Structure of PDB 5d7r Chain A Binding Site BS02

Receptor Information
>5d7r Chain A (length=193) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYA
NQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQD
LEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTET
TVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE
Ligand information
Ligand ID57Y
InChIInChI=1S/C19H16N4O4S/c1-2-3-10-12(24)5-4-11-15(10)22-23-16(11)14-8-21-18(28-14)9-6-13(25)17(19(26)27)20-7-9/h4-8,24-25H,2-3H2,1H3,(H,22,23)(H,26,27)
InChIKeyYZWBQSFGTLQFTB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1c2c(c(CCC)c(c1)O)nnc2c4cnc(c3cc(c(nc3)C(=O)O)O)s4
OpenEye OEToolkits 1.9.2CCCc1c(ccc2c1n[nH]c2c3cnc(s3)c4cc(c(nc4)C(=O)O)O)O
CACTVS 3.385CCCc1c(O)ccc2c([nH]nc12)c3sc(nc3)c4cnc(C(O)=O)c(O)c4
FormulaC19 H16 N4 O4 S
Name3-hydroxy-5-[5-(6-hydroxy-7-propyl-2H-indazol-3-yl)-1,3-thiazol-2-yl]pyridine-2-carboxylic acid
ChEMBLCHEMBL3739628
DrugBank
ZINCZINC000263621320
PDB chain5d7r Chain A Residue 306 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5d7r Discovery of Indazole Derivatives as a Novel Class of Bacterial Gyrase B Inhibitors.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		I51 N54 S55 E58 V79 D81 R84 G85 I86 P87 R144 T173 I175
Binding residue
(residue number reindexed from 1)		I37 N40 S41 E44 V65 D67 R70 G71 I72 P73 R107 T136 I138
Annotation score1
Binding affinityMOAD: ic50=0.013uM
PDBbind-CN: -logKd/Ki=7.89,IC50=0.013uM
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
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Biological Process
External links
PDB RCSB:5d7r, PDBe:5d7r, PDBj:5d7r
PDBsum5d7r
PubMed26487916
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB)

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