5LSC | pdb_00005lsc

The structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.136 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.137 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

The structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor.

Christopeit, T.Yang, K.W.Yang, S.K.Leiros, H.K.

(2016) Acta Crystallogr F Struct Biol Commun 72: 813-819

  • DOI: https://doi.org/10.1107/S2053230X16016113
  • Primary Citation of Related Structures:  
    5LSC

  • PubMed Abstract: 

    The increasing number of pathogens expressing metallo-β-lactamases (MBLs), and in this way achieving resistance to β-lactam antibiotics, is a significant threat to global public health. A promising strategy to treat such resistant pathogens is the co-administration of MBL inhibitors together with β-lactam antibiotics. However, an MBL inhibitor suitable for clinical use has not yet been identified. Verona integron-encoded metallo-β-lactamase 2 (VIM-2) is a widespread MBL with a broad substrate spectrum and hence is an interesting drug target for the treatment of β-lactam-resistant infections. In this study, three triazolylthioacetamides were tested as inhibitors of VIM-2. One of the tested compounds showed clear inhibition of VIM-2, with an IC 50 of 20 µM. The crystal structure of the inhibitor in complex with VIM-2 was obtained by DMSO-free co-crystallization and was solved at a resolution of 1.50 Å. To our knowledge, this is the first structure of a triazolylthioacetamide inhibitor in complex with an MBL. Analysis of the structure shows that the inhibitor binds to the two zinc ions in the active site of VIM-2 and revealed detailed information on the interactions involved. Furthermore, the crystal structure showed that binding of the inhibitor induced a conformational change of the conserved residue Trp87.


  • Organizational Affiliation

    The Norwegian Structural Biology Centre (Norstruct), Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase VIM-2-like protein
A, B
240Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM
UniProt
Find proteins for B8QIQ9 (Pseudomonas aeruginosa)
Explore B8QIQ9 
Go to UniProtKB:  B8QIQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8QIQ9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
752
Query on 752

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B]
2-[5-[2-(1,3-benzothiazol-2-ylamino)-2-oxidanylidene-ethyl]sulfanyl-4~{H}-1,2,4-triazol-3-yl]benzoic acid
C18 H13 N5 O3 S2
XDAKTDQGVCHONK-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
N [auth B]
O [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
J [auth B]
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.136 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.137 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.624α = 90
b = 79.255β = 130.5
c = 67.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 752Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Tromso Reserach FoundationNorway--
Research Council of NorwayNorway218539, SYNKNOYT 2011 and 213808, FRIMEDBIO 2011
National Natural Science Foundation of ChinaChina21272186, 21572179 and 81361138018

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description