6Q35 | pdb_00006q35

Crystal structure of GES-5 beta-lactamase in complex with boronic inhibitor cpd 3

• PDB DOI: https://doi.org/10.2210/pdb6Q35/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-03 Released: 2019-04-24 
• Deposition Author(s): Maso, L., Quotadamo, A., Bellio, P., Montanari, M., Venturelli, A., Celenza, G., Costi, M.P., Tondi, D., Cendron, L.
• Funding Organization(s): European Communitys Seventh Framework Programme

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystallography Deciphers the Activity of Broad-Spectrum Boronic Acid beta-Lactamase Inhibitors.

Cendron, L., Quotadamo, A., Maso, L., Bellio, P., Montanari, M., Celenza, G., Venturelli, A., Costi, M.P., Tondi, D.

(2019) ACS Med Chem Lett 10: 650-655

• PubMed: 30996812 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00607
• Primary Citation Related Structures: 
  6IBS, 6IBV, 6Q2Y, 6Q30, 6Q35


• PubMed Abstract: 
  

  Recent decades have witnessed a dramatic increase of multidrug resistant (MDR) bacteria, compromising the efficacy of available antibiotics, and a continual decline in the discovery of novel antibacterials. We recently reported the first library of benzo[b]thiophen-2-ylboronic acid inhibitors sharing broad spectrum activity against β-lactamases (BLs). The ability of these compounds to inhibit structurally and mechanistically different types of β-lactamases has been here structurally investigated. An extensive X-ray crystallographic analysis of boronic acids (BAs) binding to proteins representative of serine BLs (SBLs) and metallo β-lactamases (MBLs) have been conducted to depict the role played by the boronic group in driving molecular recognition, especially in the interaction with MBLs. Our derivatives are the first case of noncyclic boronic acids active against MBLs and represent a productive route toward potent broad-spectrum inhibitors.

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Organizational Affiliation: 
• Department of Biology, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy.
Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, 41125 Modena, Italy.
Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100 L'Aquila, Italy.
TYDOCK PHARMA S.r.l., Strada Gherbella 294/b, Modena 41126, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.38 kDa 
• Atom Count: 4,608 
• Modeled Residue Count: 535 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	270	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaGES-5, pGES-GZ_027 EC: 3.5.2.6
UniProt
Find proteins for Q09HD0 (Klebsiella pneumoniae) Explore Q09HD0  Go to UniProtKB:  Q09HD0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HD5	F [auth A], U [auth B]	[5-(aminomethyl)-1-benzothiophen-2-yl]boronic acid C9 H10 B N O2 S AMRAXCBFZWIMEQ-UHFFFAOYSA-N
DMS	G [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Q [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], H [auth A], P [auth B], R [auth B], S [auth B], T [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.669	α = 90
b = 79.444	β = 90
c = 87.523	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Maso, L., Quotadamo, A., Bellio, P., Montanari, M., Venturelli, A., Celenza, G., Costi, M.P., Tondi, D., Cendron, L.

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Funding Organization	Location	Grant Number
European Communitys Seventh Framework Programme	Italy	286998

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-05-01
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary