GES-5-meropenem complex

Experimental Data Snapshot

  • Resolution: 1.62 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Restricted Rotational Flexibility of the C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the GES-5 Carbapenemase.

Stewart, N.K.Toth, M.Quan, P.Beer, M.Buynak, J.D.Smith, C.A.Vakulenko, S.B.

(2024) ACS Infect Dis 10: 1232-1249

  • DOI: https://doi.org/10.1021/acsinfecdis.3c00683
  • Primary Citation of Related Structures:  
    8V9G, 8V9H

  • PubMed Abstract: 

    Carbapenem antibiotics are used as a last-resort treatment for infections caused by multidrug-resistant bacteria. The wide spread of carbapenemases in Gram-negative bacteria has severely compromised the utility of these drugs and represents a serious public health threat. To combat carbapenemase-mediated resistance, new antimicrobials and inhibitors of these enzymes are urgently needed. Here, we describe the interaction of the atypically C5α-methyl-substituted carbapenem, NA-1-157, with the GES-5 carbapenemase. MICs of this compound against Escherichia coli , Klebsiella pneumoniae , and Acinetobacter baumannii producing the enzyme were reduced 4-16-fold when compared to MICs of the commercial carbapenems, reaching clinically sensitive breakpoints. When NA-1-157 was combined with meropenem, a strong synergistic effect was observed. Kinetic and ESI-LC/MS studies demonstrated that NA-1-157 is a potent inhibitor of GES-5, with a high inactivation efficiency of (2.9 ± 0.9) × 10 5 M -1 s -1 . Acylation of GES-5 by NA-1-157 was biphasic, with the fast phase completing within seconds, and the slow phase taking several hours and likely proceeding through a reversible tetrahedral intermediate. Deacylation was extremely slow ( k 3 = (2.4 ± 0.3) × 10 -7 s -1 ), resulting in a residence time of 48 ± 6 days. MD simulation of the GES-5-meropenem and GES-5-NA-1-157 acyl-enzyme complexes revealed that the C5α-methyl group in NA-1-157 sterically restricts rotation of the 6α-hydroxyethyl group preventing ingress of the deacylating water into the vicinity of the scissile bond of the acyl-enzyme intermediate. These data demonstrate that NA-1-157 is a potent irreversible inhibitor of the GES-5 carbapenemase.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
284Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaGES-5
Find proteins for Q09HD0 (Klebsiella pneumoniae)
Explore Q09HD0 
Go to UniProtKB:  Q09HD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09HD0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MER (Subject of Investigation/LOI)
Query on MER

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid
C17 H27 N3 O5 S
Query on IOD

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
L [auth B],
M [auth B]
Query on EDO

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D [auth A],
E [auth A],
I [auth B],
J [auth B]
C2 H6 O2
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.62 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.829α = 90
b = 80.581β = 90
c = 87.327γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI155723

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Database references