7PTF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa.

Cotman, A.E.Durcik, M.Benedetto Tiz, D.Fulgheri, F.Secci, D.Sterle, M.Mozina, S.Skok, Z.Zidar, N.Zega, A.Ilas, J.Peterlin Masic, L.Tomasic, T.Hughes, D.Huseby, D.L.Cao, S.Garoff, L.Berruga Fernandez, T.Giachou, P.Crone, L.Simoff, I.Svensson, R.Birnir, B.Korol, S.V.Jin, Z.Vicente, F.Ramos, M.C.de la Cruz, M.Glinghammar, B.Lenhammar, L.Henderson, S.R.Mundy, J.E.A.Maxwell, A.Stevenson, C.E.M.Lawson, D.M.Janssen, G.V.Sterk, G.J.Kikelj, D.

(2023) J Med Chem 66: 1380-1425

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01597
  • Primary Citation of Related Structures:  
    7P2M, 7P2W, 7PQI, 7PQL, 7PQM, 7PTF, 7PTG

  • PubMed Abstract: 

    We have developed compounds with a promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa , which are both on the WHO priority list of antibiotic-resistant bacteria. Starting from DNA gyrase inhibitor 1 , we identified compound 27 , featuring a 10-fold improved aqueous solubility, a 10-fold improved inhibition of topoisomerase IV from A. baumannii and P. aeruginosa , a 10-fold decreased inhibition of human topoisomerase IIα, and no cross-resistance to novobiocin. Cocrystal structures of 1 in complex with Escherichia coli GyrB24 and ( S )- 27 in complex with A. baumannii GyrB23 and P. aeruginosa GyrB24 revealed their binding to the ATP-binding pocket of the GyrB subunit. In further optimization steps, solubility, plasma free fraction, and other ADME properties of 27 were improved by fine-tuning of lipophilicity. In particular, analogs of 27 with retained anti-Gram-negative activity and improved plasma free fraction were identified. The series was found to be nongenotoxic, nonmutagenic, devoid of mitochondrial toxicity, and possessed no ion channel liabilities.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit B
A, B, C
221Pseudomonas 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.657α = 90
b = 47.391β = 99.49
c = 110.626γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Communitys Seventh Framework ProgrammeUnited Kingdom115583
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P012523/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description