Structure of PDB 5d6p Chain A Binding Site BS01

Receptor Information
>5d6p 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 ID57U
InChIInChI=1S/C11H14N4O2S/c1-2-12-10(17)15-11-14-8(6-16)9(18-11)7-4-3-5-13-7/h3-5,13,16H,2,6H2,1H3,(H2,12,14,15,17)
InChIKeyYLSYQKDIZQYYGN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCNC(=O)Nc1nc(c(s1)c2ccc[nH]2)CO
ACDLabs 12.01c2(sc(c1cccn1)c(CO)n2)NC(=O)NCC
CACTVS 3.385CCNC(=O)Nc1sc(c(CO)n1)c2[nH]ccc2
FormulaC11 H14 N4 O2 S
Name1-ethyl-3-[4-(hydroxymethyl)-5-(1H-pyrrol-2-yl)-1,3-thiazol-2-yl]urea
ChEMBLCHEMBL3735431
DrugBank
ZINCZINC000263621285
PDB chain5d6p Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5d6p Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		I51 S55 E58 V79 D81 R84 G85 P87 I102
Binding residue
(residue number reindexed from 1)		I36 S40 E43 V64 D66 R69 G70 P72 I87
Annotation score1
Binding affinityMOAD: ic50=2.5uM
PDBbind-CN: -logKd/Ki=5.60,IC50=2.5uM
BindingDB: IC50=2500nM
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:5d6p, PDBe:5d6p, PDBj:5d6p
PDBsum5d6p
PubMed26460684
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB)

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