8BN6

Pseudomonas aeruginosa DNA gyrase B 24kDa ATPase subdomain complexed with EBL3021


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus .

Durcik, M.Cotman, A.E.Toplak, Z.Mozina, S.Skok, Z.Szili, P.E.Czikkely, M.Maharramov, E.Vu, T.H.Piras, M.V.Zidar, N.Ilas, J.Zega, A.Trontelj, J.Pardo, L.A.Hughes, D.Huseby, D.Berruga-Fernandez, T.Cao, S.Simoff, I.Svensson, R.Korol, S.V.Jin, Z.Vicente, F.Ramos, M.C.Mundy, J.E.A.Maxwell, A.Stevenson, C.E.M.Lawson, D.M.Glinghammar, B.Sjostrom, E.Bohlin, M.Oreskar, J.Alver, S.Janssen, G.V.Sterk, G.J.Kikelj, D.Pal, C.Tomasic, T.Peterlin Masic, L.

(2023) J Med Chem 66: 3968-3994

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01905
  • Primary Citation of Related Structures:  
    8BN6

  • PubMed Abstract: 

    A new series of dual low nanomolar benzothiazole inhibitors of bacterial DNA gyrase and topoisomerase IV were developed. The resulting compounds show excellent broad-spectrum antibacterial activities against Gram-positive Enterococcus faecalis , Enterococcus faecium and multidrug resistant (MDR) Staphylococcus aureus strains [best compound minimal inhibitory concentrations (MICs): range, <0.03125-0.25 μg/mL] and against the Gram-negatives Acinetobacter baumannii and Klebsiella pneumoniae (best compound MICs: range, 1-4 μg/mL). Lead compound 7a was identified with favorable solubility and plasma protein binding, good metabolic stability, selectivity for bacterial topoisomerases, and no toxicity issues. The crystal structure of 7a in complex with Pseudomonas aeruginosa GyrB24 revealed its binding mode at the ATP-binding site. Expanded profiling of 7a and 7h showed potent antibacterial activity against over 100 MDR and non-MDR strains of A. baumannii and several other Gram-positive and Gram-negative strains. Ultimately, in vivo efficacy of 7a in a mouse model of vancomycin-intermediate S. aureus thigh infection was also demonstrated.


  • Organizational Affiliation

    Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana 1000, Slovenia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit B221Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: gyrBPA0004
EC: 5.6.2.2
UniProt
Find proteins for Q9I7C2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I7C2 
Go to UniProtKB:  Q9I7C2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I7C2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R53 (Subject of Investigation/LOI)
Query on R53

Download Ideal Coordinates CCD File 
D [auth A]2-[[3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrol-2-yl]carbonylamino]-4-morpholin-4-yl-1,3-benzothiazole-6-carboxylic acid
C18 H16 Cl2 N4 O4 S
XMRMYIYEEWALOZ-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.2α = 90
b = 115.65β = 90
c = 38.63γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-0208
Slovenian Research AgencySloveniaJ1-9192
Slovenian Research AgencySloveniaBI-HU/19-20-008
European Communitys Seventh Framework ProgrammeEuropean Union115583
Wellcome TrustUnited Kingdom110072/Z/15/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P012523/1
European Research Council (ERC)European UnionH2020-ERC-2014-CoG 648364

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 2.0: 2023-05-24
    Changes: Non-polymer description
  • Version 2.1: 2024-02-07
    Changes: Data collection, Refinement description