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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1038/nchem.2110
  • Primary Citation of Related Structures:  
    4PVT, 4PVO, 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamase class B VIM-2A, B242Pseudomonas aeruginosaMutation(s): 0 
Gene Names: bla-VIM-2blasVIM-2blaVIM-2blaVIM2vim-2bla vim-2VIM-2IPC669_36195
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Explore Q9K2N0 
Go to UniProtKB:  Q9K2N0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
S3C
Query on S3C

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
J [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], G [auth A], K [auth B], L [auth B], M [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
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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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