Structure of PDB 2xcs Chain D Binding Site BS04

Receptor Information
>2xcs Chain D (length=670) Species: 158879 (Staphylococcus aureus subsp. aureus N315) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEK
ARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHI
RTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEH
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYNERNITSEMRE
SFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARI
VGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAA
MRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLAN
GASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPT
AGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNK
ARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNN
LYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYN
LRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEK
QAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVR
DELTEIRDRFGDDRRTEIQL
Ligand information
Ligand IDRXV
InChIInChI=1S/C25H27N5O2S/c1-31-20-2-3-23-22(11-20)21(17(12-26)13-29-23)6-9-30-7-4-18(5-8-30)27-14-19-10-25-24(15-28-19)32-16-33-25/h2-3,10-11,13,15,18,27H,4-9,14,16H2,1H3
InChIKeyNKXJSCXEAVZSMF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1COc1ccc2c(c1)c(c(cn2)C#N)CCN3CCC(CC3)NCc4cc5c(cn4)OCS5
CACTVS 3.352COc1ccc2ncc(C#N)c(CCN3CCC(CC3)NCc4cc5SCOc5cn4)c2c1
ACDLabs 10.04N#Cc2cnc1c(cc(OC)cc1)c2CCN5CCC(NCc3ncc4OCSc4c3)CC5
FormulaC25 H27 N5 O2 S
Name6-METHOXY-4-(2-{4-[([1,3]OXATHIOLO[5,4-C]PYRIDIN-6-YLMETHYL)AMINO]PIPERIDIN-1-YL}ETHYL)QUINOLINE-3-CARBONITRILE
ChEMBLCHEMBL1235773
DrugBank
ZINCZINC000058650072
PDB chain2xcs Chain F Residue 1021 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2xcs Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		D1083 M1121
Binding residue
(residue number reindexed from 1)		D263 M301
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.85,IC50=14nM
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:2xcs, PDBe:2xcs, PDBj:2xcs
PDBsum2xcs
PubMed20686482
UniProtP66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB);
Q99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)

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