Structure of PDB 6f96 Chain A Binding Site BS01

Receptor Information
>6f96 Chain A (length=187) Species: 83334 (Escherichia coli O157:H7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIH
ADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLGVGVSVVNALSQKLEL
VIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEF
EYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYE
Ligand information
Ligand IDD0K
InChIInChI=1S/C21H22N6O3/c1-3-23-21(29)27-19-11-18(25-14-6-8-16(30-2)9-7-14)17(13-24-19)20(28)26-15-5-4-10-22-12-15/h4-13H,3H2,1-2H3,(H,26,28)(H3,23,24,25,27,29)
InChIKeyFSOAZMGZMXDGQX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCNC(=O)Nc1cc(c(cn1)C(=O)Nc2cccnc2)Nc3ccc(cc3)OC
CACTVS 3.385CCNC(=O)Nc1cc(Nc2ccc(OC)cc2)c(cn1)C(=O)Nc3cccnc3
FormulaC21 H22 N6 O3
Name6-(ethylcarbamoylamino)-4-[(4-methoxyphenyl)amino]-~{N}-pyridin-3-yl-pyridine-3-carboxamide
ChEMBLCHEMBL4581035
DrugBank
ZINC
PDB chain6f96 Chain A Residue 500 [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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PDB6f96 New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		V43 N46 E50 V71 D73 R76 G77 I78 P79 I94 R136
Binding residue
(residue number reindexed from 1)		V29 N32 E36 V57 D59 R62 G63 I64 P65 I80 R104
Annotation score1
Binding affinityMOAD: ic50=0.019uM
PDBbind-CN: -logKd/Ki=7.72,IC50=19nM
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:6f96, PDBe:6f96, PDBj:6f96
PDBsum6f96
PubMed31257079
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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