6VHS | pdb_00006vhs

Crystal structure of CTX-M-14 in complex with beta-lactamase inhibitor ETX1317


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 
    0.148 (Depositor), 0.152 (DCC) 
  • R-Value Work: 
    0.129 (Depositor), 0.133 (DCC) 
  • R-Value Observed: 
    0.130 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Discovery of an Orally Available Diazabicyclooctane Inhibitor (ETX0282) of Class A, C, and D Serine beta-Lactamases.

Durand-Reville, T.F.Comita-Prevoir, J.Zhang, J.Wu, X.May-Dracka, T.L.Romero, J.A.C.Wu, F.Chen, A.Shapiro, A.B.Carter, N.M.McLeod, S.M.Giacobbe, R.A.Verheijen, J.C.Lahiri, S.D.Sacco, M.D.Chen, Y.O'Donnell, J.P.Miller, A.A.Mueller, J.P.Tommasi, R.A.

(2020) J Med Chem 63: 12511-12525

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00579
  • Primary Citation Related Structures: 
    6VHS

  • PubMed Abstract: 

    Multidrug resistant Gram-negative bacterial infections are an increasing public health threat due to rapidly rising resistance toward β-lactam antibiotics. The hydrolytic enzymes called β-lactamases are responsible for a large proportion of the resistance phenotype. β-Lactamase inhibitors (BLIs) can be administered in combination with β-lactam antibiotics to negate the action of the β-lactamases, thereby restoring activity of the β-lactam. Newly developed BLIs offer some advantage over older BLIs in terms of enzymatic spectrum but are limited to the intravenous route of administration. Reported here is a novel, orally bioavailable diazabicyclooctane (DBO) β-lactamase inhibitor. This new DBO, ETX1317, contains an endocyclic carbon-carbon double bond and a fluoroacetate activating group and exhibits broad spectrum activity against class A, C, and D serine β-lactamases. The ester prodrug of ETX1317, ETX0282, is orally bioavailable and, in combination with cefpodoxime proxetil, is currently in development as an oral therapy for multidrug resistant and carbapenem-resistant Enterobacterales infections.


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

Macromolecule Content 

  • Total Structure Weight: 56.99 kDa 
  • Atom Count: 5,124 
  • Modeled Residue Count: 525 
  • Deposited Residue Count: 526 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
263Escherichia coliMutation(s): 0 
Gene Names: blaCTX-M-14
EC: 3.5.2.6
UniProt
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X57
(Subject of Investigation/LOI)

Query on X57



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
(2R)-({[(3R,6S)-6-carbamoyl-1-formyl-4-methyl-1,2,3,6-tetrahydropyridin-3-yl]amino}oxy)(fluoro)acetic acid
C10 H14 F N3 O5
NOCLDVJNWBTORY-FXQIFTODSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free:  0.148 (Depositor), 0.152 (DCC) 
  • R-Value Work:  0.129 (Depositor), 0.133 (DCC) 
  • R-Value Observed: 0.130 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.25α = 90
b = 106.92β = 101.81
c = 47.87γ = 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: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Structure summary
  • Version 1.2: 2020-11-25
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary