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 

wwPDB Validation 3D Report Full Report


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:  

  • 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 inv ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
227Aeromonas hydrophilaMutation(s): 1 
Gene Names: cphA
EC: 3.5.2.6
Find proteins for P26918 (Aeromonas hydrophila)
Go to UniProtKB:  P26918
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SDF
Query on SDF

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Download CCD File 
A
[(R)-(2,4-dichlorophenyl)(sulfanyl)methyl]phosphonic acid
alpha-Sulfanyl(2,4-dichlorobenzyl)phosphonic acid
C7 H7 Cl2 O3 P S
WJVBVZOYOCLGPI-SSDOTTSWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SDFKi: 5000 nM (99) BINDINGDB
SDFIC50: 3000 nM BINDINGMOAD
SDFKi: 3000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.143 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 42.727α = 90.00
b = 100.877β = 90.00
c = 117.559γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SCALAdata scaling
PHASERphasing
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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