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Structure of PDB 6kzv Chain A Binding Site BS01

Receptor Information
>6kzv Chain A (length=198) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGH
CKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAVGVSV
VNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPS
LETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEG
Ligand information
Ligand IDE0F
InChIInChI=1S/C24H27N3O2/c1-27(19-11-3-2-4-12-19)16-18-10-6-8-14-22(18)26-24(29)20-15-17-9-5-7-13-21(17)25-23(20)28/h5-10,13-15,19H,2-4,11-12,16H2,1H3,(H,25,28)(H,26,29)
InChIKeyHXOAPOMHVOADBB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 2.0.7		CN(Cc1ccccc1NC(=O)C2=Cc3ccccc3NC2=O)C4CCCCC4
FormulaC24 H27 N3 O2
Name~{N}-[2-[[cyclohexyl(methyl)amino]methyl]phenyl]-2-oxidanylidene-1~{H}-quinoline-3-carboxamide;
N-(2-{[cyclohexyl(methyl)amino]methyl}phenyl)-2-oxo-1,2-dihydroquinoline-3-carboxamide
ChEMBL
DrugBank
ZINCZINC000036390838
PDB chain6kzv 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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PDB6kzv Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		N46 E50 D73 R76 G77 I78 P79
Binding residue
(residue number reindexed from 1)		N41 E45 D68 R71 G72 I73 P74
Annotation score1
Binding affinityMOAD: ic50=5.4uM
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:6kzv, PDBe:6kzv, PDBj:6kzv
PDBsum6kzv
PubMed32391502
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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