9QN6 | pdb_00009qn6

APH(2'')-IVa with a fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.278 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Fragment-based drug design of a bacterial kinase inhibitor capable of increasing the antibiotic sensitivity of clinical isolates.

Kowalewski, J.Deutscher, R.Richardoz, M.Tomaszczyk, M.Gelin, M.Labesse, G.Hausch, F.Wright, G.D.Dunyach-Remy, C.Guichou, J.F.Lionne, C.

(2025) Commun Chem 8: 417-417

  • DOI: https://doi.org/10.1038/s42004-025-01795-6
  • Primary Citation of Related Structures:  
    9QMR, 9QN6, 9QNN, 9QNQ, 9QNS, 9QNW, 9QNX, 9QNY, 9QOD, 9QOE, 9QOK, 9QOL, 9QOM, 9QOS, 9QP9, 9QPB, 9QPD, 9QPL

  • PubMed Abstract: 

    According to the World Health Organization (WHO), antimicrobial resistance is a serious global health issue. Overcoming antibiotic resistance involves several strategies, including the inhibition of resistance mechanisms. Among the various resistance mechanisms, aminoglycoside phosphotransferases (APHs) catalyze the transfer of the γ-phosphate from a nucleotide donor to various aminoglycosides, leading to their inactivation. In this work, using a fragment-based drug design (FBDD) approach, we have identified and characterized a promising APH inhibitor capable of increasing the sensitivity of Pseudomonas aeruginosa and Staphylococcus aureus resistant to aminoglycosides. It is therefore a good candidate for the future development of APH inhibitors to be prescribed in combination with aminoglycosides. This molecule is a competitive inhibitor of adenosine 5'-triphosphate (ATP), the phosphate donor of APHs. Further studies are required to optimize this molecule to improve its specificity for APHs and its bioavailability in bacteria.


  • Organizational Affiliation
    • Centre de Biologie Structurale (CBS), University of Montpellier, CNRS UMR 5048, INSERM U1054, Montpellier, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
APH(2'')-Id
A, B
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: 2.30 Å
  • R-Value Free:  0.278 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.31α = 90
b = 65.39β = 91.39
c = 77.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-02-11
    Changes: Database references