2Q9N

4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design, Synthesis and Biological Activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

4-Substituted Trinems as Broad Spectrum beta-Lactamase Inhibitors: Structure-Based Design, Synthesis, and Biological Activity

Plantan, I.Selic, L.Mesar, T.Anderluh, P.S.Oblak, M.Prezelj, A.Hesse, L.Andrejasic, M.Vilar, M.Turk, D.Kocijan, A.Prevec, T.Vilfan, G.Kocjan, D.Copar, A.Urleb, U.Solmajer, T.

(2007) J Med Chem 50: 4113-4121

  • DOI: https://doi.org/10.1021/jm0703237
  • Primary Citation of Related Structures:  
    2Q9M, 2Q9N

  • PubMed Abstract: 

    A wide variety of pathogens have acquired antimicrobial resistance as an inevitable evolutionary response to the extensive use of antibacterial agents. In particular, one of the most widely used antibiotic structural classes is the beta-lactams, in which the most common and the most efficient mechanism of bacterial resistance is the synthesis of beta-lactamases. Class C beta-lactamase enzymes are primarily cephalosporinases, mostly chromosomally encoded, and are inducible by exposure to some beta-lactam agents and resistant to inhibition by marketed beta-lactamase inhibitors. In an ongoing effort to alleviate this problem a series of novel 4-substituted trinems was designed and synthesized. Significant in vitro inhibitory activity was measured against the bacterial beta-lactamases of class C and additionally against class A. The lead compound LK-157 was shown to be a potent mechanism-based inactivator. Acylation of the active site Ser 64 of the class C enzyme beta-lactamase was observed in the solved crystal structures of two inhibitors complexes to AmpC enzyme from E. cloacae. Structure-activity relationships in the series reveal the importance of the trinem scaffold for inhibitory activity and the interesting potential of the series for further development.


  • Organizational Affiliation

    Drug Discovery, Lek Pharmaceuticals d.d., Verovskova 57, SI-1526 Ljubljana, Slovenia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase359Enterobacter cloacaeMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for P05364 (Enterobacter cloacae)
Explore P05364 
Go to UniProtKB:  P05364
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05364
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LK5
Query on LK5

Download Ideal Coordinates CCD File 
B [auth A](1S,4R,7AR)-4-BUTOXY-1-[(1R)-1-FORMYLPROPYL]-2,4,5,6,7,7A-HEXAHYDRO-1H-ISOINDOLE-3-CARBOXYLIC ACID
C17 H27 N O4
WRBRCIHZCYLBFW-KYEXWDHISA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
LK5 PDBBind:  2Q9N IC50: 430 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.377α = 90
b = 68.984β = 90
c = 62.02γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
MAINrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description