6UR3

Serendipitous Discovery of Aryl Boronic Acids as beta-Lactamase Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb6UR3/pdb

• Classification: ANTIBIOTIC
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-10-22 Released: 2019-10-30 
• Deposition Author(s): Scapin, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.179 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Literature

Serendipitous discovery of aryl boronic acids as beta-lactamase inhibitors.

Yang, S.W., Pan, J., Root, Y., Scapin, G., Xiao, L., Su, J.

(2020) Bioorg Med Chem Lett 30: 126795-126795

• PubMed: 31759850 
• DOI: https://doi.org/10.1016/j.bmcl.2019.126795
• Primary Citation of Related Structures:  
  6UQS, 6UQT, 6UQU, 6UR3


• PubMed Abstract: 
  

  High throughput screening for β-lactamase inhibitors afforded biphenyl hits such as 1. Hit confirmation and X-ray soaking experiments with Pseudomonas Aeruginosa AmpC enzyme led to the identification of an aryl boronic acid-serine complex 4, which was formed from phenyl boronic acid 8 (an impurity in compound 1) and ethylene glycol (the cryoprotectant in the soaking experiment).

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Organizational Affiliation: 

Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 41.35 kDa 
• Atom Count: 3,154 
• Modelled Residue Count: 363 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	375	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: ampC, RW109_RW109_01564 EC: 3.5.2.6
UniProt
Find proteins for P24735 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P24735  Go to UniProtKB:  P24735

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QFP (Subject of Investigation/LOI)	B [auth A]	2-hydroxyethyl hydrogen phenylboronate C8 H11 B O3 MCBDCMMJWCRCFZ-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.179 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.731	α = 90
b = 71.46	β = 90
c = 104.763	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Scapin, G.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Database references
• Version 1.2: 2020-01-15
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary