Structure of PDB 4plb Chain B Binding Site BS03

Receptor Information
>4plb Chain B (length=672) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEK
ARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHI
RTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEH
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANERNITSEMR
ESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSAR
IVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAA
AMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLA
NGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFP
TAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVN
KARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILN
NLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQY
NLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSE
KQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLV
RDELTEIRDRFGDDRRTEIQLG
Ligand information
Ligand ID31N
InChIInChI=1S/C26H28FN5O5/c1-35-22-5-3-18-23(32-22)16(17(27)12-28-18)10-20(33)26-8-6-25(7-9-26,14-37-26)29-11-15-2-4-19-24(30-15)31-21(34)13-36-19/h2-5,12,20,29,33H,6-11,13-14H2,1H3,(H,30,31,34)/t20-,25-,26-/m0/s1
InChIKeyJWCUKLIKGBNEKA-XZZVZQAVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2COc1ccc2c(n1)c(c(cn2)F)C[C@@H](C34CCC(CC3)(CO4)NCc5ccc6c(n5)NC(=O)CO6)O
ACDLabs 12.01Fc2cnc1c(nc(OC)cc1)c2CC(O)C56OCC(NCc4nc3c(OCC(=O)N3)cc4)(CC5)CC6
CACTVS 3.385COc1ccc2ncc(F)c(C[C@H](O)C34CCC(CC3)(CO4)NCc5ccc6OCC(=O)Nc6n5)c2n1
OpenEye OEToolkits 1.9.2COc1ccc2c(n1)c(c(cn2)F)CC(C34CCC(CC3)(CO4)NCc5ccc6c(n5)NC(=O)CO6)O
CACTVS 3.385COc1ccc2ncc(F)c(C[CH](O)C34CCC(CC3)(CO4)NCc5ccc6OCC(=O)Nc6n5)c2n1
FormulaC26 H28 F N5 O5
Name6-[({(1r,4S)-1-[(1S)-2-(3-fluoro-6-methoxy-1,5-naphthyridin-4-yl)-1-hydroxyethyl]-2-oxabicyclo[2.2.2]oct-4-yl}amino)methyl]-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one
ChEMBL
DrugBank
ZINC
PDB chain4plb Chain F 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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PDB4plb Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad spectrum antibacterial agents.
Resolution2.69 Å
Binding residue
(original residue number in PDB)		A1068 M1121
Binding residue
(residue number reindexed from 1)		A249 M302
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4plb, PDBe:4plb, PDBj:4plb
PDBsum4plb
PubMed24900889
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB);
P20831

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