5MGI

Crystal structure of KPC-2 carbapenemase in complex with a phenyl boronic inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Phenylboronic Acid Derivatives as Validated Leads Active in Clinical Strains Overexpressing KPC-2: A Step against Bacterial Resistance.

Celenza, G.Vicario, M.Bellio, P.Linciano, P.Perilli, M.Oliver, A.Blazquez, J.Cendron, L.Tondi, D.

(2018) ChemMedChem 13: 713-724

  • DOI: https://doi.org/10.1002/cmdc.201700788
  • Primary Citation of Related Structures:  
    5LL7, 5MGI

  • PubMed Abstract: 

    The emergence and dissemination of multidrug resistant (MDR) pathogens resistant to nearly all available antibiotics poses a significant threat in clinical therapy. Among them, Klebsiella pneumoniae clinical isolates overexpressing KPC-2 carbapenemase are the most worrisome, extending bacterial resistance to last-resort carbapenems. In this study, we investigate the molecular recognition requirements in the KPC-2 active site by small phenylboronic acid derivatives. Four new phenylboronic acid derivatives were designed and tested against KPC-2. For the most active, despite their simple chemical structures, nanomolar affinity was achieved. The new derivatives restored susceptibility to meropenem in clinical strains overexpressing KPC-2. Moreover, no cytotoxicity was detected in cell-viability assays, which further validated the designed leads. Two crystallographic binary complexes of the best inhibitors binding KPC-2 were obtained at high resolution. Kinetic descriptions of slow binding, time-dependent inhibition, and interaction geometries in KPC-2 were fully investigated. This study will ultimately lead toward the optimization and development of more-effective KPC-2 inhibitors.


  • Organizational Affiliation

    Dipartimento di Scienze Cliniche Applicate e Biotecnologie, Università dell'Aquila, Via Vetoio 1, 67100, L'Aquila, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbapenem-hydrolyzing beta-lactamase KPC264Klebsiella oxytocaMutation(s): 0 
Gene Names: blakpckpc2
EC: 3.5.2.6
UniProt
Find proteins for Q848S6 (Klebsiella oxytoca)
Explore Q848S6 
Go to UniProtKB:  Q848S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ848S6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6YV
Query on 6YV

Download Ideal Coordinates CCD File 
B [auth A](~{E})-3-[2-(dihydroxyboranyl)phenyl]prop-2-enoic acid
C9 H9 B O4
OPFDGNUJQALQFL-AATRIKPKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.409α = 90
b = 66.218β = 90
c = 72.344γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description