3O8A

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with novel Inhibitor Genz667348


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase with anti-malarial activity in the mouse model.

Booker, M.L.Bastos, C.M.Kramer, M.L.Barker, R.H.Skerlj, R.Sidhu, A.B.Deng, X.Celatka, C.Cortese, J.F.Guerrero Bravo, J.E.Crespo Llado, K.N.Serrano, A.E.Angulo-Barturen, I.Jimenez-Diaz, M.B.Viera, S.Garuti, H.Wittlin, S.Papastogiannidis, P.Lin, J.W.Janse, C.J.Khan, S.M.Duraisingh, M.Coleman, B.Goldsmith, E.J.Phillips, M.A.Munoz, B.Wirth, D.F.Klinger, J.D.Wiegand, R.Sybertz, E.

(2010) J.Biol.Chem. 285: 33054-33064

  • DOI: 10.1074/jbc.M110.162081

  • PubMed Abstract: 
  • Plasmodium falciparum, the causative agent of the most deadly form of human malaria, is unable to salvage pyrimidines and must rely on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHODH) catalyzes the rate-limiting step in the pyr ...

    Plasmodium falciparum, the causative agent of the most deadly form of human malaria, is unable to salvage pyrimidines and must rely on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHODH) catalyzes the rate-limiting step in the pyrimidine biosynthetic pathway and represents a potential target for anti-malarial therapy. A high throughput screen and subsequent medicinal chemistry program identified a series of N-alkyl-5-(1H-benzimidazol-1-yl)thiophene-2-carboxamides with low nanomolar in vitro potency against DHODH from P. falciparum, P. vivax, and P. berghei. The compounds were selective for the parasite enzymes over human DHODH, and x-ray structural data on the analog Genz-667348, demonstrated that species selectivity could be attributed to amino acid differences in the inhibitor-binding site. Compounds from this series demonstrated in vitro potency against the 3D7 and Dd2 strains of P. falciparum, good tolerability and oral exposure in the mouse, and ED(50) values in the 4-day murine P. berghei efficacy model of 13-21 mg/kg/day with oral twice-daily dosing. In particular, treatment with Genz-667348 at 100 mg/kg/day resulted in sterile cure. Two recent analogs of Genz-667348 are currently undergoing pilot toxicity testing to determine suitability as clinical development candidates.


    Organizational Affiliation

    Genzyme Corporation, Waltham, Massachusetts 02451, USA. michael.booker@genzyme.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase homolog, mitochondrial
A
415Plasmodium falciparumMutation(s): 0 
EC: 1.3.5.2
Find proteins for Q08210 (Plasmodium falciparum)
Go to UniProtKB:  Q08210
Small Molecules
Ligands 4 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
LDA
Query on LDA

Download SDF File 
Download CCD File 
A
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-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
O8A
Query on O8A

Download SDF File 
Download CCD File 
A
N-cyclopropyl-5-[2-methyl-5-(trifluoromethoxy)-1H-benzimidazol-1-yl]thiophene-2-carboxamide
C17 H14 F3 N3 O2 S
ACFOZQUWTKSSQQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
O8AIC50: 64 nM (92) BINDINGDB
O8AIC50: 22 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 85.287α = 90.00
b = 85.287β = 90.00
c = 138.719γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-23
    Type: Refinement description, Source and taxonomy