4IGH

High resolution crystal structure of human dihydroorotate dehydrogenase bound with 4-quinoline carboxylic acid analog

• PDB DOI: https://doi.org/10.2210/pdb4IGH/pdb

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


• Deposited: 2012-12-17 Released: 2013-08-21 
• Deposition Author(s): Deng, X., Das, P., Fontoura, B.M.A., Phillips, M.A., De Brabander, J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.148 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 

Literature

SAR Based Optimization of a 4-Quinoline Carboxylic Acid Analog with Potent Anti-Viral Activity.

Das, P., Deng, X., Zhang, L., Roth, M.G., Fontoura, B.M., Phillips, M.A., De Brabander, J.K.

(2013) ACS Med Chem Lett 4: 517-521

• PubMed: 23930152 
• DOI: https://doi.org/10.1021/ml300464h
• Primary Citation of Related Structures:  
  4IGH


• PubMed Abstract: 
  

  It is established that drugs targeting viral proteins are at risk of generating resistant strains. However, drugs targeting host factors can potentially avoid this problem. Herein we report structure-activity relationship studies leading to the discovery of a very potent lead compound 6-fluoro-2-(5-isopropyl-2-methyl-4-phenoxyphenyl)quinoline-4-carboxylic acid ( C44 ) that inhibits human dihydroorotate dehydrogenase (DHODH) with an IC ₅₀ of 1 nM, and viral replication of VSV and WSN-Influenza with an EC ₅₀ of 2 nM and 41 nM. We also solved the X-ray structure of human DHODH bound to C44 , providing structural insight into the potent inhibition of biaryl ether analogs of brequinar.

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Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390.

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: 42.14 kDa 
• Atom Count: 3,282 
• Modelled Residue Count: 356 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone), mitochondrial	A	372	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	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
1EA	D [auth A]	6-fluoro-2-[2-methyl-4-phenoxy-5-(propan-2-yl)phenyl]quinoline-4-carboxylic acid C26 H22 F N O3 KOLKCHJGWGJCTG-UHFFFAOYSA-N
ZWI	E [auth A]	3-[decyl(dimethyl)ammonio]propane-1-sulfonate C15 H33 N O3 S WKALLSVICJPZTM-UHFFFAOYSA-N
ORO	C [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1EA	Binding MOAD:  4IGH	IC50: 1 (nM) from 1 assay(s)
	BindingDB:  4IGH	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.148 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.786	α = 90
b = 90.786	β = 90
c = 122.485	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Deng, X., Das, P., Fontoura, B.M.A., Phillips, M.A., De Brabander, J.K.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description