4PVO

Crystal Structure of VIM-2 metallo-beta-lactamase in complex with ML302 and ML302F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.141 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Rhodanine hydrolysis leads to potent thioenolate mediated metallo-beta-lactamase inhibition.

Brem, J.van Berkel, S.S.Aik, W.Rydzik, A.M.Avison, M.B.Pettinati, I.Umland, K.D.Kawamura, A.Spencer, J.Claridge, T.D.McDonough, M.A.Schofield, C.J.

(2014) Nat Chem 6: 1084-1090

  • DOI: https://doi.org/10.1038/nchem.2110
  • Primary Citation of Related Structures:  
    4PVO, 4PVT, 4TYT

  • PubMed Abstract: 

    The use of β-lactam antibiotics is compromised by resistance, which is provided by β-lactamases belonging to both metallo (MBL)- and serine (SBL)-β-lactamase subfamilies. The rhodanines are one of very few compound classes that inhibit penicillin-binding proteins (PBPs), SBLs and, as recently reported, MBLs. Here, we describe crystallographic analyses of the mechanism of inhibition of the clinically relevant VIM-2 MBL by a rhodanine, which reveal that the rhodanine ring undergoes hydrolysis to give a thioenolate. The thioenolate is found to bind via di-zinc chelation, mimicking the binding of intermediates in β-lactam hydrolysis. Crystallization of VIM-2 in the presence of the intact rhodanine led to observation of a ternary complex of MBL, a thioenolate fragment and rhodanine. The crystallographic observations are supported by kinetic and biophysical studies, including (19)F NMR analyses, which reveal the rhodanine-derived thioenolate to be a potent broad-spectrum MBL inhibitor and a lead structure for the development of new types of clinically useful MBL inhibitors.


  • Organizational Affiliation

    Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase class B VIM-2
A, B
242Pseudomonas aeruginosaMutation(s): 0 
Gene Names: bla-VIM-2blasVIM-2blaVIM-2blaVIM2VIM-2
EC: 3.5.2.6
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SVB
Query on SVB

Download Ideal Coordinates CCD File 
F [auth A]N-(4-methylpiperazin-1-yl)-2-[(5Z)-4-oxo-2-thioxo-5-(2,3,6-trichlorobenzylidene)-1,3-thiazolidin-3-yl]acetamide
C17 H17 Cl3 N4 O2 S2
GTHJLNHVDYJCCB-JYRVWZFOSA-N
S3C
Query on S3C

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E [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 
J [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
G [auth A]
K [auth B]
L [auth B]
C [auth A],
D [auth A],
G [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 
H [auth A],
I [auth A],
N [auth B],
O [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SVB BindingDB:  4PVO IC50: 498 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.141 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.57α = 90
b = 79.239β = 131.57
c = 67.967γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
GDAdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description