Structure of PDB 5iwi Chain C Binding Site BS03

Receptor Information
>5iwi Chain C (length=481) Species: 158879 (Staphylococcus aureus subsp. aureus N315) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMT
PDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGN
FGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSV
LPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAEL
MEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRI
VVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVR
KDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQ
KTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAME
SLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETIL
ADEEVLLQLVRDELTEIRDRFGDDRRTEIQL
Ligand information
Ligand ID6EJ
InChIInChI=1S/C24H26FN5O3/c25-19-3-1-15-2-4-21(31)30-14-16(22(19)23(15)30)13-29-7-5-17(6-8-29)26-12-18-11-20-24(28-27-18)33-10-9-32-20/h1-4,11,16-17,26H,5-10,12-14H2/t16-/m1/s1
InChIKeySRICOHRDRMZREQ-MRXNPFEDSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1ccc2C=CC(=O)N3C[CH](CN4CCC(CC4)NCc5cc6OCCOc6nn5)c1c23
CACTVS 3.385Fc1ccc2C=CC(=O)N3C[C@@H](CN4CCC(CC4)NCc5cc6OCCOc6nn5)c1c23
OpenEye OEToolkits 2.0.4c1cc(c2c3c1C=CC(=O)N3CC2CN4CCC(CC4)NCc5cc6c(nn5)OCCO6)F
OpenEye OEToolkits 2.0.4c1cc(c2c3c1C=CC(=O)N3C[C@H]2CN4CCC(CC4)NCc5cc6c(nn5)OCCO6)F
ACDLabs 12.01c6c1c2c(C(CN2C(C=C1)=O)CN3CCC(CC3)NCc5cc4OCCOc4nn5)c(c6)F
FormulaC24 H26 F N5 O3
Name(1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
ChEMBLCHEMBL3793226
DrugBankDB15345
ZINCZINC000138115734
PDB chain5iwi Chain E 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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PDB5iwi Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		A68 G72 M75 D83
Binding residue
(residue number reindexed from 1)		A59 G63 M66 D74
Annotation score1
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:0006259 DNA metabolic process
GO:0006265 DNA topological change

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Molecular Function
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Biological Process
External links
PDB RCSB:5iwi, PDBe:5iwi, PDBj:5iwi
PDBsum5iwi
PubMed27055939
UniProtQ99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)

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