6TS9 | pdb_00006ts9

Crystal structure of GES-5 carbapenemase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.204 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.193 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Targeting the Class A Carbapenemase GES-5 via Virtual Screening.

Klein, R.Cendron, L.Montanari, M.Bellio, P.Celenza, G.Maso, L.Tondi, D.Brenk, R.

(2020) Biomolecules 10

  • DOI: https://doi.org/10.3390/biom10020304
  • Primary Citation Related Structures: 
    6TS9

  • PubMed Abstract: 

    The worldwide spread of β-lactamases able to hydrolyze last resort carbapenems contributes to the antibiotic resistance problem and menaces the successful antimicrobial treatment of clinically relevant pathogens. Class A carbapenemases include members of the KPC and GES families. While drugs against KPC-type carbapenemases have recently been approved, for GES-type enzymes, no inhibitors have yet been introduced in therapy. Thus, GES carbapenemases represent important drug targets. Here, we present an in silico screening against the most prevalent GES carbapenemase, GES-5, using a lead-like compound library of commercially available compounds. The most promising candidates were selected for in vitro validation in biochemical assays against recombinant GES-5 leading to four derivatives active as high micromolar competitive inhibitors. For the best inhibitors, the ability to inhibit KPC-2 was also evaluated. The discovered inhibitors constitute promising starting points for hit to lead optimization.


  • Organizational Affiliation
    • Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, 55122 Mainz, Germany.

Macromolecule Content 

  • Total Structure Weight: 62.98 kDa 
  • Atom Count: 4,829 
  • Modeled Residue Count: 537 
  • Deposited Residue Count: 574 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
287Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaGES-5pGES-GZ_027
EC: 3.5.2.6
UniProt
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR

Query on BR



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
H [auth B],
I [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
DMS
(Subject of Investigation/LOI)

Query on DMS



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.204 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.193 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.3α = 90
b = 80.36β = 90
c = 87.85γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary