Structure of PDB 5d7c Chain A Binding Site BS01

Receptor Information
>5d7c Chain A (length=192) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYAN
QIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDL
EVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETT
VYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE
Ligand information
Ligand ID57W
InChIInChI=1S/C20H18N6O/c1-2-22-20(27)25-16-13-26(18-7-3-4-9-23-18)17-10-15(12-24-19(16)17)14-6-5-8-21-11-14/h3-13H,2H2,1H3,(H2,22,25,27)
InChIKeyFRDSIJNIQUPVHU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCNC(=O)Nc1cn(c2c1ncc(c2)c3cccnc3)c4ccccn4
CACTVS 3.385CCNC(=O)Nc1cn(c2ccccn2)c3cc(cnc13)c4cccnc4
ACDLabs 12.01O=C(NCC)Nc3c2ncc(c1cnccc1)cc2n(c3)c4ncccc4
FormulaC20 H18 N6 O
Name1-ethyl-3-[1-(pyridin-2-yl)-6-(pyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-3-yl]urea
ChEMBLCHEMBL3736222
DrugBank
ZINCZINC000263620434
PDB chain5d7c Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5d7c Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		S55 E58 V79 D81 R84 G85 I86 P87 I102 R144 T173 I175
Binding residue
(residue number reindexed from 1)		S40 E43 V64 D66 R69 G70 I71 P72 I87 R106 T135 I137
Annotation score1
Binding affinityMOAD: ic50=0.14uM
PDBbind-CN: -logKd/Ki=6.85,IC50=0.14uM
BindingDB: IC50=140nM
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:5d7c, PDBe:5d7c, PDBj:5d7c
PDBsum5d7c
PubMed26460684
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB)

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