OXA-48 bound to inhibitor CDD-2725

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Exploiting the Carboxylate-Binding Pocket of beta-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library.

Park, S.Fan, J.Chamakuri, S.Palaniappan, M.Sharma, K.Qin, X.Wang, J.Tan, Z.Judge, A.Hu, L.Sankaran, B.Li, F.Prasad, B.V.V.Matzuk, M.M.Palzkill, T.

(2024) J Med Chem 67: 620-642

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01834
  • Primary Citation of Related Structures:  
    8SQF, 8SQG

  • PubMed Abstract: 

    β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 10 6 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.

  • Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamaseA [auth B],
B [auth A]
265Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bla OXA-48
Find proteins for Q6XEC0 (Klebsiella pneumoniae)
Explore Q6XEC0 
Go to UniProtKB:  Q6XEC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XEC0
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on KCX
A [auth B],
B [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.083α = 90
b = 123.083β = 90
c = 161.759γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

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 StatesAI143832

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Database references