7OUK | pdb_00007ouk

BDM88855 inhibitor bound to the transmembrane domain of AcrB

PDB DOI: https://doi.org/10.2210/pdb7OUK/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12, synthetic construct
Expression System: Escherichia coli BL21(DE3), Escherichia coli K-12
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2021-06-12 Released: 2021-12-29
Deposition Author(s): Tam, H.K., Foong, W.E., Pos, K.M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.263 (Depositor), 0.262 (DCC)
R-Value Work:
0.236 (Depositor), 0.237 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
View more details

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

PubMed: 35013254 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-27726-2
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 389.72 kDa
Atom Count: 26,935
Modeled Residue Count: 3,411
Deposited Residue Count: 3,509
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	A, B, C	1,057	Escherichia coli K-12	Mutation(s): 0 Gene Names: acrB, acrE, b0462, JW0451 Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224 Go to UniProtKB: P31224
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPIN	D, E	169	synthetic construct	Mutation(s): 0 Gene Names: Artificial gene

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain RA [auth C] SDF format, chain P [auth A] SDF format, chain MA [auth C] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain BA [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain BA [auth B]	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		Interactions Focus chain BA [auth B] Focus chain F [auth A] Focus chain H [auth A] Focus chain MA [auth C] Focus chain P [auth A] Focus chain RA [auth C] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain BA [auth B] Focus chain F [auth A] Focus chain H [auth A] Focus chain MA [auth C] Focus chain P [auth A] Focus chain RA [auth C] Focus chain U [auth B] Focus chain V [auth B]
LPX Query on LPX Download:Ideal Coordinates CCD File SDF format, chain QA [auth C] SDF format, chain OA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain OA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain OA [auth C]	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		Interactions Focus chain OA [auth C] Focus chain QA [auth C] Interactions & Density Focus chain OA [auth C] Focus chain QA [auth C]
DDR Query on DDR Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain Z [auth B]	Z [auth B]	(2S)-3-hydroxypropane-1,2-diyl didecanoate C₂₃ H₄₄ O₅ GNSDEDOVXZDMKM-NRFANRHFSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
1K8 (Subject of Investigation/LOI) Query on 1K8 Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain G [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain G [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain G [auth A]	G [auth A], HA [auth B]	3-chloranyl-2-piperazin-1-yl-quinoline C₁₃ H₁₄ Cl N₃ JJZVQFQJCHXCFQ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain HA [auth B] Interactions & Density Focus chain G [auth A] Focus chain HA [auth B]
DDQ Query on DDQ Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain GA [auth B]	GA [auth B]	DECYLAMINE-N,N-DIMETHYL-N-OXIDE C₁₂ H₂₇ N O ZRKZFNZPJKEWPC-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Interactions & Density Focus chain GA [auth B]
C14 Query on C14 Download:Ideal Coordinates CCD File SDF format, chain PA [auth C] SDF format, chain M [auth A] SDF format, chain K [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A]	K [auth A], M [auth A], PA [auth C]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth A] Focus chain PA [auth C] Interactions & Density Focus chain K [auth A] Focus chain M [auth A] Focus chain PA [auth C]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain NA [auth C] SDF format, chain KA [auth C] SDF format, chain J [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain J [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain J [auth A]	J [auth A], KA [auth C], NA [auth C]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain KA [auth C] Focus chain NA [auth C] Interactions & Density Focus chain J [auth A] Focus chain KA [auth C] Focus chain NA [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain WA [auth C] SDF format, chain JA [auth B] SDF format, chain IA [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B]	IA [auth B], JA [auth B], WA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain WA [auth C] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain WA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain SA [auth C] SDF format, chain L [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain AA [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain AA [auth B]	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		Interactions Focus chain AA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain L [auth A] Focus chain SA [auth C] Focus chain T [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain L [auth A] Focus chain SA [auth C] Focus chain T [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain S [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain LA [auth C] SDF format, chain I [auth A] SDF format, chain FA [auth B] SDF format, chain EA [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B]	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		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain I [auth A] Focus chain LA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain I [auth A] Focus chain LA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain X [auth B] Focus chain Y [auth B]