5N58

di-Zinc VIM-5 metallo-beta-lactamase in complex with (1-chloro-4-hydroxyisoquinoline-3-carbonyl)-D-tryptophan (Compound 1)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Crystallographic analyses of isoquinoline complexes reveal a new mode of metallo-beta-lactamase inhibition.

Li, G.B., Brem, J., Lesniak, R., Abboud, M.I., Lohans, C.T., Clifton, I.J., Yang, S.Y., Jimenez-Castellanos, J.C., Avison, M.B., Spencer, J., McDonough, M.A., Schofield, C.J.

(2017) Chem Commun (Camb) 53: 5806-5809

  • DOI: https://doi.org/10.1039/c7cc02394d
  • Primary Citation of Related Structures:  
    5N4S, 5N4T, 5N55, 5N58, 5NAI

  • PubMed Abstract: 

    Crystallographic analyses of the VIM-5 metallo-β-lactamase (MBL) with isoquinoline inhibitors reveal non zinc ion binding modes. Comparison with other MBL-inhibitor structures directed addition of a zinc-binding thiol enabling identification of potent B1 MBL inhibitors. The inhibitors potentiate meropenem activity against clinical isolates harboring MBLs.

    • Organizational Affiliation: 

    Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. [email protected] [email protected].


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Class B metallo-beta-lactamase
A, B
266Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaVIM-5
EC: 3.5.2.6
UniProt
Find proteins for Q8GKX2 (Klebsiella pneumoniae)
Explore Q8GKX2 
Go to UniProtKB:  Q8GKX2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GKX2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
93W
Query on 93W
Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]		(2~{R})-2-[(1-chloranyl-4-oxidanyl-isoquinolin-3-yl)carbonylamino]-3-(1~{H}-indol-3-yl)propanoic acid
C21 H16 Cl N3 O4
PVDFWPDMZYPBMH-MRXNPFEDSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
G [auth A],
H [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.471α = 90
b = 81.54β = 90
c = 95.892γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description