9HAO | pdb_00009hao

BDM91531 inhibitor bound to the transmembrane domain of AcrB

PDB DOI: https://doi.org/10.2210/pdb9HAO/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12, synthetic construct
Expression System: Escherichia coli B, Escherichia coli K-12
Mutation(s): No

Deposited: 2024-11-04 Released: 2025-11-12
Deposition Author(s): Mueller, R.T., Herrmann, A., Pos, K.M.
Funding Organization(s): German Federal Ministry for Education and Research, Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.225 (Depositor), 0.225 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps

Boernsen, C., Mueller, R.T., Pos, K.M.

To be published.

Macromolecule Content

Total Structure Weight: 394.71 kDa
Atom Count: 28,454
Modeled Residue Count: 3,407
Deposited Residue Count: 3,509
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 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
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224 Go to UniProtKB: P31224
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPIN	D, E	169	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain UB [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain UB [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain UB [auth C]	F [auth A] G [auth A] IA [auth B] J [auth A] JA [auth B] F [auth A], G [auth A], IA [auth B], J [auth A], JA [auth B], PA [auth B], PB [auth C], UB [auth C]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain UB [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain UB [auth C]
LPX Query on LPX Download Ideal Coordinates CCD File SDF format, chain RB [auth C] SDF format, chain TB [auth C] MOL2 format, chain RB [auth C] MOL2 format, chain TB [auth C] mmCIF format, chain RB [auth C] mmCIF format, chain TB [auth C]	RB [auth C], TB [auth C]	(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate C₂₁ H₄₄ N O₇ P YVYMBNSKXOXSKW-FQEVSTJZSA-N		Interactions Focus chain RB [auth C] Focus chain TB [auth C] Interactions & Density Focus chain RB [auth C] Focus chain TB [auth C]
DDR Query on DDR Download Ideal Coordinates CCD File SDF format, chain NA [auth B] MOL2 format, chain NA [auth B] mmCIF format, chain NA [auth B]	NA [auth B]	(2S)-3-hydroxypropane-1,2-diyl didecanoate C₂₃ H₄₄ O₅ GNSDEDOVXZDMKM-NRFANRHFSA-N		Interactions Focus chain NA [auth B] Interactions & Density Focus chain NA [auth B]
XE9 (Subject of Investigation/LOI) Query on XE9 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain AA [auth A]	AA [auth A]	[3-(3-chloranyl-2-piperazin-1-yl-quinolin-6-yl)phenyl]methanamine C₂₀ H₂₁ Cl N₄ PMBAQAZUQBDHLD-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Interactions & Density Focus chain AA [auth A]
DDQ Query on DDQ Download Ideal Coordinates CCD File SDF format, chain OC [auth C] SDF format, chain UA [auth B] MOL2 format, chain OC [auth C] MOL2 format, chain UA [auth B] mmCIF format, chain OC [auth C] mmCIF format, chain UA [auth B]	OC [auth C], UA [auth B]	DECYLAMINE-N,N-DIMETHYL-N-OXIDE C₁₂ H₂₇ N O ZRKZFNZPJKEWPC-UHFFFAOYSA-N		Interactions Focus chain OC [auth C] Focus chain UA [auth B] Interactions & Density Focus chain OC [auth C] Focus chain UA [auth B]
C14 Query on C14 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain SB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain SB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain SB [auth C]	I [auth A], SB [auth C]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain SB [auth C] Interactions & Density Focus chain I [auth A] Focus chain SB [auth C]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain W [auth A] SDF format, chain Y [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A]	BB [auth B], CB [auth B], W [auth A], Y [auth A]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain BB [auth B] Focus chain CB [auth B] Focus chain W [auth A] Focus chain Y [auth A] Interactions & Density Focus chain BB [auth B] Focus chain CB [auth B] Focus chain W [auth A] Focus chain Y [auth A]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain KA [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain KA [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain KA [auth B]	CA [auth A], KA [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain KA [auth B] Interactions & Density Focus chain CA [auth A] Focus chain KA [auth B]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain AC [auth C] SDF format, chain GC [auth C] SDF format, chain H [auth A] SDF format, chain KB [auth B] SDF format, chain L [auth A] SDF format, chain MB [auth C] SDF format, chain QB [auth C] SDF format, chain QC [auth C] MOL2 format, chain AC [auth C] MOL2 format, chain GC [auth C] MOL2 format, chain H [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain MB [auth C] MOL2 format, chain QB [auth C] MOL2 format, chain QC [auth C] mmCIF format, chain AC [auth C] mmCIF format, chain GC [auth C] mmCIF format, chain H [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain MB [auth C] mmCIF format, chain QB [auth C] mmCIF format, chain QC [auth C]	AC [auth C] GC [auth C] H [auth A] KB [auth B] L [auth A] AC [auth C], GC [auth C], H [auth A], KB [auth B], L [auth A], MB [auth C], QB [auth C], QC [auth C]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain AC [auth C] Focus chain GC [auth C] Focus chain H [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain MB [auth C] Focus chain QB [auth C] Focus chain QC [auth C] Interactions & Density Focus chain AC [auth C] Focus chain GC [auth C] Focus chain H [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain MB [auth C] Focus chain QB [auth C] Focus chain QC [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain FC [auth C] SDF format, chain VA [auth B] SDF format, chain ZB [auth C] MOL2 format, chain FC [auth C] MOL2 format, chain VA [auth B] MOL2 format, chain ZB [auth C] mmCIF format, chain FC [auth C] mmCIF format, chain VA [auth B] mmCIF format, chain ZB [auth C]	FC [auth C], VA [auth B], ZB [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FC [auth C] Focus chain VA [auth B] Focus chain ZB [auth C] Interactions & Density Focus chain FC [auth C] Focus chain VA [auth B] Focus chain ZB [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BC [auth C] SDF format, chain CC [auth C] SDF format, chain