7UDQ

Crystal structure of COQ8A-CA157 inhibitor complex in space group P1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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, mitochondrial
A, B
393Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.273α = 109.79
b = 54.859β = 94.62
c = 80.012γ = 92.11
Software Package:
Software NamePurpose
PHENIXrefinement
JBluIce-EPICSdata collection
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
PHASERphasing

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