6EWE

Crystal structure of BCII Metallo-beta-lactamase in complex with DZ-308


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

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Ligand Structure Quality Assessment 


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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: 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 ...

    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. Electronic address: christopher.schofield@chem.ox.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metallo-beta-lactamase type 2A227Bacillus cereusMutation(s): 0 
Gene Names: blm
EC: 3.5.2.6
UniProt
Find proteins for P04190 (Bacillus cereus)
Explore P04190 
Go to UniProtKB:  P04190
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04190
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C0W
Query on C0W

Download Ideal Coordinates CCD File 
E [auth A](~{Z})-3-(1-benzothiophen-3-yl)-2-sulfanyl-prop-2-enoic acid
C11 H8 O2 S2
RAMCKYVBVNEIFT-UITAMQMPSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C0W BindingDB:  6EWE IC50: 3100 (nM) from 1 assay(s)
Binding MOAD:  6EWE IC50: 3100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.19α = 90
b = 61.01β = 92.99
c = 69.54γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release