4DE3

CTX-M-9 class A beta-lactamase complexed with compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1021/jm2014138
  • Primary Citation of Related Structures:  
    4DDS, 4DDY, 4DE0, 4DE1, 4DE2, 4DE3

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
263Escherichia coliMutation(s): 0 
Gene Names: blaCTX-M-9blaCTX-M-9ablaCTX-M-9bCTX-M
EC: 3.5.2.6
UniProt
Find proteins for Q9L5C8 (Escherichia coli)
Explore Q9L5C8 
Go to UniProtKB:  Q9L5C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L5C8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DN8
Query on DN8

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
3-bromo-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide
C14 H10 Br N5 O
HXGCQRJRUHDKKD-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLN
Binding Affinity Annotations 
IDSourceBinding Affinity
DN8 PDBBind:  4DE3 Ki: 3000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.174α = 90
b = 107.188β = 100.38
c = 47.487γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 2.0: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description
  • Version 2.1: 2024-10-09
    Changes: Structure summary