7UDP

Crystal structure of COQ8A-CA157 inhibitor complex in space group C2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Small-molecule inhibition of the archetypal UbiB protein COQ8.

Murray, N.H.Asquith, C.R.M.Fang, Z.East, M.P.Ptak, N.Smith, R.W.Vasta, J.D.Zimprich, C.A.Corona, C.R.Robers, M.B.Johnson, G.L.Bingman, C.A.Pagliarini, D.J.

(2023) Nat Chem Biol 19: 230-238

  • DOI: https://doi.org/10.1038/s41589-022-01168-3
  • Primary Citation of Related Structures:  
    7UDP, 7UDQ

  • PubMed Abstract: 

    Small-molecule tools have enabled mechanistic investigations and therapeutic targeting of the protein kinase-like (PKL) superfamily. However, such tools are still lacking for many PKL members, including the highly conserved and disease-related UbiB family. Here, we sought to develop and characterize an inhibitor for the archetypal UbiB member COQ8, whose function is essential for coenzyme Q (CoQ) biosynthesis. Guided by crystallography, activity assays and cellular CoQ measurements, we repurposed the 4-anilinoquinoline scaffold to selectively inhibit human COQ8A in cells. Our chemical tool promises to lend mechanistic insights into the activities of these widespread and understudied proteins and to offer potential therapeutic strategies for human diseases connected to their dysfunction.


  • Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Atypical kinase COQ8A, mitochondrial393Homo sapiensMutation(s): 0 
Gene Names: COQ8AADCK3CABC1PP265
EC: 2.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NI60 (Homo sapiens)
Explore Q8NI60 
Go to UniProtKB:  Q8NI60
PHAROS:  Q8NI60
GTEx:  ENSG00000163050 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NI60
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MVS (Subject of Investigation/LOI)
Query on MVS

Download Ideal Coordinates CCD File 
B [auth A]4-[(3,4,5-trimethoxyphenyl)amino]quinoline-7-carbonitrile
C19 H17 N3 O3
BLWQIEISIMYCHD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.21α = 90
b = 56.379β = 98.39
c = 48.684γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata processing
JBluIce-EPICSdata collection

Structure Validation

View Full Validation Report



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 StatesR35GM131795
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008505
National Science Foundation (NSF, United States)United StatesDGE-1747503

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description