3IOG

Crystal structure of CphA N220G mutant with inhibitor 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Mercaptophosphonate Compounds as Broad-Spectrum Inhibitors of the Metallo-beta-lactamases

Lassaux, P.Hamel, M.Gulea, M.Delbruck, H.Mercuri, P.S.Horsfall, L.Dehareng, D.Kupper, M.Frere, J.-M.Hoffmann, K.Galleni, M.Bebrone, C.

(2010) J Med Chem 53: 4862-4876

  • DOI: 10.1021/jm100213c
  • Primary Citation of Related Structures:  
    2WRS, 3IOF, 3IOG

  • PubMed Abstract: 
  • Although commercialized inhibitors of active site serine beta-lactamases are currently used in coadministration with antibiotic therapy, no clinically useful inhibitors of metallo-beta-lactamases (MBLs) have yet been discovered. In this paper, we investigated the inhibitory effect of mercaptophosphonate derivatives against the three subclasses of MBLs (B1, B2, and B3) ...

    Although commercialized inhibitors of active site serine beta-lactamases are currently used in coadministration with antibiotic therapy, no clinically useful inhibitors of metallo-beta-lactamases (MBLs) have yet been discovered. In this paper, we investigated the inhibitory effect of mercaptophosphonate derivatives against the three subclasses of MBLs (B1, B2, and B3). All 14 tested mercaptophosphonates, with the exception of 1a, behaved as competitive inhibitors for the three subclasses. Apart from 13 and 21, all the mercaptophosphonates tested exhibit a good inhibitory effect on the subclass B2 MBL CphA with low inhibition constants (K(i) < 15 muM). Interestingly, compound 18 turned out to be a potent broad spectrum MBL inhibitor. The crystallographic structures of the CphA-10a and CphA-18 complexes indicated that the sulfur atom of 10a and the phosphonato group of 18 interact with the Zn(2+) ion, respectively. Molecular modeling studies of the interactions between compounds 10a and 18 and the VIM-4 (B1), CphA (B2), and FEZ-1 (B3) enzymes brought to light different binding modes depending on the enzyme and the inhibitor, consistent with the crystallographic structures.


    Organizational Affiliation

    Laboratory of Biological Macromolecules, University of Liège, Allée du 6 Août B6, Sart-Tilman, 4000 Liège, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA227Aeromonas hydrophilaMutation(s): 1 
Gene Names: cphA
EC: 3.5.2.6
UniProt
Find proteins for P26918 (Aeromonas hydrophila)
Explore P26918 
Go to UniProtKB:  P26918
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
SDF PDBBind:  3IOG Ki: 3000 (nM) from 1 assay(s)
BindingDB:  3IOG Ki: 5000 (nM) from 1 assay(s)
Binding MOAD:  3IOG Ki: 3000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.727α = 90
b = 100.877β = 90
c = 117.559γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance