Structure of PDB 5cph Chain B Binding Site BS01

Receptor Information
>5cph Chain B (length=186) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEV
VIEKDNWIKVTDNGRGIPVDIQGRPAVEVILTSSVVNALSQDLEVYVHRN
ETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETL
QQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG
Ligand information
Ligand IDEVO
InChIInChI=1S/C14H10N2O/c17-14-12(8-10-4-3-7-15-9-10)11-5-1-2-6-13(11)16-14/h1-9H,(H,16,17)/b12-8+
InChIKeyALVGMCFQOGIUFY-XYOKQWHBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc2c(c1)C(=Cc3cccnc3)C(=O)N2
OpenEye OEToolkits 1.9.2c1ccc2c(c1)/C(=C\c3cccnc3)/C(=O)N2
CACTVS 3.385O=C1Nc2ccccc2C1=Cc3cccnc3
ACDLabs 12.01O=C2C(c1c(cccc1)N2)=[C@H]c3cnccc3
CACTVS 3.385O=C/1Nc2ccccc2C/1=C/c3cccnc3
FormulaC14 H10 N2 O
Name(3E)-3-(pyridin-3-ylmethylidene)-1,3-dihydro-2H-indol-2-one
ChEMBLCHEMBL3760057
DrugBank
ZINCZINC000004824092
PDB chain5cph Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5cph Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB.
Resolution1.2 Å
Binding residue
(original residue number in PDB)		N54 E58 D81 I86 I102
Binding residue
(residue number reindexed from 1)		N35 E39 D62 I67 I80
Annotation score1
Binding affinityBindingDB: IC50=840000nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5cph, PDBe:5cph, PDBj:5cph
PDBsum5cph
PubMed26786695
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB)

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