6EW3

Crystal structure of the metallo-beta-lactamase VIM-2 with ML302F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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Literature

Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases.

Zhang, D.Markoulides, M.S.Stepanovs, D.Rydzik, A.M.El-Hussein, A.Bon, C.Kamps, J.J.A.G.Umland, K.D.Collins, P.M.Cahill, S.T.Wang, D.Y.von Delft, F.Brem, J.McDonough, M.A.Schofield, C.J.

(2018) Bioorg Med Chem 26: 2928-2936

  • DOI: https://doi.org/10.1016/j.bmc.2018.02.043
  • Primary Citation of Related Structures:  
    5JMX, 6EUM, 6EW3, 6EWE, 6F2N

  • PubMed Abstract: 

    Metallo-β-lactamases (MBLs) enable bacterial resistance to almost all classes of β-lactam antibiotics. We report studies on enethiol containing MBL inhibitors, which were prepared by rhodanine hydrolysis. The enethiols inhibit MBLs from different subclasses. Crystallographic analyses reveal that the enethiol sulphur displaces the di-Zn(II) ion bridging 'hydrolytic' water. In some, but not all, cases biophysical analyses provide evidence that rhodanine/enethiol inhibition involves formation of a ternary MBL enethiol rhodanine complex. The results demonstrate how low molecular weight active site Zn(II) chelating compounds can inhibit a range of clinically relevant MBLs and provide additional evidence for the potential of rhodanines to be hydrolysed to potent inhibitors of MBL protein fold and, maybe, other metallo-enzymes, perhaps contributing to the complex biological effects of rhodanines. The results imply that any medicinal chemistry studies employing rhodanines (and related scaffolds) as inhibitors should as a matter of course include testing of their hydrolysis products.


  • Organizational Affiliation

    Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase VIM-2
A, B
232Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM-2
EC: 3.5.2.6
UniProt
Find proteins for D1MEN9 (Pseudomonas aeruginosa)
Explore D1MEN9 
Go to UniProtKB:  D1MEN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1MEN9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S3C (Subject of Investigation/LOI)
Query on S3C

Download Ideal Coordinates CCD File 
H [auth A],
P [auth B]
(2Z)-2-sulfanyl-3-(2,3,6-trichlorophenyl)prop-2-enoic acid
C9 H5 Cl3 O2 S
ZCOCHUAGSBNGCP-CLTKARDFSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
Q [auth B],
R [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
K [auth B]
L [auth B]
C [auth A],
D [auth A],
E [auth A],
K [auth B],
L [auth B],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
N [auth B],
O [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
S [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.48α = 90
b = 78.91β = 130.48
c = 67.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description