7FVS | pdb_00007fvs

Crystal Structure of S. aureus gyrase in complex with 4-[[1-[(1-chloro-6,7-dihydro-5H-cyclopenta[c]pyridin-6-yl)methyl]azetidin-3-yl]methylamino]-6-fluorochromen-2-one

PDB DOI: https://doi.org/10.2210/pdb7FVS/pdb
Deposition Group: G_1002266 | Explore G_1002266
NAKB: 7FVS

Classification: ISOMERASE
Organism(s): Staphylococcus aureus subsp. aureus N315, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-04-18 Released: 2023-06-28
Deposition Author(s): Xu, B., Benz, J., Cumming, J.G., Kreis, L., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche LTD

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.221 (Depositor), 0.200 (DCC)
R-Value Work:
0.185 (Depositor), 0.175 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens.

Cumming, J.G., Kreis, L., Kuhne, H., Wermuth, R., Vercruysse, M., Kramer, C., Rudolph, M.G., Xu, Z.

(2023) ACS Med Chem Lett 14: 993-998

PubMed: 37465290 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.3c00187
Primary Citation Related Structures:
7FVS, 7FVT

PubMed Abstract:
The rise of multidrug-resistant (MDR) Gram-negative bacteria is a major global health problem necessitating the discovery of new classes of antibiotics. Novel bacterial topoisomerase inhibitors (NBTIs) target the clinically validated bacterial type II topoisomerases with a distinct binding site and mechanism of action to fluoroquinolone antibiotics, thus avoiding cross-resistance to this drug class. Here we report the discovery of a series of NBTIs incorporating a novel indane DNA binding moiety. X-ray cocrystal structures of compounds 2 and 17a bound to Staphylococcus aureus DNA gyrase-DNA were determined, revealing specific interactions with the enzyme binding pocket at the GyrA dimer interface and a long-range electrostatic interaction between the basic amine in the linker and the carboxylate of Asp83. Exploration of the structure-activity relationship within the series led to the identification of lead compound 18c , which showed potent broad-spectrum activity against a panel of MDR Gram-negative bacteria.

Organizational Affiliation

Roche Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 169.16 kDa
Atom Count: 11,927
Modeled Residue Count: 1,381
Deposited Residue Count: 1,424
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B,DNA gyrase subunit A Chimera	A, B	692	Staphylococcus aureus subsp. aureus N315	Mutation(s): 1 Gene Names: gyrB, SA0005, gyrA, SA0006 EC: 5.6.2.2
UniProt
Find proteins for P66937 (Staphylococcus aureus (strain N315)) Explore P66937 Go to UniProtKB: P66937
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315)) Explore Q99XG5 Go to UniProtKB: Q99XG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q99XG5 P66937
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(APGPCPCPGPTPAPGPGPGPCPCPCPTPAPCPGPGPCPT)-3')	C, D	20	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
61I (Subject of Investigation/LOI) Query on 61I Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	4-{[(1-{[(6R)-1-chloro-6,7-dihydro-5H-cyclopenta[c]pyridin-6-yl]methyl}azetidin-3-yl)methyl]amino}-6-fluoro-2H-1-benzopyran-2-one C₂₂ H₂₁ Cl F N₃ O₂ HCXCXUYRFPJWRR-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]