Structure of PDB 5d7d Chain B Binding Site BS03

Receptor Information
>5d7d Chain B (length=189) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEV
VIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDLEVYV
HRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNY
ETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG
Ligand information
Ligand ID57X
InChIInChI=1S/C17H15N5OS/c1-2-8-22-14(23)6-5-12-15(20-21-16(12)22)13-10-19-17(24-13)11-4-3-7-18-9-11/h3-7,9-10H,2,8H2,1H3,(H,20,21)
InChIKeyVOOCDNWLHBWIJZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCN1C(=O)C=Cc2c1[nH]nc2c3sc(nc3)c4cccnc4
ACDLabs 12.01C=1C(N(c2c(C=1)c(nn2)c4sc(c3cccnc3)nc4)CCC)=O
OpenEye OEToolkits 1.9.2CCCN1c2c(c(n[nH]2)c3cnc(s3)c4cccnc4)C=CC1=O
FormulaC17 H15 N5 O S
Name7-propyl-3-[2-(pyridin-3-yl)-1,3-thiazol-5-yl]-1,7-dihydro-6H-pyrazolo[3,4-b]pyridin-6-one
ChEMBLCHEMBL3810359
DrugBank
ZINCZINC000205861192
PDB chain5d7d Chain B Residue 308 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5d7d Discovery of Indazole Derivatives as a Novel Class of Bacterial Gyrase B Inhibitors.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		N54 S55 E58 V79 D81 R84 G85 I86 P87 R144 T173 I175
Binding residue
(residue number reindexed from 1)		N35 S36 E39 V60 D62 R65 G66 I67 P68 R102 T131 I133
Annotation score1
Binding affinityBindingDB: IC50=6.0nM
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
Biological Process
GO:0006265 DNA topological change

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5d7d, PDBe:5d7d, PDBj:5d7d
PDBsum5d7d
PubMed26487916
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB)

[Back to BioLiP]