5VFD | pdb_00005vfd

Diazabicyclooctenone ETX2514 bound to Class D beta lactamase OXA-24 from A. baumannii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.206 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

ETX2514 is a broad-spectrum beta-lactamase inhibitor for the treatment of drug-resistant Gram-negative bacteria including Acinetobacter baumannii.

Durand-Reville, T.F.Guler, S.Comita-Prevoir, J.Chen, B.Bifulco, N.Huynh, H.Lahiri, S.Shapiro, A.B.McLeod, S.M.Carter, N.M.Moussa, S.H.Velez-Vega, C.Olivier, N.B.McLaughlin, R.Gao, N.Thresher, J.Palmer, T.Andrews, B.Giacobbe, R.A.Newman, J.V.Ehmann, D.E.de Jonge, B.O'Donnell, J.Mueller, J.P.Tommasi, R.A.Miller, A.A.

(2017) Nat Microbiol 2: 17104-17104

  • DOI: https://doi.org/10.1038/nmicrobiol.2017.104
  • Primary Citation Related Structures: 
    5VFD

  • PubMed Abstract: 

    Multidrug-resistant (MDR) bacterial infections are a serious threat to public health. Among the most alarming resistance trends is the rapid rise in the number and diversity of β-lactamases, enzymes that inactivate β-lactams, a class of antibiotics that has been a therapeutic mainstay for decades. Although several new β-lactamase inhibitors have been approved or are in clinical trials, their spectra of activity do not address MDR pathogens such as Acinetobacter baumannii. This report describes the rational design and characterization of expanded-spectrum serine β-lactamase inhibitors that potently inhibit clinically relevant class A, C and D β-lactamases and penicillin-binding proteins, resulting in intrinsic antibacterial activity against Enterobacteriaceae and restoration of β-lactam activity in a broad range of MDR Gram-negative pathogens. One of the most promising combinations is sulbactam-ETX2514, whose potent antibacterial activity, in vivo efficacy against MDR A. baumannii infections and promising preclinical safety demonstrate its potential to address this significant unmet medical need.


  • Organizational Affiliation
    • Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA.

Macromolecule Content 

  • Total Structure Weight: 28.62 kDa 
  • Atom Count: 2,258 
  • Modeled Residue Count: 244 
  • Deposited Residue Count: 244 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase244Acinetobacter baumanniiMutation(s): 0 
Gene Names: blaOXA-33bla-OXA-40blaOXA-24blaOXA-40oxa-24oxa40A8G88_08245
UniProt
Find proteins for Q8RLA6 (Acinetobacter baumannii)
Explore Q8RLA6 
Go to UniProtKB:  Q8RLA6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RLA6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9CP

Query on 9CP



Download:Ideal Coordinates CCD File
G [auth A](2S,5R)-1-formyl-4-methyl-5-[(sulfooxy)amino]-1,2,5,6-tetrahydropyridine-2-carboxamide
C8 H13 N3 O6 S
XVMABMMPQCPJKI-BQBZGAKWSA-N
9CM

Query on 9CM



Download:Ideal Coordinates CCD File
H [auth A](2S,5R)-4-methyl-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]oct-3-ene-2-carboxamide
C8 H11 N3 O6 S
WHFPRPRSXFJXMN-WDSKDSINSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.206 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.68α = 90
b = 102.68β = 90
c = 84.77γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2025-03-26
    Changes: Data collection, Structure summary