7T6C

E. coli dihydroorotate dehydrogenase bound to the ubiquinone surrogate DCIP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insights into inhibition of the drug target dihydroorotate dehydrogenase by bacterial hydroxyalkylquinolines.

Horwitz, S.M.Blue, T.C.Ambarian, J.A.Hoshino, S.Seyedsayamdost, M.R.Davis, K.M.

(2022) RSC Chem Biol 3: 420-425

  • DOI: https://doi.org/10.1039/d1cb00255d
  • Primary Citation of Related Structures:  
    7T5K, 7T5Y, 7T6C, 7T6H

  • PubMed Abstract: 

    Hydroxyalkylquinolines (HAQs) are ubiquitious natural products but their interactions with associated protein targets remain elusive. We report X-ray crystal structures of two HAQs in complex with dihydroorotate dehydrogenase (DHODH). Our results reveal the structural basis of DHODH inhibition by HAQs and open the door to downstream structure-activity relationship studies.


  • Organizational Affiliation

    Department of Chemistry, Emory University Atlanta GA 30322 USA katherine.davis@emory.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone)
A, B
368Escherichia coli K-12Mutation(s): 0 
Gene Names: pyrDb0945JW0928
EC: 1.3.5.2
UniProt
Find proteins for P0A7E1 (Escherichia coli (strain K12))
Explore P0A7E1 
Go to UniProtKB:  P0A7E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7E1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
PE4
Query on PE4

Download Ideal Coordinates CCD File 
C [auth A]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
RLM (Subject of Investigation/LOI)
Query on RLM

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
2,6-bis(chloranyl)-4-[(4-hydroxyphenyl)amino]phenol
C12 H9 Cl2 N O2
IFTGQCOAUCEONK-UHFFFAOYSA-N
ORO (Subject of Investigation/LOI)
Query on ORO

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

Download Ideal Coordinates CCD File 
G [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.046α = 90
b = 169.328β = 90
c = 129.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description