Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 12)

Experimental Data Snapshot

  • Resolution: 1.36 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.144 

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High-Throughput Crystallography Reveals Boron-Containing Inhibitors of a Penicillin-Binding Protein with Di- and Tricovalent Binding Modes.

Newman, H.Krajnc, A.Bellini, D.Eyermann, C.J.Boyle, G.A.Paterson, N.G.McAuley, K.E.Lesniak, R.Gangar, M.von Delft, F.Brem, J.Chibale, K.Schofield, C.J.Dowson, C.G.

(2021) J Med Chem 64: 11379-11394

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00717
  • Primary Citation of Related Structures:  
    7ATM, 7ATO, 7ATW, 7ATX, 7AU0, 7AU1, 7AU8, 7AU9, 7AUB, 7AUH

  • PubMed Abstract: 

    The effectiveness of β-lactam antibiotics is increasingly compromised by β-lactamases. Boron-containing inhibitors are potent serine-β-lactamase inhibitors, but the interactions of boron-based compounds with the penicillin-binding protein (PBP) β-lactam targets have not been extensively studied. We used high-throughput X-ray crystallography to explore reactions of a boron-containing fragment set with the Pseudomonas aeruginosa PBP3 (PaPBP3). Multiple crystal structures reveal that boronic acids react with PBPs to give tricovalently linked complexes bonded to Ser294, Ser349, and Lys484 of PaPBP3; benzoxaboroles react with PaPBP3 via reaction with two nucleophilic serines (Ser294 and Ser349) to give dicovalently linked complexes; and vaborbactam reacts to give a monocovalently linked complex. Modifications of the benzoxaborole scaffold resulted in a moderately potent inhibition of PaPBP3, though no antibacterial activity was observed. Overall, the results further evidence the potential for the development of new classes of boron-based antibiotics, which are not compromised by β-lactamase-driven resistance.

  • Organizational Affiliation

    School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan D,D-transpeptidase FtsI537Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: ftsIpbpBPA4418
Find proteins for G3XD46 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD46 
Go to UniProtKB:  G3XD46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3XD46
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S08 (Subject of Investigation/LOI)
Query on S08

Download Ideal Coordinates CCD File 
E [auth A]2-(6-(((R)-2-amino-2-oxo-1-phenylethyl)carbamoyl)-1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acetic acid
C18 H17 B N2 O6
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth A]
C4 H10 O3
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth A]
C3 H8 O3
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A],
K [auth A]
C2 H6 O S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.36 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.038α = 90
b = 81.925β = 90
c = 88.241γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 2.0: 2021-09-22
    Changes: Data collection, Database references, Non-polymer description
  • Version 2.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description