7TI1 | pdb_00007ti1

Structure of AmpC bound to RPX-7063 at 2.0A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.214 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Broad-spectrum cyclic boronate beta-lactamase inhibitors featuring an intramolecular prodrug for oral bioavailability.

Raja Reddy, K.Totrov, M.Lomovskaya, O.Griffith, D.C.Tarazi, Z.Clifton, M.C.Hecker, S.J.

(2022) Bioorg Med Chem 62: 116722-116722

  • DOI: https://doi.org/10.1016/j.bmc.2022.116722
  • Primary Citation of Related Structures:  
    7TI0, 7TI1, 7TI2

  • PubMed Abstract: 

    Early efforts to broaden the spectrum and potency of cyclic boronic acid β-lactamase inhibitor vaborbactam included a series of 7-membered ring boronates. Exploration of stereoisomers and incorporation of heteroatoms allowed identification of the all-carbon cyclic boronate with substituents trans as the preferred core structure, showing inhibition of Class A and C enzymes. Crystal structures of one analog bound to important β-lactamase enzymes were obtained. When isolated under acidic conditions, these compounds spontaneously formed a neutral cyclic anhydride (intramolecular prodrug) which was shown to have much-improved oral bioavailability (52-69%) compared to the ring-opened carboxylate salt (9%).


  • Organizational Affiliation

    Qpex Biopharma, Inc, 6275 Nancy Ridge Dr., Suite 100, San Diego, CA 92121, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase383Enterobacter cloacaeMutation(s): 0 
Gene Names: ampC
EC: 3.5.2.6
UniProt
Find proteins for P05364 (Enterobacter cloacae)
Explore P05364 
Go to UniProtKB:  P05364
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05364
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.96α = 90
b = 77.98β = 90
c = 62.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ZXQClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary