3O8A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1074/jbc.M110.162081
  • Primary Citation of Related Structures:  
    3O8A

  • 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 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

    From Genzyme Corporation, Waltham, Massachusetts 02451. Electronic address: michael.booker@genzyme.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase homolog, mitochondrial415Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: dihydroorotate dehydrogenasePFF0160c
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 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
O8A
Query on O8A

Download Ideal Coordinates CCD File 
B [auth A]N-cyclopropyl-5-[2-methyl-5-(trifluoromethoxy)-1H-benzimidazol-1-yl]thiophene-2-carboxamide
C17 H14 F3 N3 O2 S
ACFOZQUWTKSSQQ-UHFFFAOYSA-N
LDA
Query on LDA

Download Ideal Coordinates CCD File 
E [auth A]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
ORO
Query on ORO

Download Ideal Coordinates CCD File 
D [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
O8A Binding MOAD:  3O8A IC50: 22 (nM) from 1 assay(s)
BindingDB:  3O8A IC50: 64 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.287α = 90
b = 85.287β = 90
c = 138.719γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations