6TZJ

ADC-7 in complex with boronic acid transition state inhibitor ME_096


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

1,2,3-Triazolylmethaneboronate: A Structure Activity Relationship Study of a Class of beta-Lactamase Inhibitors againstAcinetobacter baumanniiCephalosporinase.

Caselli, E.Fini, F.Introvigne, M.L.Stucchi, M.Taracila, M.A.Fish, E.R.Smolen, K.A.Rather, P.N.Powers, R.A.Wallar, B.J.Bonomo, R.A.Prati, F.

(2020) ACS Infect Dis 6: 1965-1975

  • DOI: 10.1021/acsinfecdis.0c00254
  • Primary Citation of Related Structures:  
    6TZG, 6TZF, 6TZI, 6TZH, 6TZJ

  • PubMed Abstract: 
  • Boronic acid transition state inhibitors (BATSIs) are known reversible covalent inhibitors of serine β-lactamases. The selectivity and high potency of specific BATSIs bearing an amide side chain mimicking the β-lactam's amide side chain are an established and recognized synthetic strategy ...

    Boronic acid transition state inhibitors (BATSIs) are known reversible covalent inhibitors of serine β-lactamases. The selectivity and high potency of specific BATSIs bearing an amide side chain mimicking the β-lactam's amide side chain are an established and recognized synthetic strategy. Herein, we describe a new class of BATSIs where the amide group is replaced by a bioisostere triazole; these compounds were designed as molecular probes. To this end, a library of 26 α-triazolylmethaneboronic acids was synthesized and tested against the clinically concerning Acinetobacter -derived cephalosporinase, ADC-7. In steady state analyses, these compounds demonstrated K i values ranging from 90 nM to 38 μM (±10%). Five compounds were crystallized in complex with ADC-7 β-lactamase, and all the crystal structures reveal the triazole is in the putative amide binding site, thus confirming the triazole-amide bioisosterism. The easy synthetic access of these new inhibitors as prototype scaffolds allows the insertion of a wide range of chemical groups able to explore the enzyme binding site and provides insights on the importance of specific residues in recognition and catalysis. The best inhibitor identified, compound 6q ( K i 90 nM), places a tolyl group near Arg340, making favorable cation-π interactions. Notably, the structure of 6q does not resemble the natural substrate of the β-lactamase yet displays a pronounced inhibition activity, in addition to lowering the minimum inhibitory concentration (MIC) of ceftazidime against three bacterial strains expressing class C β-lactamases. In summary, these observations validate the α-triazolylboronic acids as a promising template for further inhibitor design.


    Organizational Affiliation

    Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA, B, C, D361Acinetobacter baumanniiMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for Q6DRA1 (Acinetobacter baumannii)
Explore Q6DRA1 
Go to UniProtKB:  Q6DRA1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PKV
Query on PKV

Download Ideal Coordinates CCD File 
E [auth A], G [auth B], H [auth C], J [auth D][4-[[(4-methylphenyl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]methyl-phosphonooxy-borinic acid
C11 H16 B N4 O7 P S
YPLPGLUGELKLDN-UHFFFAOYSA-N
 Ligand Interaction
GLY
Query on GLY

Download Ideal Coordinates CCD File 
F [auth A], I [auth C], K [auth D]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.477α = 90
b = 80.616β = 113.46
c = 105.105γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building

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 StatesR01 AI072219

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2020-07-22
    Changes: Database references