4ORI

Rat dihydroorotate dehydrogenase bound with DSM338 (N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fluorine Modulates Species Selectivity in the Triazolopyrimidine Class of Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors.

Deng, X.Kokkonda, S.El Mazouni, F.White, J.Burrows, J.N.Kaminsky, W.Charman, S.A.Matthews, D.Rathod, P.K.Phillips, M.A.

(2014) J.Med.Chem. 57: 5381-5394

  • DOI: 10.1021/jm500481t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Malaria is one of the most serious global infectious diseases. The pyrimidine biosynthetic enzyme Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) is an important target for antimalarial chemotherapy. We describe a detailed analysis of pr ...

    Malaria is one of the most serious global infectious diseases. The pyrimidine biosynthetic enzyme Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) is an important target for antimalarial chemotherapy. We describe a detailed analysis of protein-ligand interactions between DHODH and a triazolopyrimidine-based inhibitor series to explore the effects of fluorine on affinity and species selectivity. We show that increasing fluorination dramatically increases binding to mammalian DHODHs, leading to a loss of species selectivity. Triazolopyrimidines bind Plasmodium and mammalian DHODHs in overlapping but distinct binding sites. Key hydrogen-bond and stacking interactions underlying strong binding to PfDHODH are absent in the mammalian enzymes. Increasing fluorine substitution leads to an increase in the entropic contribution to binding, suggesting that strong binding to mammalian DHODH is a consequence of an enhanced hydrophobic effect upon binding to an apolar pocket. We conclude that hydrophobic interactions between fluorine and hydrocarbons provide significant binding energy to protein-ligand interactions. Our studies define the requirements for species-selective binding to PfDHODH and show that the triazolopyrimidine scaffold can alternatively be tuned to inhibit human DHODH, an important target for autoimmune diseases.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Boulevard, Dallas, Texas 75390-9041, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (quinone), mitochondrial
A
372Rattus norvegicusMutation(s): 0 
Gene Names: Dhodh
EC: 1.3.5.2
Find proteins for Q63707 (Rattus norvegicus)
Go to UniProtKB:  Q63707
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
2V6
Query on 2V6

Download SDF File 
Download CCD File 
A
N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine
C14 H7 F8 N5
JEEOGRYTTNEULC-UHFFFAOYSA-N
 Ligand Interaction
ORO
Query on ORO

Download SDF File 
Download CCD File 
A
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2V6IC50: 49 - 2100 nM (100) BINDINGDB
2V6IC50: 88 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.365α = 90.00
b = 43.845β = 99.96
c = 63.305γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
HKL-3000data collection
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-07-09
    Type: Database references