Crystal Structure of BcII metallo-beta-lactamase in complex with ML302F

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 3.0 of the entry. See complete history


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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase 2227Bacillus cereusMutation(s): 0 
Gene Names: blm
Find proteins for P04190 (Bacillus cereus)
Explore P04190 
Go to UniProtKB:  P04190
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04190
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
S3C BindingDB:  4TYT IC50: 80 (nM) from 1 assay(s)
Binding MOAD:  4TYT IC50: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.079α = 90
b = 61.358β = 93
c = 69.416γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
Cootmodel building
SCALEPACKdata scaling

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 KingdomG1100135

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 2.0: 2017-09-13
    Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 3.0: 2023-12-20
    Changes: Atomic model, Data collection, Database references, Refinement description