3KVK

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with amino-benzoic acid inhibitor 641 at 2.05A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KVK/pdb

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


• Deposited: 2009-11-30 Released: 2010-03-02 
• Deposition Author(s): McLean, L., Zhang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.205 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures.

McLean, L.R., Zhang, Y., Degnen, W., Peppard, J., Cabel, D., Zou, C., Tsay, J.T., Subramaniam, A., Vaz, R.J., Li, Y.

(2010) Bioorg Med Chem Lett 20: 1981-1984

• PubMed: 20153645 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.115
• Primary Citation of Related Structures:  
  3KVJ, 3KVK, 3KVL, 3KVM


• PubMed Abstract: 
  

  Amino-benzoic acid derivatives 1-4 were found to be inhibitors for DHODH by virtual screening, biochemical, and X-ray crystallographic studies. X-ray structures showed that 1 and 2 bind to DHODH as predicted by virtual screening, but 3 and 4 were found to be structurally different from the corresponding compounds initially identified by virtual screening.

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Organizational Affiliation: 

Discovery Research, Sanofi-aventis, Bridgewater, NJ 08807, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.89 kDa 
• Atom Count: 3,105 
• Modelled Residue Count: 364 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase, mitochondrial	A	390	Homo sapiens	Mutation(s): 0  Gene Names: DHODH EC: 1.3.5.2
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
6X1	F [auth A]	2-{[(3,5-dichlorophenyl)carbamoyl]amino}benzoic acid C14 H10 Cl2 N2 O3 PIWYMPXOKMFVER-UHFFFAOYSA-N
DET	E [auth A]	UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE C13 H29 N O OZHBUVQCJMARBN-UHFFFAOYSA-N
DOR	D [auth A]	(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID C5 H6 N2 O4 UFIVEPVSAGBUSI-REOHCLBHSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
6X1	BindingDB:  3KVK	IC50: 700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.205 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.908	α = 90
b = 90.908	β = 90
c = 123.077	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): McLean, L., Zhang, Y.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description