3I65

Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural plasticity of malaria dihydroorotate dehydrogenase allows selective binding of diverse chemical scaffolds.

Deng, X., Gujjar, R., El Mazouni, F., Kaminsky, W., Malmquist, N.A., Goldsmith, E.J., Rathod, P.K., Phillips, M.A.

(2009) J Biol Chem 284: 26999-27009

  • DOI: 10.1074/jbc.M109.028589
  • Primary Citation of Related Structures:  
    3I68, 3I65, 3I6R

  • PubMed Abstract: 

    • Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective ...

    Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.

    Organizational Affiliation: 

    Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9041, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase homolog, mitochondrialA415Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PFF0160c, Plasmodium falciparum
EC: 1.3.3.1 (PDB Primary Data), 1.3.5.2 (UniProt)
Membrane protein
Mpstruc		Group: 
MONOTOPIC MEMBRANE PROTEINS		Sub Group: 
Dihydroorotate Dehydrogenases (DHODH, class 2)		Protein: 
Dihydroorotate Dehydrogenase with triazolopyrimidine-based inhibitor DSM1
Find proteins for Q08210 (Plasmodium falciparum (isolate 3D7))
Explore Q08210 
Go to UniProtKB:  Q08210
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
JZ8
Query on JZ8
Download CCD File 
A
5-methyl-7-(naphthalen-2-ylamino)-1H-[1,2,4]triazolo[1,5-a]pyrimidine-3,8-diium
C16 H15 N5
GNJXIZOPHGMAQW-UHFFFAOYSA-P		 Ligand Interaction
LDA
Query on LDA
Download CCD File 
A
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N		 Ligand Interaction
ORO
Query on ORO
Download CCD File 
A
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JZ8IC50:  47   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.858α = 90
b = 85.858β = 90
c = 138.352γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance