Structure of PDB 5cdo Chain D Binding Site BS04

Receptor Information
>5cdo Chain D (length=188) 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
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAV
Ligand information
Ligand ID53L
InChIInChI=1S/C17H18N4O6/c1-8-7-20-12-4-3-11(21(25)26)5-10(12)6-17(13(20)9(2)27-8)14(22)18-16(24)19-15(17)23/h3-5,8-9,13H,6-7H2,1-2H3,(H2,18,19,22,23,24)/t8-,9+,13-/m1/s1
InChIKeyDJZPHYIXNUOVJU-VYUIOLGVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC1CN2c3ccc(cc3CC4(C2C(O1)C)C(=O)NC(=O)N=C4O)N(=O)=O
OpenEye OEToolkits 1.9.2C[C@@H]1CN2c3ccc(cc3C[C@@]4([C@H]2[C@@H](O1)C)C(=O)NC(=O)N=C4O)N(=O)=O
ACDLabs 12.01C13C(OC(CN1c2ccc(N(=O)=O)cc2CC34C(O)=NC(NC4=O)=O)C)C
CACTVS 3.385C[C@@H]1CN2[C@H]([C@H](C)O1)[C@]3(Cc4cc(ccc24)[N](=O)=O)C(=O)NC(=O)N=C3O
CACTVS 3.385C[CH]1CN2[CH]([CH](C)O1)[C]3(Cc4cc(ccc24)[N](=O)=O)C(=O)NC(=O)N=C3O
FormulaC17 H18 N4 O6
Name(2R,4S,4aS,5S)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione
ChEMBLCHEMBL1276314
DrugBank
ZINCZINC000003943078
PDB chain5cdo Chain F Residue 2101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5cdo Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		G436 R458 G459
Binding residue
(residue number reindexed from 1)		G20 R42 G43
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:0006265 DNA topological change

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5cdo, PDBe:5cdo, PDBj:5cdo
PDBsum5cdo
PubMed26640131
UniProtP66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB)

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