6TZH

ADC-7 in complex with boronic acid transition state inhibitor S06015


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 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 

  • DOI: 10.1021/acsinfecdis.0c00254
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Boronic Acids 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 have been ad ...

    Boronic Acids 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 have been advanced in several studies. 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 of the active site. A library of 26 α-triazolylmethaneboronic acids was synthesized and tested against the clinically concerning Acinetobacter-Derived Cephalosporinase ADC-7, with Ki values ranging from 90 nM to 38 μM. Five compounds were crystallized in complex with ADC-7 β-lactamase and all of 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 7q (Ki 90 nM), places a tolyl group near Arg340 making favorable cation-π interactions. Notably, the structure of 7q does not resemble the natural substrate of the β-lactamase yet displays a pronounced inhibition activity, in addition to lowering the 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

    Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan. Electronic address: thirota@itbm.nagoya-u.ac.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B, C, D
361Acinetobacter baumanniiMutation(s): 0 
EC: 3.5.2.6
Find proteins for Q6DRA1 (Acinetobacter baumannii)
Go to UniProtKB:  Q6DRA1
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERF
Query on ERF

Download CCD File 
A, B, C, D
phosphonooxy-[(4-thiophen-3-yl-1,2,3-triazol-1-yl)methyl]borinic acid
C7 H9 B N3 O5 P S
CSAHOMHDQOWLFN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GLY
Query on GLY

Download CCD File 
A, B, C, D
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.554α = 90
b = 81.464β = 113.1
c = 105.665γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata 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 

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