7P2M

E.coli GyrB24 with inhibitor LMD43 (EBL2560)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

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 B220Escherichia coli K-12Mutation(s): 0 
Gene Names: gyrBacrBcouhimBhisUnalCparApcbAb3699JW5625
EC: 5.6.2.2
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12))
Explore P0AES6 
Go to UniProtKB:  P0AES6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AES6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N1N (Subject of Investigation/LOI)
Query on N1N

Download Ideal Coordinates CCD File 
C [auth A]2-[[3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrol-2-yl]carbonylamino]-4-phenylmethoxy-1,3-benzothiazole-6-carboxylic acid
C21 H15 Cl2 N3 O4 S
QJJVAUMJKWWKTD-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.647α = 90
b = 50.33β = 102.25
c = 52.697γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines InitiativeSwitzerlandGrant No. 115583
Wellcome TrustUnited Kingdom110072/Z/15/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBBSRC Institute Strategic Programme Grant
European Communitys Seventh Framework ProgrammeEuropean Union(FP7/2007-2013)
Slovenian Research AgencySloveniaP1-0208

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description