3SFK

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM267


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-Guided Lead Optimization of Triazolopyrimidine-Ring Substituents Identifies Potent Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors with Clinical Candidate Potential.

Coteron, J.M.Marco, M.Esquivias, J.Deng, X.White, K.L.White, J.Koltun, M.El Mazouni, F.Kokkonda, S.Katneni, K.Bhamidipati, R.Shackleford, D.M.Angulo-Barturen, I.Ferrer, S.B.Jimenez-Diaz, M.B.Gamo, F.J.Goldsmith, E.J.Charman, W.N.Bathurst, I.Floyd, D.Matthews, D.Burrows, J.N.Rathod, P.K.Charman, S.A.Phillips, M.A.

(2011) J.Med.Chem. 54: 5540-5561

  • DOI: 10.1021/jm200592f

  • PubMed Abstract: 
  • Drug therapy is the mainstay of antimalarial therapy, yet current drugs are threatened by the development of resistance. In an effort to identify new potential antimalarials, we have undertaken a lead optimization program around our previously identi ...

    Drug therapy is the mainstay of antimalarial therapy, yet current drugs are threatened by the development of resistance. In an effort to identify new potential antimalarials, we have undertaken a lead optimization program around our previously identified triazolopyrimidine-based series of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. The X-ray structure of PfDHODH was used to inform the medicinal chemistry program allowing the identification of a potent and selective inhibitor (DSM265) that acts through DHODH inhibition to kill both sensitive and drug resistant strains of the parasite. This compound has similar potency to chloroquine in the humanized SCID mouse P. falciparum model, can be synthesized by a simple route, and rodent pharmacokinetic studies demonstrated it has excellent oral bioavailability, a long half-life and low clearance. These studies have identified the first candidate in the triazolopyrimidine series to meet previously established progression criteria for efficacy and ADME properties, justifying further development of this compound toward clinical candidate status.


    Organizational Affiliation

    GlaxoSmithKline, Diseases of the Developing World (DDW)-Tres Cantos Medicines Development Campus, Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (quinone), mitochondrial
A
400Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 1.3.5.2
Find proteins for Q08210 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q08210
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
D67
Query on D67

Download SDF File 
Download CCD File 
A
2-(1,1-difluoroethyl)-5-methyl-N-[4-(trifluoromethyl)phenyl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine
C15 H12 F5 N5
CUCVTDOXQYMYKL-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 %)
D67IC50: 38 nM (92) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.224 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 86.586α = 90.00
b = 86.586β = 90.00
c = 138.167γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-3000data collection
REFMACrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-06-13 
  • Released Date: 2011-07-06 
  • Deposition Author(s): Deng, X., Phillips, M.

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-17
    Type: Database references
  • Version 1.3: 2017-07-26
    Type: Refinement description, Source and taxonomy