6Q35

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


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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

  • DOI: 10.1021/acsmedchemlett.8b00607
  • Primary Citation of 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) ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA, B270Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaGES-5pGES-GZ_027
EC: 3.5.2.6
UniProt
Find proteins for Q09HD0 (Klebsiella pneumoniae)
Explore Q09HD0 
Go to UniProtKB:  Q09HD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09HD0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HD5
Query on HD5

Download Ideal Coordinates CCD File 
F [auth A],
U [auth B]
[5-(aminomethyl)-1-benzothiophen-2-yl]boronic acid
C9 H10 B N O2 S
AMRAXCBFZWIMEQ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
G [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
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
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
H [auth A],
P [auth B],
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.669α = 90
b = 79.444β = 90
c = 87.523γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Communitys Seventh Framework ProgrammeItaly286998

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references