9QP2 | pdb_00009qp2

APH(2'')-IVa with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.254 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9QP2

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 76.25 kDa 
  • Atom Count: 4,992 
  • Modeled Residue Count: 594 
  • Deposited Residue Count: 642 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I8W
(Subject of Investigation/LOI)

Query on A1I8W



Download:Ideal Coordinates CCD File
C [auth B],
G [auth A]
(2~{R})-3-[4-(5-chloranyl-1~{H}-pyrrolo[2,3-b]pyridin-4-yl)-1,2,3-triazol-1-yl]-2-methyl-propan-1-ol
C13 H14 Cl N5 O
AHVJTVIIVOMNQW-MRVPVSSYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
D [auth B]
E [auth B]
F [auth B]
H [auth A]
I [auth A]
D [auth B],
E [auth B],
F [auth B],
H [auth A],
I [auth A],
J [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.254 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.737α = 90
b = 64.838β = 91.47
c = 77.234γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2026-02-11
    Type: Initial release