating global infectious diseases. The pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) has been identified as a new malaria drug target, and a triazolopyrimidine-based DHODH inhibitor 1 (DSM265) is in clinical development. We sought to identify compounds with higher potency against Plasmodium DHODH while showing greater selectivity toward animal DHODHs. Herein we describe a series of novel triazolopyrimidines wherein the p-SF5-aniline was replaced with substituted 1,2,3,4-tetrahydro-2-naphthyl or 2-indanyl amines. These compounds showed strong species selectivity, and several highly potent tetrahydro-2-naphthyl derivatives were identified. Compounds with halogen substitutions displayed sustained plasma levels after oral dosing in rodents leading to efficacy in the P. falciparum SCID mouse malaria model. These data suggest that tetrahydro-2-naphthyl derivatives have the potential to be efficacious for the treatment of malaria, but due to higher metabolic clearance than 1, they most likely would need to be part of a multidose regimen.


    Organizational Affiliation

    Departments of Chemistry and Global Health, University of Washington , Seattle, Washington 98195, United States.




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
5Y5
Query on 5Y5

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Download CCD File 
A
2-[1,1-bis(fluoranyl)ethyl]-~{N}-[(2~{S})-7-bromanyl-1,2,3,4-tetrahydronaphthalen-2-yl]-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine
C18 H18 Br F2 N5
WSMWEZWUWJDREU-AWEZNQCLSA-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
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: 2.32 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.180 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 86.147α = 90.00
b = 86.147β = 90.00
c = 139.053γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesU01AI075594

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations