6ZXI | pdb_00006zxi

Crystal Structure of the OXA-48 Carbapenem-Hydrolyzing Class D beta-Lactamase in Complex with the DBO inhibitor ANT3310


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.217 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.172 (Depositor) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery of ANT3310 , a Novel Broad-Spectrum Serine beta-Lactamase Inhibitor of the Diazabicyclooctane Class, Which Strongly Potentiates Meropenem Activity against Carbapenem-Resistant Enterobacterales and Acinetobacter baumannii.

Davies, D.T.Leiris, S.Zalacain, M.Sprynski, N.Castandet, J.Bousquet, J.Lozano, C.Llanos, A.Alibaud, L.Vasa, S.Pattipati, R.Valige, R.Kummari, B.Pothukanuri, S.De Piano, C.Morrissey, I.Holden, K.Warn, P.Marcoccia, F.Benvenuti, M.Pozzi, C.Tassone, G.Mangani, S.Docquier, J.D.Pallin, D.Elliot, R.Lemonnier, M.Everett, M.

(2020) J Med Chem 63: 15802-15820

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01535
  • Primary Citation Related Structures: 
    6ZXI

  • PubMed Abstract: 

    The diazabicyclooctanes (DBOs) are a class of serine β-lactamase (SBL) inhibitors that use a strained urea moiety as the warhead to react with the active serine residue in the active site of SBLs. The first in-class drug, avibactam, as well as several other recently approved DBOs (e.g., relebactam) or those in clinical development (e.g., nacubactam and zidebactam) potentiate activity of β-lactam antibiotics, to various extents, against carbapenem-resistant Enterobacterales (CRE) carrying class A, C, and D SBLs; however, none of these are able to rescue the activity of β-lactam antibiotics against carbapenem-resistant Acinetobacter baumannii (CRAB), a WHO "critical priority pathogen" producing class D OXA-type SBLs. Herein, we describe the chemical optimization and resulting structure-activity relationship, leading to the discovery of a novel DBO, ANT3310 , which uniquely has a fluorine atom replacing the carboxamide and stands apart from the current DBOs in restoring carbapenem activity against OXA-CRAB as well as SBL-carrying CRE pathogens.


  • Organizational Affiliation
    • Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France.

Macromolecule Content 

  • Total Structure Weight: 61.48 kDa 
  • Atom Count: 4,450 
  • Modeled Residue Count: 485 
  • Deposited Residue Count: 530 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
265Klebsiella pneumoniaeMutation(s): 0 
Gene Names: 
EC: 3.5.2.6
UniProt
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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QS8
(Subject of Investigation/LOI)

Query on QS8



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
[[(3~{R},6~{R})-6-fluoranyl-1-methanoyl-piperidin-3-yl]amino] hydrogen sulfate
C6 H11 F N2 O5 S
NHFNUMMVPZGHRV-RITPCOANSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO2

Query on CO2



Download:Ideal Coordinates CCD File
F [auth A]CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.217 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.172 (Depositor) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.798α = 90
b = 105.106β = 90
c = 125.426γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary