5FI8 | pdb_00005fi8

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 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/acs.jmedchem.6b00275
  • Primary Citation Related Structures: 
    5FI8

  • 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 (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.

Macromolecule Content 

  • Total Structure Weight: 46.65 kDa 
  • Atom Count: 3,031 
  • Modeled Residue Count: 363 
  • Deposited Residue Count: 401 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial401Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PFF0160c
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / 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
5Y5

Query on 5Y5



Download:Ideal Coordinates CCD File
B [auth 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
LDA

Query on LDA



Download:Ideal Coordinates CCD File
E [auth A]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
ORO

Query on ORO



Download:Ideal Coordinates CCD File
D [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.222 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.147α = 90
b = 86.147β = 90
c = 139.053γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU01AI075594

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description