6VTN | pdb_00006vtn

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM557


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.219 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6VTN

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Lead Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series for the Treatment of Malaria.

Kokkonda, S.Deng, X.White, K.L.El Mazouni, F.White, J.Shackleford, D.M.Katneni, K.Chiu, F.C.K.Barker, H.McLaren, J.Crighton, E.Chen, G.Angulo-Barturen, I.Jimenez-Diaz, M.B.Ferrer, S.Huertas-Valentin, L.Martinez-Martinez, M.S.Lafuente-Monasterio, M.J.Chittimalla, R.Shahi, S.P.Wittlin, S.Waterson, D.Burrows, J.N.Matthews, D.Tomchick, D.Rathod, P.K.Palmer, M.J.Charman, S.A.Phillips, M.A.

(2020) J Med Chem 63: 4929-4956

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00311
  • Primary Citation Related Structures: 
    6VTN, 6VTY

  • PubMed Abstract: 

    Malaria puts at risk nearly half the world's population and causes high mortality in sub-Saharan Africa, while drug resistance threatens current therapies. The pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is a validated target for malaria treatment based on our finding that triazolopyrimidine DSM265 ( 1 ) showed efficacy in clinical studies. Herein, we describe optimization of a pyrrole-based series identified using a target-based DHODH screen. Compounds with nanomolar potency versus Plasmodium DHODH and Plasmodium parasites were identified with good pharmacological properties. X-ray studies showed that the pyrroles bind an alternative enzyme conformation from 1 leading to improved species selectivity versus mammalian enzymes and equivalent activity on Plasmodium falciparum and Plasmodium vivax DHODH. The best lead DSM502 ( 37 ) showed in vivo efficacy at similar levels of blood exposure to 1 , although metabolic stability was reduced. Overall, the pyrrole-based DHODH inhibitors provide an attractive alternative scaffold for the development of new antimalarial compounds.


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

Macromolecule Content 

  • Total Structure Weight: 46.34 kDa 
  • Atom Count: 3,110 
  • Modeled Residue Count: 375 
  • 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 3 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
RL7
(Subject of Investigation/LOI)

Query on RL7



Download:Ideal Coordinates CCD File
B [auth A]N-cyclopropyl-4-{[2-fluoro-4-(trifluoromethyl)phenyl]methyl}-3-methyl-1H-pyrrole-2-carboxamide
C17 H16 F4 N2 O
HLDSAPKKTAWHGH-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: 2.25 Å
  • R-Value Free:  0.219 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.751α = 90
b = 84.751β = 90
c = 137.959γ = 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 Library of Medicine (NIH/NLM)United StatesU01AI075594

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description