Structure of PDB 5cdq Chain S Binding Site BS04

Receptor Information
>5cdq Chain S (length=193) Species: 158879 (Staphylococcus aureus subsp. aureus N315) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILN
VEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDG
AHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMN
PEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYA
Ligand information
Ligand IDMFX
InChIInChI=1S/C21H24FN3O4/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11-3-2-6-23-16(11)10-24/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28)/t11-,16+/m0/s1
InChIKeyFABPRXSRWADJSP-MEDUHNTESA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(O)=O
CACTVS 3.341COc1c(N2C[CH]3CCCN[CH]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(O)=O
ACDLabs 10.04Fc2cc1C(=O)C(C(=O)O)=CN(c1c(OC)c2N4CC3CCCNC3C4)C5CC5
OpenEye OEToolkits 1.5.0COc1c2c(cc(c1N3CC4CCCNC4C3)F)C(=O)C(=CN2C5CC5)C(=O)O
OpenEye OEToolkits 1.5.0COc1c2c(cc(c1N3C[C@@H]4CCCN[C@@H]4C3)F)C(=O)C(=CN2C5CC5)C(=O)O
FormulaC21 H24 F N3 O4
Name1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid;
moxifloxacin
ChEMBLCHEMBL32
DrugBankDB00218
ZINCZINC000003826253
PDB chain5cdq Chain V Residue 2101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5cdq Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		R458 G459
Binding residue
(residue number reindexed from 1)		R45 G46
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5cdq, PDBe:5cdq, PDBj:5cdq
PDBsum5cdq
PubMed26640131
UniProtP66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB)

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