8FQP | pdb_00008fqp

apo ADC-162 beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8FQP

This is version 1.3 of the entry. See complete history

Literature

Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter -Derived Cephalosporinase Variants with an Expanded-Substrate Spectrum.

Powers, R.A.June, C.M.Fernando, M.C.Fish, E.R.Maurer, O.L.Baumann, R.M.Beardsley, T.J.Taracila, M.A.Rudin, S.D.Hujer, K.M.Hujer, A.M.Santi, N.Villamil, V.Introvigne, M.L.Prati, F.Caselli, E.Bonomo, R.A.Wallar, B.J.

(2023) J Med Chem 66: 8510-8525

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00144
  • Primary Citation Related Structures: 
    8FQM, 8FQN, 8FQO, 8FQP, 8FQQ, 8FQR, 8FQS, 8FQT, 8FQU, 8FQV, 8FQW

  • PubMed Abstract: 

    Class C Acinetobacter -derived cephalosporinases (ADCs) represent an important target for inhibition in the multidrug-resistant pathogen Acinetobacter baumannii . Many ADC variants have emerged, and characterization of their structural and functional differences is essential. Equally as important is the development of compounds that inhibit all prevalent ADCs despite these differences. The boronic acid transition state inhibitor, MB076 , a novel heterocyclic triazole with improved plasma stability, was synthesized and inhibits seven different ADC β-lactamase variants with K i values <1 μM. MB076 acted synergistically in combination with multiple cephalosporins to restore susceptibility. ADC variants containing an alanine duplication in the Ω-loop, specifically ADC-33, exhibited increased activity for larger cephalosporins, such as ceftazidime, cefiderocol, and ceftolozane. X-ray crystal structures of ADC variants in this study provide a structural context for substrate profile differences and show that the inhibitor adopts a similar conformation in all ADC variants, despite small changes near their active sites.


  • Organizational Affiliation
    • Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States.

Macromolecule Content 

  • Total Structure Weight: 81.7 kDa 
  • Atom Count: 6,240 
  • Modeled Residue Count: 714 
  • Deposited Residue Count: 722 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamaseA [auth B],
B [auth A]
361Acinetobacter baumanniiMutation(s): 0 
Gene Names: blaADC
EC: 3.5.2.6
UniProt
Find proteins for A0A2H4PPJ8 (Acinetobacter baumannii)
Explore A0A2H4PPJ8 
Go to UniProtKB:  A0A2H4PPJ8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2H4PPJ8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.054α = 90
b = 83.633β = 90
c = 204.338γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
autoPROCdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI072219

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2023-07-26
    Changes: Database references
  • Version 1.3: 2024-05-22
    Changes: Data collection