DA [auth A] SDF format, chain DC [auth C] SDF format, chain EA [auth A] SDF format, chain EC [auth C] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HC [auth C] SDF format, chain IC [auth C] SDF format, chain JC [auth C] SDF format, chain KC [auth C] SDF format, chain LC [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain P [auth A] SDF format, chain PC [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain RC [auth D] SDF format, chain S [auth A] SDF format, chain SC [auth D] SDF format, chain T [auth A] SDF format, chain TC [auth D] SDF format, chain U [auth A] SDF format, chain UC [auth D] SDF format, chain V [auth A] SDF format, chain VB [auth C] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BC [auth C] MOL2 format, chain CC [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain DC [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain EC [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HC [auth C] MOL2 format, chain IC [auth C] MOL2 format, chain JC [auth C] MOL2 format, chain KC [auth C] MOL2 format, chain LC [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PC [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain RC [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SC [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TC [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UC [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth C] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain BC [auth C] mmCIF format, chain CC [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain DC [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain EC [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HC [auth C] mmCIF format, chain IC [auth C] mmCIF format, chain JC [auth C] mmCIF format, chain KC [auth C] mmCIF format, chain LC [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PC [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain RC [auth D] mmCIF format, chain S [auth A] mmCIF format, chain SC [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TC [auth D] mmCIF format, chain U [auth A] mmCIF format, chain UC [auth D] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth C] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B]	AB [auth B] BC [auth C] CC [auth C] DA [auth A] DC [auth C] AB [auth B], BC [auth C], CC [auth C], DA [auth A], DC [auth C], EA [auth A], EC [auth C], FA [auth A], GA [auth A], HC [auth C], IC [auth C], JC [auth C], KC [auth C], LC [auth C], M [auth A], N [auth A], O [auth A], OA [auth B], OB [auth C], P [auth A], PC [auth C], Q [auth A], QA [auth B], R [auth A], RA [auth B], RC [auth D], S [auth A], SC [auth D], T [auth A], TC [auth D], U [auth A], UC [auth D], V [auth A], VB [auth C], WA [auth B], XA [auth B], YA [auth B], Z [auth A], ZA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain BC [auth C] Focus chain CC [auth C] Focus chain DA [auth A] Focus chain DC [auth C] Focus chain EA [auth A] Focus chain EC [auth C] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HC [auth C] Focus chain IC [auth C] Focus chain JC [auth C] Focus chain KC [auth C] Focus chain LC [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PC [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VB [auth C] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BC [auth C] Focus chain CC [auth C] Focus chain DA [auth A] Focus chain DC [auth C] Focus chain EA [auth A] Focus chain EC [auth C] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HC [auth C] Focus chain IC [auth C] Focus chain JC [auth C] Focus chain KC [auth C] Focus chain LC [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PC [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VB [auth C] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain DB [auth B] SDF format, chain EB [auth B] SDF format, chain JB [auth B] SDF format, chain MC [auth C] SDF format, chain NB [auth C] SDF format, chain NC [auth C] SDF format, chain X [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain MC [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain NC [auth C] MOL2 format, chain X [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain JB [auth B] mmCIF format, chain MC [auth C] mmCIF format, chain NB [auth C] mmCIF format, chain NC [auth C] mmCIF format, chain X [auth A]	BA [auth A] DB [auth B] EB [auth B] JB [auth B] MC [auth C] BA [auth A], DB [auth B], EB [auth B], JB [auth B], MC [auth C], NB [auth C], NC [auth C], X [auth A]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain JB [auth B] Focus chain MC [auth C] Focus chain NB [auth C] Focus chain NC [auth C] Focus chain X [auth A] Interactions & Density Focus chain BA [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain JB [auth B] Focus chain MC [auth C] Focus chain NB [auth C] Focus chain NC [auth C] Focus chain X [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FB [auth B] SDF format, chain GB [auth B] SDF format, chain HA [auth B] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain K [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain MA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain WB [auth C] SDF format, chain XB [auth C] SDF format, chain YB [auth C] MOL2 format, chain FB [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain WB [auth C] MOL2 format, chain XB [auth C] MOL2 format, chain YB [auth C] mmCIF format, chain FB [auth B] mmCIF format, chain GB [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain WB [auth C] mmCIF format, chain XB [auth C] mmCIF format, chain YB [auth C]	FB [auth B] GB [auth B] HA [auth B] HB [auth B] IB [auth B] FB [auth B], GB [auth B], HA [auth B], HB [auth B], IB [auth B], K [auth A], LA [auth B], LB [auth C], MA [auth B], SA [auth B], TA [auth B], WB [auth C], XB [auth C], YB [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HA [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain K [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain WB [auth C] Focus chain XB [auth C] Focus chain YB [auth C] Interactions & Density Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HA [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain K [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain WB [auth C] Focus chain XB [auth C] Focus chain YB [auth C]