5LL7 | pdb_00005ll7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.197 (DCC) 
  • R-Value Work: 
    0.183 (DCC) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 28.77 kDa 
  • Atom Count: 2,177 
  • Modeled Residue Count: 264 
  • Deposited Residue Count: 268 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase268Escherichia coliMutation(s): 0 
Gene Names: blaKPC-18
EC: 3.5.2.6
UniProt
Find proteins for A0A0H4IUK8 (Escherichia coli)
Explore A0A0H4IUK8 
Go to UniProtKB:  A0A0H4IUK8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H4IUK8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.197 (DCC) 
  • R-Value Work:  0.183 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.033α = 90
b = 65.764β = 90
c = 72.21γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fondo Ateneo Ricerca University of Modena and Reggio EmiliaItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary