2B0M

Human dihydroorotate dehydrogenase bound to a novel inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Brequinar derivatives and species-specific drug design for dihydroorotate dehydrogenase.

Hurt, D.E.Sutton, A.E.Clardy, J.

(2006) Bioorg.Med.Chem.Lett. 16: 1610-1615

  • DOI: 10.1016/j.bmcl.2005.12.029

  • PubMed Abstract: 
  • Therapeutic agents brequinar sodium and leflunomide (Arava) work by binding in a hydrophobic tunnel formed by a highly variable N-terminus of family 2 dihydroorotate dehydrogenase (DHODH). The X-ray crystallographic structure of an analog of brequina ...

    Therapeutic agents brequinar sodium and leflunomide (Arava) work by binding in a hydrophobic tunnel formed by a highly variable N-terminus of family 2 dihydroorotate dehydrogenase (DHODH). The X-ray crystallographic structure of an analog of brequinar bound to human DHODH was determined. In silico screening of a library of compounds suggested another subset of brequinar analogs that do not inhibit human DHODH as potentially effective inhibitors of Plasmodium falciparum DHODH.


    Related Citations: 
    • Structure of Plasmodium falciparum dihyroorotate dehydrogenase with a bound inhibitor
      Hurt, D.E.,Widom, J.,Clardy, J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase, mitochondrial
A
393Homo sapiensMutation(s): 0 
Gene Names: DHODH
EC: 1.3.5.2
Find proteins for Q02127 (Homo sapiens)
Go to Gene View: DHODH
Go to UniProtKB:  Q02127
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
201
Query on 201

Download SDF File 
Download CCD File 
A
3-AMIDO-5-BIPHENYL-BENZOIC ACID
5-(AMINOCARBONYL)-1,1':4',1''-TERPHENYL-3-CARBOXYLIC ACID
C20 H15 N O3
LAZPCGBRHLARSI-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 %)
201Ki: 2800 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.398α = 90.00
b = 90.398β = 90.00
c = 123.332γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
CNSrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance