Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 4

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Structure-based design, synthesis, and characterization of inhibitors of human and Plasmodium falciparum dihydroorotate dehydrogenases

Davies, M.Heikkila, T.McConkey, G.A.Fishwick, C.W.G.Parsons, M.R.Johnson, A.P.

(2009) J Med Chem 52: 2683-2693

  • DOI: https://doi.org/10.1021/jm800963t
  • Primary Citation of Related Structures:  
    3F1Q, 3FJ6, 3FJL, 3G0U, 3G0X

  • PubMed Abstract: 

    Pyrimidine biosynthesis is an attractive drug target in a variety of organisms, including humans and the malaria parasite Plasmodium falciparum. Dihydroorotate dehydrogenase, an enzyme catalyzing the only redox reaction of the pyrimidine biosynthesis pathway, is a well-characterized target for chemotherapeutical intervention. In this study, we have applied SPROUT-LeadOpt, a software package for structure-based drug discovery and lead optimization, to improve the binding of the active metabolite of the anti-inflammatory drug leflunomide to the target cavities of the P. falciparum and human dihydroorotate dehydrogenases. Following synthesis of a library of compounds based upon the SPROUT-optimized molecular scaffolds, a series of inhibitors generally showing good inhibitory activity was obtained, in keeping with the SPROUT-LeadOpt predictions. Furthermore, cocrystal structures of five of these SPROUT-designed inhibitors bound in the ubiquinone binding cavity of the human dihydroorotate dehydrogenase are also analyzed.

  • Organizational Affiliation

    School of Chemistry, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase367Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q02127 (Homo sapiens)
Explore Q02127 
Go to UniProtKB:  Q02127
PHAROS:  Q02127
GTEx:  ENSG00000102967 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02127
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FMN

Download Ideal Coordinates CCD File 
C17 H21 N4 O9 P
Query on MDY

Download Ideal Coordinates CCD File 
D [auth A](2Z)-N-(3-chloro-2'-methoxybiphenyl-4-yl)-2-cyano-3-hydroxybut-2-enamide
C18 H15 Cl N2 O3
Query on ORO

Download Ideal Coordinates CCD File 
C5 H4 N2 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
MDY BindingDB:  3G0U Ki: 25 (nM) from 1 assay(s)
IC50: 200 (nM) from 1 assay(s)
Binding MOAD:  3G0U IC50: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.752α = 90
b = 90.752β = 90
c = 122.799γ = 120
Software Package:
Software NamePurpose
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description