6WAA

K. pneumoniae Topoisomerase IV (ParE-ParC) in complex with DNA and compound 34 (7-[(1S,5R)-1-amino-3-azabicyclo[3.1.0]hexan-3-yl]-4-(aminomethyl)-1-cyclopropyl-3,6-difluoro-8-methylquinolin-2(1H)-one)

Summary for 6WAA

• Entry DOI: 10.2210/pdb6waa/pdb
• Descriptor: DNA topoisomerase 4 subunit B,DNA topoisomerase (ATP-hydrolyzing) chimera, DNA (5'-D(*TP*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3'), DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3'), ... (8 entities in total)
• Functional Keywords: dna-topoisomerase, isomerase-dna-isomerase inhibitor complex, isomerase/dna/isomerase inhibitor
• Biological source: Klebsiella pneumoniae 342; More
• Total number of polymer chains: 12
• Total formula weight: 371367.74

Authors

Noeske, J.,Shu, W.,Bellamacina, C. (deposition date: 2020-03-24, release date: 2020-07-15, Last modification date: 2024-12-25)

Primary citation

Skepper, C.K.,Armstrong, D.,Balibar, C.J.,Bauer, D.,Bellamacina, C.,Benton, B.M.,Bussiere, D.,De Pascale, G.,De Vicente, J.,Dean, C.R.,Dhumale, B.,Fisher, L.M.,Fuller, J.,Fulsunder, M.,Holder, L.M.,Hu, C.,Kantariya, B.,Lapointe, G.,Leeds, J.A.,Li, X.,Lu, P.,Lvov, A.,Ma, S.,Madhavan, S.,Malekar, S.,McKenney, D.,Mergo, W.,Metzger, L.,Moser, H.E.,Mutnick, D.,Noeske, J.,Osborne, C.,Patel, A.,Patel, D.,Patel, T.,Prajapati, K.,Prosen, K.R.,Reck, F.,Richie, D.L.,Rico, A.,Sanderson, M.R.,Satasia, S.,Sawyer, W.S.,Selvarajah, J.,Shah, N.,Shanghavi, K.,Shu, W.,Thompson, K.V.,Traebert, M.,Vala, A.,Vala, L.,Veselkov, D.A.,Vo, J.,Wang, M.,Widya, M.,Williams, S.L.,Xu, Y.,Yue, Q.,Zang, R.,Zhou, B.,Rivkin, A.
Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria.
J.Med.Chem., 63:7773-7816, 2020

PubMed Abstract: Since their discovery over 5 decades ago, quinolone antibiotics have found enormous success as broad spectrum agents that exert their activity through dual inhibition of bacterial DNA gyrase and topoisomerase IV. Increasing rates of resistance, driven largely by target-based mutations in the GyrA/ParC quinolone resistance determining region, have eroded the utility and threaten the future use of this vital class of antibiotics. Herein we describe the discovery and optimization of a series of 4-(aminomethyl)quinolin-2(1)-ones, exemplified by , that inhibit bacterial DNA gyrase and topoisomerase IV and display potent activity against ciprofloxacin-resistant Gram-negative pathogens. X-ray crystallography reveals that occupies the classical quinolone binding site in the topoisomerase IV-DNA cleavage complex but does not form significant contacts with residues in the quinolone resistance determining region.

PubMed: 32634310
DOI: 10.1021/acs.jmedchem.0c00347

Experimental method

X-RAY DIFFRACTION (3.2 Å)