ISDA: 6QX1

Deposition Date 2019-03-06

Release Date 2019-04-17

Last Version Date 2024-01-24

Entry Detail

PDB ID:

6QX1

Keywords:

ISOMERASE

Title:

2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA.

Biological Source:

Source Organism(s):

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

Expression System(s):

Escherichia coli, Synthetic construct

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.65 Å

R-Value Free:

0.20

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 61

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit A
Gene (Uniprot):gyrA
Chain IDs:B (auth: A), D (auth: C)
Chain Length:490
Number of Molecules:2
Biological Source:Staphylococcus aureus

UniProt ID:Q99XG5 Pfam ID:PF00521 EC:5.6.2.2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B
Chain IDs:A (auth: B), C (auth: D)
Chain Length:202
Number of Molecules:2
Biological Source:Staphylococcus aureus

UniProt ID:P0A0K8 Pfam ID:PF01751

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

Ligand Molecules

GLY

GOL

JK8

Primary Citation

Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.

Thalji, R.K, Raha, K, Andreotti, D, Checchia, A, Cui, H, Meneghelli, G, Profeta, R, Tonelli, F, Tommasi, S, Bakshi, T, Donovan, B.T, Howells, A, Jain, S, Nixon, C, Quinque, G, McCloskey, L, Bax, B.D, Neu, M, Chan, P.F, Stavenger, R.A.Show

Bioorg.Med.Chem.Lett. 29 1407 1412 (2019)

PMID: 30962087 DOI: 10.1016/j.bmcl.2019.03.029

Abstact

A series of DNA gyrase inhibitors were designed based on the X-ray structure of a parent thiophene scaffold with the objective to improve biochemical and whole-cell antibacterial activity, while reducing cardiac ion channel activity. The binding mode and overall design hypothesis of one series was confirmed with a co-crystal structure with DNA gyrase. Although some analogs retained both biochemical activity and whole-cell antibacterial activity, we were unable to significantly improve the activity of the series and analogs retained activity against the cardiac ion channels, therefore we stopped optimization efforts.

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Disease

Primary Citation of related structures

Abstact

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