Structural basis for the inhibition of bacterial multidrug exporters

Experimental Data Snapshot

  • Resolution: 3.05 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Structural basis for the inhibition of bacterial multidrug exporters

Nakashima, R.Sakurai, K.Yamasaki, S.Hayashi, K.Nagata, C.Hoshino, K.Onodera, Y.Nishino, K.Yamaguchi, A.

(2013) Nature 500: 102-106

  • DOI: https://doi.org/10.1038/nature12300
  • Primary Citation of Related Structures:  
    3W9H, 3W9I, 3W9J

  • PubMed Abstract: 

    The multidrug efflux transporter AcrB and its homologues are important in the multidrug resistance of Gram-negative pathogens. However, despite efforts to develop efflux inhibitors, clinically useful inhibitors are not available at present. Pyridopyrimidine derivatives are AcrB- and MexB-specific inhibitors that do not inhibit MexY; MexB and MexY are principal multidrug exporters in Pseudomonas aeruginosa. We have previously determined the crystal structure of AcrB in the absence and presence of antibiotics. Drugs were shown to be exported by a functionally rotating mechanism through tandem proximal and distal multisite drug-binding pockets. Here we describe the first inhibitor-bound structures of AcrB and MexB, in which these proteins are bound by a pyridopyrimidine derivative. The pyridopyrimidine derivative binds tightly to a narrow pit composed of a phenylalanine cluster located in the distal pocket and sterically hinders the functional rotation. This pit is a hydrophobic trap that branches off from the substrate-translocation channel. Phe 178 is located at the edge of this trap in AcrB and MexB and contributes to the tight binding of the inhibitor molecule through a π-π interaction with the pyridopyrimidine ring. The voluminous side chain of Trp 177 located at the corresponding position in MexY prevents inhibitor binding. The structure of the hydrophobic trap described in this study will contribute to the development of universal inhibitors of MexB and MexY in P. aeruginosa.

  • Organizational Affiliation

    Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acriflavine resistance protein B
A, B, C
1,033Escherichia coli K-12Mutation(s): 0 
Gene Names: acrBacrEb0462JW0451
Membrane Entity: Yes 
Find proteins for P31224 (Escherichia coli (strain K12))
Explore P31224 
Go to UniProtKB:  P31224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31224
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on P9D

Download Ideal Coordinates CCD File 
D [auth B][{2-[({[(3R)-1-{8-[(4-tert-butyl-1,3-thiazol-2-yl)carbamoyl]-4-oxo-3-[(E)-2-(1H-tetrazol-5-yl)ethenyl]-4H-pyrido[1,2-a]pyrimidin-2-yl}piperidin-3-yl]oxy}carbonyl)amino]ethyl}(dimethyl)ammonio]acetate
C31 H39 N11 O6 S
Experimental Data & Validation

Experimental Data

  • Resolution: 3.05 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226.279α = 90
b = 134.16β = 97.83
c = 162.202γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description