6RPN

Structure of metallo beta lactamase VIM-2 with cyclic boronate APC308.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Broad Spectrum beta-Lactamase Inhibition by a Thioether Substituted Bicyclic Boronate.

Parkova, A.Lucic, A.Krajnc, A.Brem, J.Calvopina, K.Langley, G.W.McDonough, M.A.Trapencieris, P.Schofield, C.J.

(2020) ACS Infect Dis 6: 1398-1404

  • DOI: https://doi.org/10.1021/acsinfecdis.9b00330
  • Primary Citation of Related Structures:  
    6RPN

  • PubMed Abstract: 

    β-Lactamases comprise the most widely used mode of resistance to β-lactam antibiotics. Cyclic boronates have shown promise as a new class of β-lactamase inhibitor, with pioneering potential to potently inhibit both metallo- and serine-β-lactamases. We report studies concerning a bicyclic boronate ester with a thioether rather than the more typical β-lactam antibiotic "C-6/C-7" acylamino type side chain, which is present in the penicillin/cephalosporin antibiotics. The thioether bicyclic boronate ester was tested for activity against representative serine- and metallo-β-lactamases. The results support the broad inhibition potential of bicyclic boronate based inhibitors with different side chains, including against metallo-β-lactamases from B1, B2, and B3 subclasses. Combined with previous crystallographic studies, analysis of a crystal structure of the thioether inhibitor with the clinically relevant VIM-2 metallo-β-lactamase implies that further SAR work will expand the already broad scope of β-lactamase inhibition by bicyclic boronates.


  • Organizational Affiliation

    Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase VIM-2
A, B
242Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM-2bla vim-2bla-VIM-2blasVIM-2blaVIM2blmVIM-2PAERUG_P32_London_17_VIM_2_10_11_06255
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Explore Q9K2N0 
Go to UniProtKB:  Q9K2N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K2N0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KL8
Query on KL8

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
(3~{S})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid
C16 H16 B O5 S
NCOFNSDHLWCKKT-CQSZACIVSA-N
KDZ
Query on KDZ

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
(3~{R})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid
C16 H16 B O5 S
NCOFNSDHLWCKKT-AWEZNQCLSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
S [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
L [auth B]
M [auth B]
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
O [auth B],
P [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
Q [auth B],
R [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KL8 Binding MOAD:  6RPN IC50: 200 (nM) from 1 assay(s)
KDZ Binding MOAD:  6RPN IC50: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.081α = 90
b = 79.155β = 130.03
c = 67.746γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 2.0: 2020-04-15
    Changes: Non-polymer description, Refinement description
  • Version 2.1: 2020-06-24
    Changes: Database references
  • Version 2.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description