9CSI

A. baumannii MsbA Bound to Cerastecin Compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Cerastecin Inhibition of the Lipooligosaccharide Transporter MsbA to Combat Acinetobacter baumannii : From Screening Impurity to In Vivo Efficacy.

Skudlarek, J.W.Cooke, A.J.Mitchell, H.J.Babaoglu, K.Shaw, A.W.Tong, L.Nomland, A.B.Labroli, M.Sha, D.Mulhearn, J.J.Wu, C.Li, S.W.Beshore, D.C.Hughes, J.M.E.Jouffroy, M.Wang, H.Balibar, C.J.Painter, R.E.Shen, P.Lange, H.S.Ishchenko, A.Chen, Y.T.Klein, D.J.Tracy, R.W.Miller, R.R.Cabalu, T.D.Wu, Z.Leithead, A.Scapin, G.Hruza, A.W.Dzhekieva, L.Bukhtiyarova, M.Homsher, M.F.Xu, M.Bahnck-Teets, C.McKenney, D.Buevich, A.V.Liu, J.Zhang, L.K.Meng, T.Kelly, T.DiNunzio, E.Soisson, S.Cheng, R.K.Y.Hennig, M.Raheem, I.Walker, S.S.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01277
  • Primary Citation of Related Structures:  
    9CSG, 9CSI

  • PubMed Abstract: 

    Acinetobacter baumannii , a commonly multidrug-resistant Gram-negative bacterium responsible for large numbers of bloodstream and lung infections worldwide, is increasingly difficult to treat and constitutes a growing threat to human health. Structurally novel antibacterial chemical matter that can evade existing resistance mechanisms is essential for addressing this critical medical need. Herein, we describe our efforts to inhibit the essential A. baumannii lipooligosaccharide (LOS) ATP-binding cassette (ABC) transporter MsbA. An unexpected impurity from a phenotypic screening was optimized as a series of dimeric compounds, culminating with 1 (cerastecin D), which exhibited antibacterial activity in the presence of human serum and a pharmacokinetic profile sufficient to achieve efficacy against A. baumannii in murine septicemia and lung infection models.


  • Organizational Affiliation

    Merck & Co., Inc., Rahway, New Jersey 07065, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipid A export ATP-binding/permease protein MsbA598Acinetobacter baumanniiMutation(s): 0 
Gene Names: msbA
UniProt
Find proteins for A0A6F8TGG1 (Acinetobacter baumannii)
Explore A0A6F8TGG1 
Go to UniProtKB:  A0A6F8TGG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6F8TGG1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AZS (Subject of Investigation/LOI)
Query on A1AZS

Download Ideal Coordinates CCD File 
E [auth A]3,3'-[(1,4-dioxobutane-1,4-diyl)bis(azanediyl)]bis[(4-butylbenzene-1-sulfonamido)benzoic acid]
C38 H42 N4 O10 S2
MZGNMODGUUOXBI-UHFFFAOYSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MVC
Query on MVC

Download Ideal Coordinates CCD File 
C [auth A]MONOVACCENIN
C21 H40 O4
KJHYUSLWTPMFTN-WHXUGTBJSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.277α = 90
b = 83.157β = 90
c = 338.094γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release