5ENT

Minocycline bound structure of bacterial efflux pump.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives.

Sjuts, H.Vargiu, A.V.Kwasny, S.M.Nguyen, S.T.Kim, H.S.Ding, X.Ornik, A.R.Ruggerone, P.Bowlin, T.L.Nikaido, H.Pos, K.M.Opperman, T.J.

(2016) Proc Natl Acad Sci U S A 113: 3509-3514

  • DOI: https://doi.org/10.1073/pnas.1602472113
  • Primary Citation of Related Structures:  
    5EN5, 5ENO, 5ENP, 5ENQ, 5ENR, 5ENS, 5ENT

  • PubMed Abstract: 

    The Escherichia coli AcrAB-TolC efflux pump is the archetype of the resistance nodulation cell division (RND) exporters from Gram-negative bacteria. Overexpression of RND-type efflux pumps is a major factor in multidrug resistance (MDR), which makes these pumps important antibacterial drug discovery targets. We have recently developed novel pyranopyridine-based inhibitors of AcrB, which are orders of magnitude more powerful than the previously known inhibitors. However, further development of such inhibitors has been hindered by the lack of structural information for rational drug design. Although only the soluble, periplasmic part of AcrB binds and exports the ligands, the presence of the membrane-embedded domain in AcrB and its polyspecific binding behavior have made cocrystallization with drugs challenging. To overcome this obstacle, we have engineered and produced a soluble version of AcrB [AcrB periplasmic domain (AcrBper)], which is highly congruent in structure with the periplasmic part of the full-length protein, and is capable of binding substrates and potent inhibitors. Here, we describe the molecular basis for pyranopyridine-based inhibition of AcrB using a combination of cellular, X-ray crystallographic, and molecular dynamics (MD) simulations studies. The pyranopyridines bind within a phenylalanine-rich cage that branches from the deep binding pocket of AcrB, where they form extensive hydrophobic interactions. Moreover, the increasing potency of improved inhibitors correlates with the formation of a delicate protein- and water-mediated hydrogen bond network. These detailed insights provide a molecular platform for the development of novel combinational therapies using efflux pump inhibitors for combating multidrug resistant Gram-negative pathogens.


  • Organizational Affiliation

    Institute of Biochemistry, Goethe University Frankfurt, D-60438 Frankfurt, Germany;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrB,Multidrug efflux pump subunit AcrB
A, B, C
609Escherichia coli K-12Mutation(s): 0 
Gene Names: acrBacrEb0462JW0451
UniProt
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DARPin
D, E, F
169synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MIY
Query on MIY

Download Ideal Coordinates CCD File 
G [auth C](4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE
C23 H27 N3 O7
DYKFCLLONBREIL-KVUCHLLUSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.557α = 90
b = 145.409β = 90
c = 175.612γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-04-13
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2018-04-25
    Changes: Data collection
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary