8P1I

Single particle cryo-EM co-structure of Klebsiella pneumoniae AcrB with the BDM91288 efflux pump inhibitor at 2.97 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae.

Vieira Da Cruz, A.Jimenez-Castellanos, J.C.Bornsen, C.Van Maele, L.Compagne, N.Pradel, E.Muller, R.T.Meurillon, V.Soulard, D.Piveteau, C.Biela, A.Dumont, J.Leroux, F.Deprez, B.Willand, N.Pos, K.M.Frangakis, A.S.Hartkoorn, R.C.Flipo, M.

(2024) EMBO Mol Med 16: 93-111

  • DOI: https://doi.org/10.1038/s44321-023-00007-9
  • Primary Citation of Related Structures:  
    8P1I

  • PubMed Abstract: 

    Antimicrobial resistance is a global problem, rendering conventional treatments less effective and requiring innovative strategies to combat this growing threat. The tripartite AcrAB-TolC efflux pump is the dominant constitutive system by which Enterobacterales like Escherichia coli and Klebsiella pneumoniae extrude antibiotics. Here, we describe the medicinal chemistry development and drug-like properties of BDM91288, a pyridylpiperazine-based AcrB efflux pump inhibitor. In vitro evaluation of BDM91288 confirmed it to potentiate the activity of a panel of antibiotics against K. pneumoniae as well as revert clinically relevant antibiotic resistance mediated by acrAB-tolC overexpression. Using cryo-EM, BDM91288 binding to the transmembrane region of K. pneumoniae AcrB was confirmed, further validating the mechanism of action of this inhibitor. Finally, proof of concept studies demonstrated that oral administration of BDM91288 significantly potentiated the in vivo efficacy of levofloxacin treatment in a murine model of K. pneumoniae lung infection.


  • Organizational Affiliation

    Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Efflux pump membrane transporter
A, B, C
1,056Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940Mutation(s): 0 
Gene Names: UUU_08720
Membrane Entity: Yes 
UniProt
Find proteins for A0A332Z023 (Klebsiella pneumoniae)
Explore A0A332Z023 
Go to UniProtKB:  A0A332Z023
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A332Z023
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WR6
Query on WR6

Download Ideal Coordinates CCD File 
E [auth B][(2~{R})-1-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-3-undecanoyloxy-propan-2-yl] tricosanoate
C40 H79 O10 P
QVTMHGKJALUQCM-XPSQVAKYSA-N
PG8
Query on PG8

Download Ideal Coordinates CCD File 
F [auth C],
G [auth C]
1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)
C22 H42 O10 P
BQEXNLVNNRZNEI-WOJBJXKFSA-M
WQW (Subject of Investigation/LOI)
Query on WQW

Download Ideal Coordinates CCD File 
D [auth A]3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline
C17 H24 Cl N5
WOZFYSNOHHYUAU-UHFFFAOYSA-P
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermanyBMBF- 16GW0236K
Agence Nationale de la Recherche (ANR)FranceANR-19-AMRB-0007

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references