5O7N | pdb_00005o7n

Beta-lactamase VIM-2 in complex with (2R)-1-(2-Benzyl-3-mercaptopropanoyl)piperidine-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.211 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5O7N

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Challenges in the Development of a Thiol-Based Broad-Spectrum Inhibitor for Metallo-beta-Lactamases.

Buttner, D.Kramer, J.S.Klingler, F.M.Wittmann, S.K.Hartmann, M.R.Kurz, C.G.Kohnhauser, D.Weizel, L.Bruggerhoff, A.Frank, D.Steinhilber, D.Wichelhaus, T.A.Pogoryelov, D.Proschak, E.

(2018) ACS Infect Dis 4: 360-372

  • DOI: https://doi.org/10.1021/acsinfecdis.7b00129
  • Primary Citation Related Structures: 
    5O7N

  • PubMed Abstract: 

    Pathogens, expressing metallo-β-lactamases (MBLs), become resistant against most β-lactam antibiotics. Besides the dragging search for new antibiotics, development of MBL inhibitors would be an alternative weapon against resistant bacterial pathogens. Inhibition of resistance enzymes could restore the antibacterial activity of β-lactams. Various approaches to MBL inhibitors are described; among others, the promising motif of a zinc coordinating thiol moiety is very popular. Nevertheless, since the first report of a thiol-based MBL inhibitor (thiomandelic acid) in 2001, no steps in development of thiol based MBL inhibitors were reported that go beyond clinical isolate testing. In this study, we report on the synthesis and biochemical characterization of thiol-based MBL inhibitors and highlight the challenges behind the development of thiol-based compounds, which exhibit good in vitro activity toward a broad spectrum of MBLs, selectivity against human off-targets, and reasonable activity against clinical isolates.


  • Organizational Affiliation
    • Institute of Medical Microbiology and Infection Control , Goethe University Hospital , Paul-Ehrlich-Straße 40 , 60596 Frankfurt , Germany.

Macromolecule Content 

  • Total Structure Weight: 56.33 kDa 
  • Atom Count: 3,988 
  • Modeled Residue Count: 463 
  • Deposited Residue Count: 508 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase VIM-2
A, B
254Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaVIM-2
EC: 3.5.2.6
UniProt
Find proteins for A0A173FE28 (Klebsiella pneumoniae)
Explore A0A173FE28 
Go to UniProtKB:  A0A173FE28
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A173FE28
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9NK

Query on 9NK



Download:Ideal Coordinates CCD File
G [auth A],
Q [auth B]
(2~{R})-1-[(2~{S})-2-(phenylmethyl)-3-sulfanyl-propanoyl]piperidine-2-carboxylic acid
C16 H21 N O3 S
BUVJKPXAJVVXFT-ZIAGYGMSSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
M [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



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

Query on FMT



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
K [auth A]
R [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.211 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.989α = 90
b = 79.308β = 130.45
c = 67.645γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AutoSolphasing
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations