4X69

Crystal structure of OP0595 complexed with CTX-M-44


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

OP0595, a new diazabicyclooctane: mode of action as a serine beta-lactamase inhibitor, antibiotic and beta-lactam 'enhancer'

Morinaka, A.Tsutsumi, Y.Yamada, M.Suzuki, K.Watanabe, T.Abe, T.Furuuchi, T.Inamura, S.Sakamaki, Y.Mitsuhashi, N.Ida, T.Livermore, D.M.

(2015) J Antimicrob Chemother 70: 2779-2786

  • DOI: https://doi.org/10.1093/jac/dkv166
  • Primary Citation of Related Structures:  
    4X68, 4X69

  • PubMed Abstract: 

    The production of a growing diversity of β-lactamases by Gram-negative bacteria challenges antimicrobial chemotherapy. OP0595, discovered separately by each of Meiji Seika Pharma and Fedora Pharmaceuticals, is a new diazabicyclooctane serine β-lactamase inhibitor that also acts as an antibiotic and as a β-lactamase-independent β-lactam 'enhancer'. Inhibitory activity against serine β-lactamases and affinity for PBPs were determined using nitrocefin and Bocillin FL, respectively. MICs alone and in combination with β-lactam agents were measured according to CLSI recommendations. Morphological changes in Escherichia coli were examined by phase-contrast microscopy. IC50s of OP0595 for class A and C β-lactamases were <1000 nM, with covalent binding demonstrated to the active-site serine of CTX-M-44 and AmpC enzymes. OP0595 also had direct antibiotic activity against many Enterobacteriaceae, associated with inhibition of PBP2 and conversion of the bacteria into spherical forms. Synergy between OP0595 and β-lactam agents was seen against strains producing class A and C β-lactamases vulnerable to inhibition. Lastly, OP0595 lowered the MICs of PBP3-targeted partner β-lactam agents for a non-β-lactamase-producing E. coli mutant that was resistant to OP0595 itself, indicating β-lactamase-independent 'enhancer'-based synergy. OP0595 acts in three ways: (i) as an inhibitor of class A and C β-lactamases, covalently binding at their active sites; (ii) as an antibacterial, by inhibiting PBP2 of several Enterobacteriaceae; and (iii) as an 'enhancer' of β-lactam agents that bind to other PBPs besides PBP2 for several Enterobacteriaceae. OP0595 has considerable potential to overcome resistance when it is combined with various β-lactam agents.


  • Organizational Affiliation

    Meiji Seika Pharma Co., Ltd, Yokohama, Japan akihiro.morinaka@meiji.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase Toho-1
A, B
262Escherichia coliMutation(s): 1 
Gene Names: bla
EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli)
Explore Q47066 
Go to UniProtKB:  Q47066
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47066
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.533α = 90
b = 72.982β = 109.29
c = 63.052γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Derived calculations
  • Version 1.2: 2015-10-14
    Changes: Database references
  • Version 1.3: 2020-02-05
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary