Structure of PDB 5bs3 Chain D Binding Site BS04

Receptor Information
>5bs3 Chain D (length=670) Species: 1280 (Staphylococcus aureus) [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 IDWCP
InChIInChI=1S/C26H26FN5O5/c27-16-10-28-17-2-4-20(34)32-13-26(35,21(16)22(17)32)12-25-7-5-24(6-8-25,14-37-25)29-9-15-1-3-18-23(30-15)31-19(33)11-36-18/h1-4,10,29,35H,5-9,11-14H2,(H,30,31,33)/t24-,25-,26-/m0/s1
InChIKeyXTHQMKOHGLBSON-GSDHBNRESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc2c(nc1CNC34CCC(CC3)(OC4)C[C@@]5(CN6c7c5c(cnc7C=CC6=O)F)O)NC(=O)CO2
CACTVS 3.385O[C@]1(CN2C(=O)C=Cc3ncc(F)c1c23)CC45CCC(CC4)(CO5)NCc6ccc7OCC(=O)Nc7n6
ACDLabs 12.01O=C5C=Cc7ncc(c6C(O)(CC21OCC(CC1)(CC2)NCc4nc3NC(=O)COc3cc4)CN5c67)F
OpenEye OEToolkits 1.9.2c1cc2c(nc1CNC34CCC(CC3)(OC4)CC5(CN6c7c5c(cnc7C=CC6=O)F)O)NC(=O)CO2
CACTVS 3.385O[C]1(CN2C(=O)C=Cc3ncc(F)c1c23)CC45CCC(CC4)(CO5)NCc6ccc7OCC(=O)Nc7n6
FormulaC26 H26 F N5 O5
Name(4R)-3-fluoro-4-hydroxy-4-{[(1r,4R)-4-{[(3-oxo-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-6-yl)methyl]amino}-2-oxabicyclo[2.2.2]oct-1-yl]methyl}-4,5-dihydro-7H-pyrrolo[3,2,1-de][1,5]naphthyridin-7-one
ChEMBL
DrugBank
ZINC
PDB chain5bs3 Chain F Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5bs3 Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2).
Resolution2.65 Å
Binding residue
(original residue number in PDB)
A1068 G1072 D1083
Binding residue
(residue number reindexed from 1)
A248 G252 D263
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:5bs3, PDBe:5bs3, PDBj:5bs3
PDBsum5bs3
PubMed25851938
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB);
P20831

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