9QOZ | pdb_00009qoz

APH(2'')-IVa with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.263 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Targeting bacterial kinases as a strategy to counteract antibiotic resistance.

Buffa, V.Kowalewski, J.Qi, G.Deutscher, R.Cica, M.Richardoz, M.Tomaszczyk, M.Kramer, A.Knapp, S.Dunyach-Remy, C.Rox, K.Guichou, J.F.Lionne, C.Hausch, F.

(2025) Commun Chem 8: 390-390

  • DOI: https://doi.org/10.1038/s42004-025-01794-7
  • Primary Citation of Related Structures:  
    9QOR, 9QOT, 9QOU, 9QOW, 9QOX, 9QOZ, 9QP0, 9QP1, 9QP2, 9QP3, 9QP5, 9QP6, 9QP7, 9QPA, 9QQJ, 9RL1

  • PubMed Abstract: 

    Antibiotic resistance is rapidly emerging as one of the most critical health threats, with resistant microorganisms progressively diminishing the effectiveness of established antibiotics. As a result, the development of therapeutic approaches that effectively target resistant pathogens is of utmost importance. In this study, we developed inhibitors for APH(2")-IVa, a bacterial kinase conveying resistance to aminoglycoside antibiotics. Starting from a hit of a fragment-based screening, we explored the inhibitory motif by structure-based design, ultimately leading to a series of triazole analogues. Advanced analogues displayed promising ADME properties, emerging selectivity vs a panel of human kinases, permeability in both Gram-positive and Gram-negative bacteria, and a moderate antibiotic efficacy for clinical strains of P. aeruginosa. Taken together, our results suggest inhibition of bacterial kinases could be a promising option to reinstall the efficacy of aminoglycoside antibiotics.


  • Organizational Affiliation
    • Department of Chemistry, Institute of Organic Chemistry and Biochemistry, Technical University Darmstadt, Peter-Grünberg-Straße 4, Darmstadt, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
APH(2'')-IdA [auth B],
B [auth A]
321Enterococcus casseliflavusMutation(s): 0 
Gene Names: aph(2'')-Id
UniProt
Find proteins for O68183 (Enterococcus casseliflavus)
Explore O68183 
Go to UniProtKB:  O68183
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68183
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.464α = 90
b = 64.706β = 90.03
c = 78.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-19-AMRB-0001
Agence Nationale de la Recherche (ANR)France(ANR-10-INBS-0004
Agence Nationale de la Recherche (ANR)France(ANR-10-INBS-0005

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-11
    Type: Initial release