5WAG

ADC-7 in complex with boronic acid transition state inhibitor S06017


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.931 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Analysis of Boronic Acids as Inhibitors of Acinetobacter-Derived Cephalosporinase-7, a Unique Class C beta-Lactamase.

Bouza, A.A.Swanson, H.C.Smolen, K.A.VanDine, A.L.Taracila, M.A.Romagnoli, C.Caselli, E.Prati, F.Bonomo, R.A.Powers, R.A.Wallar, B.J.

(2018) ACS Infect Dis 4: 325-336

  • DOI: 10.1021/acsinfecdis.7b00152
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acinetobacter baumannii is a multidrug resistant pathogen that infects more than 12 000 patients each year in the US. Much of the resistance to β-lactam antibiotics in Acinetobacter spp. is mediated by class C β-lactamases known as Acinetobacter-deri ...

    Acinetobacter baumannii is a multidrug resistant pathogen that infects more than 12 000 patients each year in the US. Much of the resistance to β-lactam antibiotics in Acinetobacter spp. is mediated by class C β-lactamases known as Acinetobacter-derived cephalosporinases (ADCs). ADCs are unaffected by clinically used β-lactam-based β-lactamase inhibitors. In this study, five boronic acid transition state analog inhibitors (BATSIs) were evaluated for inhibition of the class C cephalosporinase ADC-7. Our goal was to explore the properties of BATSIs designed to probe the R1 binding site. Ki values ranged from low micromolar to subnanomolar, and circular dichroism (CD) demonstrated that each inhibitor stabilizes the β-lactamase-inhibitor complexes. Additionally, X-ray crystal structures of ADC-7 in complex with five inhibitors were determined (resolutions from 1.80 to 2.09 Å). In the ADC-7/CR192 complex, the BATSI with the lowest Ki (0.45 nM) and greatest ΔTm (+9 °C), a trifluoromethyl substituent, interacts with Arg340. Arg340 is unique to ADCs and may play an important role in the inhibition of ADC-7. The ADC-7/BATSI complexes determined in this study shed light into the unique recognition sites in ADC enzymes and also offer insight into further structure-based optimization of these inhibitors.


    Organizational Affiliation

    Department of Chemistry, Grand Valley State University , 1 Campus Drive, Allendale, Michigan 49401, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
B, A, C, D
361Acinetobacter baumanniiMutation(s): 0 
EC: 3.5.2.6
Find proteins for Q6DRA1 (Acinetobacter baumannii)
Go to UniProtKB:  Q6DRA1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN

Download SDF File 
Download CCD File 
A
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
A0V
Query on A0V

Download SDF File 
Download CCD File 
A, B, C, D
1-{[hydroxy(phosphonooxy)boranyl]methyl}-1H-1,2,3-triazole-4-carboxylic acid
C4 H7 B N3 O7 P
AEBNZGMSDDIREX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.931 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 88.665α = 90.00
b = 80.896β = 113.36
c = 105.338γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI072219

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-20
    Type: Database references
  • Version 1.2: 2018-03-21
    Type: Database references