Structure of PDB 6yd9 Chain A Binding Site BS01

Receptor Information
>6yd9 Chain A (length=198) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALA
GHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHGVGV
SVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFW
PSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY
Ligand information
Ligand IDON2
InChIInChI=1S/C16H15Cl2N5O2S/c1-7-12(17)13(18)14(20-7)15(25)23-16-22-9-3-2-8(6-10(9)26-16)21-11(24)4-5-19/h2-3,6,20H,4-5,19H2,1H3,(H,21,24)(H,22,23,25)
InChIKeyRVKKBUSSKLNKTC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c(c(c([nH]1)C(=O)Nc2nc3ccc(cc3s2)NC(=O)CCN)Cl)Cl
CACTVS 3.385Cc1[nH]c(C(=O)Nc2sc3cc(NC(=O)CCN)ccc3n2)c(Cl)c1Cl
FormulaC16 H15 Cl2 N5 O2 S
NameN-[6-(3-azanylpropanoylamino)-1,3-benzothiazol-2-yl]-3,4-bis(chloranyl)-5-methyl-1H-pyrrole-2-carboxamide
ChEMBLCHEMBL4803858
DrugBank
ZINC
PDB chain6yd9 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6yd9 Exploring the Chemical Space of Benzothiazole-Based DNA Gyrase B Inhibitors.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		N46 E50 D73 R76 G77 I78 P79 R136 T165
Binding residue
(residue number reindexed from 1)		N43 E47 D70 R73 G74 I75 P76 R116 T145
Annotation score1
Binding affinityMOAD: ic50=110nM
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:6yd9, PDBe:6yd9, PDBj:6yd9
PDBsum6yd9
PubMed33329764
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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