4IGH

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


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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial372Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02127
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
1EA
Query on 1EA

Download Ideal Coordinates CCD File 
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
Query on ZWI

Download Ideal Coordinates CCD File 
E [auth A]3-[decyl(dimethyl)ammonio]propane-1-sulfonate
C15 H33 N O3 S
WKALLSVICJPZTM-UHFFFAOYSA-N
ORO
Query on ORO

Download Ideal Coordinates CCD File 
C [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
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 = 90.786α = 90
b = 90.786β = 90
c = 122.485γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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