CTX-M-9 in complex with the broad spectrum inhibitor 3-(2- carboxyvinyl)benzo(b)thiophene-2-boronic acid

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

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This is version 1.4 of the entry. See complete history


Targeting Class A and C Serine beta-Lactamases with a Broad-Spectrum Boronic Acid Derivative.

Tondi, D.Venturelli, A.Bonnet, R.Pozzi, C.Shoichet, B.K.Costi, M.P.

(2014) J Med Chem 57: 5449-5458

  • DOI: https://doi.org/10.1021/jm5006572
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Production of β-lactamases (BLs) is the most widespread resistance mechanism adopted by bacteria to fight β-lactam antibiotics. The substrate spectrum of BLs has become increasingly broad, posing a serious health problem. Thus, there is an urgent need for novel BL inhibitors. Boronic acid transition-state analogues are able to reverse the resistance conferred by class A and C BLs. We describe a boronic acid analogue possessing interesting and potent broad-spectrum activity vs class A and C serine-based BLs. Starting from benzo(b)thiophene-2-boronic acid (BZBTH2B), a nanomolar non-β-lactam inhibitor of AmpC that can potentiate the activity of a third-generation cephalosporin against AmpC-producing resistant bacteria, we designed a novel broad-spectrum nanomolar inhibitor of class A and C BLs. Structure-based drug design (SBDD), synthesis, enzymology data, and X-ray crystallography results are discussed. We clarified the inhibitor binding geometry responsible for broad-spectrum activity vs serine-active BLs using double mutant thermodynamic cycle studies.

  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco , 600 16th Street San Francisco, California 94143-2240, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
263Escherichia coliMutation(s): 0 
Gene Names: blaCTX-M-9blaCTX-M-9ablaCTX-M-9a blaCTX-M-9 blaCTX-M-9bblaCTX-M-9b
Find proteins for Q9L5C8 (Escherichia coli)
Explore Q9L5C8 
Go to UniProtKB:  Q9L5C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L5C8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2GK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2E)-3-[2-(dihydroxyboranyl)-1-benzothiophen-3-yl]prop-2-enoic acid
C11 H9 B O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.116α = 90
b = 106.595β = 102.03
c = 47.68γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2014-06-18 
  • Deposition Author(s): Tondi, D.

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-16
    Changes: Database references
  • Version 1.2: 2016-10-19
    Changes: Structure summary
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description