4DE1

CTX-M-9 class A beta-lactamase complexed with compound 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-Based Design of Potent and Ligand-Efficient Inhibitors of CTX-M Class A Beta-Lactamase

Nichols, D.A.Jaishankar, P.Larson, W.Smith, E.Liu, G.Beyrouthy, R.Bonnet, R.Renslo, A.R.Chen, Y.

(2012) J.Med.Chem. 55: 2163-2172

  • DOI: 10.1021/jm2014138
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The emergence of CTX-M class A extended-spectrum β-lactamases poses a serious health threat to the public. We have applied structure-based design to improve the potency of a novel noncovalent tetrazole-containing CTX-M inhibitor (K(i) = 21 μM) more t ...

    The emergence of CTX-M class A extended-spectrum β-lactamases poses a serious health threat to the public. We have applied structure-based design to improve the potency of a novel noncovalent tetrazole-containing CTX-M inhibitor (K(i) = 21 μM) more than 200-fold via structural modifications targeting two binding hot spots, a hydrophobic shelf formed by Pro167 and a polar site anchored by Asp240. Functional groups contacting each binding hot spot independently in initial designs were later combined to produce analogues with submicromolar potencies, including 6-trifluoromethyl-3H-benzoimidazole-4-carboxylic acid [3-(1H-tetrazol-5-yl)-phenyl]-amide, which had a K(i) value of 89 nM and reduced the MIC of cefotaxime by 64-fold in CTX-M-9 expressing Escherichia coli . The in vitro potency gains were accompanied by improvements in ligand efficiency (from 0.30 to 0.39) and LipE (from 1.37 to 3.86). These new analogues represent the first nM-affinity noncovalent inhibitors of a class A β-lactamase. Their complex crystal structures provide valuable information about ligand binding for future inhibitor design.


    Organizational Affiliation

    University of South Florida College of Medicine, Department of Molecular Medicine, 12901 Bruce B. Downs Boulevard, MDC 3522, Tampa, Florida 33612, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
263Escherichia coliMutation(s): 0 
Gene Names: blaCTX-M-9a (blaCTX-M-9, blaCTX-M-9b)
EC: 3.5.2.6
Find proteins for Q9L5C8 (Escherichia coli)
Go to UniProtKB:  Q9L5C8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
0J6
Query on 0J6

Download SDF File 
Download CCD File 
A, B
N-[3-(1H-tetrazol-5-yl)phenyl]-2H-indazole-5-carboxamide
C15 H11 N7 O
UWMWXBXKWPTZOO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0J6Ki: 1100 nM BINDINGMOAD
0J6Ki: 1100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.123 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.166α = 90.00
b = 106.567β = 101.86
c = 47.825γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-28
    Type: Initial release