7OUK

BDM88855 inhibitor bound to the transmembrane domain of AcrB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps.

Ple, C.Tam, H.K.Vieira Da Cruz, A.Compagne, N.Jimenez-Castellanos, J.C.Muller, R.T.Pradel, E.Foong, W.E.Malloci, G.Ballee, A.Kirchner, M.A.Moshfegh, P.Herledan, A.Herrmann, A.Deprez, B.Willand, N.Vargiu, A.V.Pos, K.M.Flipo, M.Hartkoorn, R.C.

(2022) Nat Commun 13: 115-115

  • DOI: https://doi.org/10.1038/s41467-021-27726-2
  • Primary Citation of Related Structures:  
    7OUK, 7OUL, 7OUM

  • PubMed Abstract: 

    Efflux transporters of the RND family confer resistance to multiple antibiotics in Gram-negative bacteria. Here, we identify and chemically optimize pyridylpiperazine-based compounds that potentiate antibiotic activity in E. coli through inhibition of its primary RND transporter, AcrAB-TolC. Characterisation of resistant E. coli mutants and structural biology analyses indicate that the compounds bind to a unique site on the transmembrane domain of the AcrB L protomer, lined by key catalytic residues involved in proton relay. Molecular dynamics simulations suggest that the inhibitors access this binding pocket from the cytoplasm via a channel exclusively present in the AcrB L protomer. Thus, our work unveils a class of allosteric efflux-pump inhibitors that likely act by preventing the functional catalytic cycle of the RND pump.


  • Organizational Affiliation

    Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000, Lille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrB
A, B, C
1,057Escherichia coli K-12Mutation(s): 0 
Gene Names: acrBacrEb0462JW0451
Membrane Entity: Yes 
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
169synthetic constructMutation(s): 0 
Gene Names: Artificial gene
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
BA [auth B]
F [auth A]
H [auth A]
MA [auth C]
P [auth A]
BA [auth B],
F [auth A],
H [auth A],
MA [auth C],
P [auth A],
RA [auth C],
U [auth B],
V [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LPX
Query on LPX

Download Ideal Coordinates CCD File 
OA [auth C],
QA [auth C]
(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
C21 H44 N O7 P
YVYMBNSKXOXSKW-FQEVSTJZSA-N
DDR
Query on DDR

Download Ideal Coordinates CCD File 
Z [auth B](2S)-3-hydroxypropane-1,2-diyl didecanoate
C23 H44 O5
GNSDEDOVXZDMKM-NRFANRHFSA-N
1K8 (Subject of Investigation/LOI)
Query on 1K8

Download Ideal Coordinates CCD File 
G [auth A],
HA [auth B]
3-chloranyl-2-piperazin-1-yl-quinoline
C13 H14 Cl N3
JJZVQFQJCHXCFQ-UHFFFAOYSA-N
DDQ
Query on DDQ

Download Ideal Coordinates CCD File 
GA [auth B]DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
C14
Query on C14

Download Ideal Coordinates CCD File 
K [auth A],
M [auth A],
PA [auth C]
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
D10
Query on D10

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W [auth B]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT
Query on OCT

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J [auth A],
KA [auth C],
NA [auth C]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
IA [auth B],
JA [auth B],
WA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
CA [auth B]
DA [auth B]
L [auth A]
SA [auth C]
AA [auth B],
CA [auth B],
DA [auth B],
L [auth A],
SA [auth C],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth B]
FA [auth B]
I [auth A]
LA [auth C]
N [auth A]
EA [auth B],
FA [auth B],
I [auth A],
LA [auth C],
N [auth A],
O [auth A],
Q [auth A],
R [auth A],
S [auth B],
TA [auth C],
UA [auth C],
VA [auth C],
X [auth B],
Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.126α = 90
b = 159.647β = 90
c = 245.499γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB 807, Transport and Communication across Biological Membranes

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description