Structure of PDB 6rks Chain A Binding Site BS03

Receptor Information
>6rks Chain A (length=508) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGN
DWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQG
NFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPD
VMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEG
LMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDARETII
VHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRD
AVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRRE
VVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTAL
VANPWQLGNVAAAGDDAARPEWLEPEFGVGLYYLTEQQAQAILDLRLQKL
TGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGDK
RRTEITAN
Ligand information
Ligand IDJHN
InChIInChI=1S/C24H28N6O3/c31-22-4-3-20-24-29(22)15-19(30(24)23(32)13-27-20)14-28-7-5-17(6-8-28)25-11-18-10-16-2-1-9-33-21(16)12-26-18/h3-4,10,12-13,17,19,25H,1-2,5-9,11,14-15H2/t19-/m1/s1
InChIKeyPZFAZQUREQIODZ-LJQANCHMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1c2c(cnc1CNC3CCN(CC3)C[C@@H]4CN5C(=O)C=CC6=C5N4C(=O)C=N6)OCCC2
OpenEye OEToolkits 2.0.7c1c2c(cnc1CNC3CCN(CC3)CC4CN5C(=O)C=CC6=C5N4C(=O)C=N6)OCCC2
CACTVS 3.385O=C1C=CC2=C3N1C[CH](CN4CCC(CC4)NCc5cc6CCCOc6cn5)N3C(=O)C=N2
CACTVS 3.385O=C1C=CC2=C3N1C[C@@H](CN4CCC(CC4)NCc5cc6CCCOc6cn5)N3C(=O)C=N2
FormulaC24 H28 N6 O3
Name(3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione
ChEMBLCHEMBL3317856
DrugBankDB12134
ZINC
PDB chain6rks Chain G Residue 101 [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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PDB6rks Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		D82 M120
Binding residue
(residue number reindexed from 1)		D75 M113
Annotation score1
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003916 DNA topoisomerase activity
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0034335 DNA negative supercoiling activity
GO:0042802 identical protein binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006261 DNA-templated DNA replication
GO:0006265 DNA topological change
GO:0006351 DNA-templated transcription
GO:0009410 response to xenobiotic stimulus
GO:0046677 response to antibiotic
GO:0051276 chromosome organization
GO:2000104 negative regulation of DNA-templated DNA replication
Cellular Component
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009330 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
GO:0016020 membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6rks, PDBe:6rks, PDBj:6rks
PDBsum6rks
PubMed31666516
UniProtP0AES4|GYRA_ECOLI DNA gyrase subunit A (Gene Name=gyrA)

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