5DEL

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM59


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The X-ray structure of Plasmodium falciparum dihydroorotate dehydrogenase bound to a potent and selective N-phenylbenzamide inhibitor reveals novel binding-site interactions.

Deng, X.Matthews, D.Rathod, P.K.Phillips, M.A.

(2015) Acta Crystallogr.,Sect.F 71: 553-559

  • DOI: 10.1107/S2053230X15000989
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plasmodium species are protozoan parasites that are the causative agent of malaria. Malaria is a devastating disease, and its treatment and control have been hampered by the propensity of the parasite to become drug-resistant. Dihydroorotate dehydrog ...

    Plasmodium species are protozoan parasites that are the causative agent of malaria. Malaria is a devastating disease, and its treatment and control have been hampered by the propensity of the parasite to become drug-resistant. Dihydroorotate dehydrogenase (DHODH) has been identified as a promising new target for the development of antimalarial agents. Here, the X-ray structure of P. falciparum DHODH bound to a potent and selective N-phenylbenzamide-based inhibitor (DSM59) is described at 2.3 Å resolution. The structure elucidates novel binding-site interactions and shows how conformational flexibility of the enzyme leads to the ability to bind diverse chemical structures with high affinity. This information provides new insight into the design of high-affinity DHODH inhibitors for the treatment of malaria.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (quinone), mitochondrial
A
401Plasmodium 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
LDA
Query on LDA

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Download CCD File 
A
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
D59
Query on D59

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Download CCD File 
A
N-(3,5-dichlorophenyl)-2-methyl-3-nitrobenzamide
C14 H10 Cl2 N2 O3
NKIJNFMSYDSAJK-UHFFFAOYSA-N
 Ligand Interaction
ORO
Query on ORO

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Download CCD File 
A
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D59IC50: 16 - 130000 nM (92) BINDINGDB
D59Ki: 30 nM (92) BINDINGDB
D59IC50: 16 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 85.046α = 90.00
b = 85.046β = 90.00
c = 137.704γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-08-25 
  • Released Date: 2015-10-07 
  • Deposition Author(s): Phillips, M., Deng, X.
  • This entry supersedes: 4RYH

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release