6QX2 image
Deposition Date 2019-03-06
Release Date 2019-04-17
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6QX2
Keywords:
ISOMERASE
Title:
3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA
Biological Source:
Source Organism:
Staphylococcus aureus (Taxon ID: 1280)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.40 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 1 21 1
6QX2 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit A
Gene (Uniprot):gyrA
Mutations:123 phosphotyrosine
Chain IDs:B (auth: A), D (auth: C), J (auth: L), N (auth: R), P (auth: T), T (auth: a), V (auth: c), Z (auth: j), BA (auth: l), FA (auth: r), HA (auth: t)
Chain Length:490
Number of Molecules:11
Biological Source:Staphylococcus aureus
UniProt ID:Q99XG5 Pfam ID:PF00521 EC:5.6.2.2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit B
Gene (Uniprot):gyrB
Chain IDs:A (auth: B), M (auth: S), S (auth: b), EA (auth: s)
Chain Length:186
Number of Molecules:4
Biological Source:Staphylococcus aureus
UniProt ID:P0A0K8 Pfam ID:PF01751, PF00986 EC:5.6.2.2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit B
Gene (Uniprot):gyrB
Chain IDs:C (auth: D), O (auth: U), AA (auth: m)
Chain Length:181
Number of Molecules:3
Biological Source:Staphylococcus aureus
UniProt ID:P0A0K8 Pfam ID:PF01751, PF00986 EC:5.6.2.2
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
Chain IDs:E, F, K (auth: N), L (auth: O), R (auth: W), W (auth: e), CA (auth: n), IA (auth: v), JA (auth: w)
Chain Length:20
Number of Molecules:9
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit A
Gene (Uniprot):gyrA
Chain IDs:H (auth: J)
Chain Length:490
Number of Molecules:1
Biological Source:Staphylococcus aureus
UniProt ID:Q99XG5 Pfam ID:PF00521 EC:5.6.2.2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit B
Chain IDs:G (auth: K)
Chain Length:187
Number of Molecules:1
Biological Source:Staphylococcus aureus
UniProt ID:P0A0K8 Pfam ID:PF01751, PF00986
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit B
Chain IDs:I (auth: M)
Chain Length:189
Number of Molecules:1
Biological Source:Staphylococcus aureus
UniProt ID:P0A0K8 Pfam ID:PF01751, PF00986
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
Chain IDs:Q (auth: V), DA (auth: o)
Chain Length:19
Number of Molecules:2
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit B
Chain IDs:U (auth: d)
Chain Length:181
Number of Molecules:1
Biological Source:Staphylococcus aureus
UniProt ID:P0A0K8 Pfam ID:PF01751, PF00986
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
Chain IDs:X (auth: f)
Chain Length:20
Number of Molecules:1
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit B
Chain IDs:Y (auth: k)
Chain Length:187
Number of Molecules:1
Biological Source:Staphylococcus aureus
UniProt ID:P0A0K8 Pfam ID:PF01751, PF00986
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit B
Chain IDs:GA (auth: u)
Chain Length:188
Number of Molecules:1
Biological Source:Staphylococcus aureus
UniProt ID:P0A0K8 Pfam ID:PF01751, PF00986
Ligand Molecules
JK8
Primary Citation
Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.
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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Primary Citation of related structures
6QX1