5O7N

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 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.1 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: 10.1021/acsinfecdis.7b00129
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamase VIM-2A, B254Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaVIM-2
UniProt
Find proteins for A0A173FE28 (Klebsiella pneumoniae)
Explore A0A173FE28 
Go to UniProtKB:  A0A173FE28
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9NK (Subject of Investigation/LOI)
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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
EDO
Query on EDO

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

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • 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