Structure of PDB 6f94 Chain A Binding Site BS01

Receptor Information
>6f94 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 IDD0H
InChIInChI=1S/C23H25N5O2/c1-4-24-23(30)28-21-13-20(26-17-9-5-7-15(2)11-17)19(14-25-21)22(29)27-18-10-6-8-16(3)12-18/h5-14H,4H2,1-3H3,(H,27,29)(H3,24,25,26,28,30)
InChIKeyXQEFOQFUHGWPSD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCNC(=O)Nc1cc(c(cn1)C(=O)Nc2cccc(c2)C)Nc3cccc(c3)C
CACTVS 3.385CCNC(=O)Nc1cc(Nc2cccc(C)c2)c(cn1)C(=O)Nc3cccc(C)c3
FormulaC23 H25 N5 O2
Name6-(ethylcarbamoylamino)-~{N}-(3-methylphenyl)-4-[(3-methylphenyl)amino]pyridine-3-carboxamide
ChEMBLCHEMBL3329291
DrugBank
ZINCZINC000144675530
PDB chain6f94 Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6f94 New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		V43 A47 E50 D73 R76 G77 I78 I94 R136
Binding residue
(residue number reindexed from 1)		V29 A33 E36 D59 R62 G63 I64 I80 R104
Annotation score1
Binding affinityMOAD: ic50=0.099uM
PDBbind-CN: -logKd/Ki=7.00,IC50=99nM
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:6f94, PDBe:6f94, PDBj:6f94
PDBsum6f94
PubMed31257079
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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