7SEL

E. coli MsbA in complex with LPS and inhibitor G7090 (compound 3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Inhibitors of the Lipopolysaccharide Transporter MsbA: From a Screening Hit to Potent Wild-Type Gram-Negative Activity.

Verma, V.A.Wang, L.Labadie, S.S.Liang, J.Sellers, B.D.Wang, J.Dong, L.Wang, Q.Zhang, S.Xu, Z.Zhang, Y.Niu, Y.Wang, X.Wai, J.Koehler, M.F.T.Hu, H.Alexander, M.K.Nishiyama, M.Miu, A.Xu, Y.Pang, J.Katakam, A.K.Reichelt, M.Austin, C.D.Ho, H.Payandeh, J.Koth, C.M.

(2022) J Med Chem 65: 4085-4120

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01909
  • Primary Citation of Related Structures:  
    7SEL

  • PubMed Abstract: 

    The dramatic increase in the prevalence of multi-drug resistant Gram-negative bacterial infections and the simultaneous lack of new classes of antibiotics is projected to result in approximately 10 million deaths per year by 2050. We report on efforts to target the Gram-negative ATP-binding cassette (ABC) transporter MsbA, an essential inner membrane protein that transports lipopolysaccharide from the inner leaflet to the periplasmic face of the inner membrane. We demonstrate the improvement of a high throughput screening hit into compounds with on-target single digit micromolar (μM) minimum inhibitory concentrations against wild-type uropathogenic Escherichia coli , Klebsiella pneumoniae , and Enterobacter cloacae . A 2.98 Å resolution X-ray crystal structure of MsbA complexed with an inhibitor revealed a novel mechanism for inhibition of an ABC transporter. The identification of a fully encapsulated membrane binding site in Gram-negative bacteria led to unique physicochemical property requirements for wild-type activity.


  • Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent lipid A-core flippase
A, B
599Escherichia coliMutation(s): 0 
Gene Names: msbAECBD_2681
EC: 7.5.2.6
Membrane Entity: Yes 
UniProt
Find proteins for P60752 (Escherichia coli (strain K12))
Explore P60752 
Go to UniProtKB:  P60752
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60752
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KDL (Subject of Investigation/LOI)
Query on KDL

Download Ideal Coordinates CCD File 
E [auth B](2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
C110 H202 N2 O39 P2
DIXUKJUHGLIZGU-OIPVZEHTSA-N
95X (Subject of Investigation/LOI)
Query on 95X

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2E)-3-{7-[(1S)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-1-methylnaphthalen-2-yl}prop-2-enoic acid
C22 H17 Cl2 F O3
RHZRLFIWQWRTKH-PPOCWRSBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.446α = 90
b = 91.99β = 90.31
c = 110.655γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
F. Hoffmann-La Roche LTDSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection