ISDA

Deposition Date 2021-05-15

Release Date 2021-10-20

Last Version Date 2023-10-18

Entry Detail

PDB ID:

7MVS

Keywords:

ISOMERASE/DNA/ANTIBIOTIC

Title:

DNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A resolution

Biological Source:

Source Organism:

Staphylococcus aureus (Taxon ID: 1280)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.60 Å

R-Value Free:

0.25

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 61

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit A
Gene (Uniprot):gyrB
Mutations:Y324F
Chain IDs:A, B
Chain Length:693
Number of Molecules:2
Biological Source:Staphylococcus aureus

UniProt ID:P0A0K8,P20831 Pfam ID:PF01751, PF00986, PF00521 EC:5.6.2.2

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
Chain IDs:C, D
Chain Length:20
Number of Molecules:2
Biological Source:synthetic construct

Ligand Molecules

SO4

Y1W

Primary Citation

Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA.

Lu, Y, Vibhute, S, Li, L, Okumu, A, Ratigan, S.C, Nolan, S, Papa, J.L, Mann, C.A, English, A, Chen, A, Seffernick, J.T, Koci, B, Duncan, L.R, Roth, B, Cummings, J.E, Slayden, R.A, Lindert, S, McElroy, C.A, Wozniak, D.J, Yalowich, J, Mitton-Fry, M.J.Show

J.Med.Chem. 64 15214 15249 (2021)

PMID: 34614347 DOI: 10.1021/acs.jmedchem.1c01250

Abstact

Novel bacterial topoisomerase inhibitors (NBTIs) are among the most promising new antibiotics in preclinical/clinical development. We previously reported dioxane-linked NBTIs with potent antistaphylococcal activity and reduced hERG inhibition, a key safety liability. Herein, polarity-focused optimization enabled the delineation of clear structure-property relationships for both microsomal metabolic stability and hERG inhibition, resulting in the identification of lead compound 79. This molecule demonstrates potent antibacterial activity against diverse Gram-positive pathogens, inhibition of both DNA gyrase and topoisomerase IV, a low frequency of resistance, a favorable in vitro cardiovascular safety profile, and in vivo efficacy in a murine model of methicillin-resistant Staphylococcus aureus infection.

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Primary Citation of related structures