4DFU

Inhibition of an antibiotic resistance enzyme: crystal structure of aminoglycoside phosphotransferase APH(2")-ID/APH(2")-IVA in complex with kanamycin inhibited with quercetin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A small molecule discrimination map of the antibiotic resistance kinome.

Shakya, T.Stogios, P.J.Waglechner, N.Evdokimova, E.Ejim, L.Blanchard, J.E.McArthur, A.G.Savchenko, A.Wright, G.D.

(2011) Chem.Biol. 18: 1591-1601

  • DOI: 10.1016/j.chembiol.2011.10.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Kinase-mediated resistance to antibiotics is a significant clinical challenge. These enzymes share a common protein fold characteristic of Ser/Thr/Tyr protein kinases. We screened 14 antibiotic resistance kinases against 80 chemically diverse protein ...

    Kinase-mediated resistance to antibiotics is a significant clinical challenge. These enzymes share a common protein fold characteristic of Ser/Thr/Tyr protein kinases. We screened 14 antibiotic resistance kinases against 80 chemically diverse protein kinase inhibitors to map resistance kinase chemical space. The screens identified molecules with both broad and narrow inhibition profiles, proving that protein kinase inhibitors offer privileged chemical matter with the potential to block antibiotic resistance. One example is the flavonol quercetin, which inhibited a number of resistance kinases in vitro and in vivo. This activity was rationalized by determination of the crystal structure of the aminoglycoside kinase APH(2″)-IVa in complex with quercetin and its antibiotic substrate kanamycin. Our data demonstrate that protein kinase inhibitors offer chemical scaffolds that can block antibiotic resistance, providing leads for co-drug design.


    Organizational Affiliation

    M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 3Z5, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APH(2")-Id
A, B
322Enterococcus casseliflavusMutation(s): 0 
Gene Names: aph(2'')-Id
Find proteins for O68183 (Enterococcus casseliflavus)
Go to UniProtKB:  O68183
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUE
Query on QUE

Download SDF File 
Download CCD File 
A, B
3,5,7,3',4'-PENTAHYDROXYFLAVONE
QUERCETIN
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
KAN
Query on KAN

Download SDF File 
Download CCD File 
A, B
KANAMYCIN A
C18 H36 N4 O11
SBUJHOSQTJFQJX-NOAMYHISSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QUEKi: 25000 nM BINDINGMOAD
QUEKi: 25100 nM PDBBIND
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 43.141α = 90.00
b = 101.814β = 96.86
c = 70.249γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-02-22
    Type: Structure summary