CTX-M-14 Beta Lactamase with Compound 3

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.122 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


An Empirical Study of Amide-Heteroarene pi-Stacking Interactions Using Reversible Inhibitors of a Bacterial Serine Hydrolase.

DeFrees, K.Kemp, M.T.ElHilali-Pollard, X.Zhang, X.Mohamed, A.Chen, Y.Renslo, A.R.

(2019) Org Chem Front 6: 1749-1756

  • DOI: https://doi.org/10.1039/c9qo00342h
  • Primary Citation of Related Structures:  
    6OOE, 6OOF, 6OOH, 6OOJ, 6OOK

  • PubMed Abstract: 

    Compared to aryl-aryl π-stacking interactions, the analogous stacking of heteroarenes on amide π systems is less well understood and vastly underutilized in structure-based drug design. Recent theoretical studies have delineated the important geometric coordinates of the interaction, some of which have been confirmed with synthetic model systems based on Rebek imides. Unfortunately, a broadly useful and tractable protein-ligand model system of this interaction has remained elusive. Here we employed a known inhibitor scaffold to study π-stacking of diverse heteroarene substituents on the amide face of Gly238 in the cephalosporinases CTX-M-14 and CTX-M-27. Biochemical inhibition constants ( K i ) and biophysical binding constants ( K d ) were determined for nineteen new analogues against both enzymes, while multiple high-resolution co-crystal structures revealed remarkably consistent placement of the probe heteroarene on Gly238. The data presented support the predicted importance of opposing dipoles in amide-heteroarene interactions and should be useful for evaluating other theoretical predictions concerning these interactions.

  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St., San Francisco, California 94158, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
263Escherichia coliMutation(s): 0 
Gene Names: blaCTX-M-14
Find proteins for Q9L5C7 (Escherichia coli)
Explore Q9L5C7 
Go to UniProtKB:  Q9L5C7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L5C7
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PCA
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
MZV Binding MOAD:  6OOK Kd: 8140 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.122 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.003α = 90
b = 106.725β = 101.73
c = 47.736γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI103158

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description