2B0M

Human dihydroorotate dehydrogenase bound to a novel inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2B0M/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-14 Released: 2005-09-27 
• Deposition Author(s): Hurt, D.E., Sutton, A.E., Clardy, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 

Starting Model: experimental

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

• PubMed: 16406782 
• DOI: https://doi.org/10.1016/j.bmcl.2005.12.029
• Primary Citation of Related Structures:  
  2B0M


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.94 kDa 
• Atom Count: 2,964 
• Modelled Residue Count: 361 
• Deposited Residue Count: 393 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase, mitochondrial	A	393	Homo sapiens	Mutation(s): 0  Gene Names: DHODH EC: 1.3.3.1 (PDB Primary Data), 1.3.5.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q02127 (Homo sapiens) Explore Q02127  Go to UniProtKB:  Q02127
PHAROS:  Q02127 GTEx:  ENSG00000102967

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
201	B [auth A]	3-AMIDO-5-BIPHENYL-BENZOIC ACID C20 H15 N O3 LAZPCGBRHLARSI-UHFFFAOYSA-N
ORO	D [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
201	BindingDB:  2B0M	Ki: 2800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.398	α = 90
b = 90.398	β = 90
c = 123.332	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Hurt, D.E., Sutton, A.E., Clardy, J.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description