Structure of PDB 2xct Chain B Binding Site BS04

Receptor Information
>2xct Chain B (length=669) 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
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNANERNITSEMRESF
LDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVG
DVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMR
FTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGA
SGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAG
LILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKAR
MIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLY
KQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLR
KAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQA
QAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDE
LTEIRDRFGDDRRTEIQLG
Ligand information
Ligand IDCPF
InChIInChI=1S/C17H18FN3O3/c18-13-7-11-14(8-15(13)20-5-3-19-4-6-20)21(10-1-2-10)9-12(16(11)22)17(23)24/h7-10,19H,1-6H2,(H,23,24)
InChIKeyMYSWGUAQZAJSOK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC(=O)C1=CN(C2CC2)c3cc(N4CCNCC4)c(F)cc3C1=O
ACDLabs 12.01O=C(O)C=3C(=O)c1c(cc(c(F)c1)N2CCNCC2)N(C=3)C4CC4
OpenEye OEToolkits 1.7.0c1c2c(cc(c1F)N3CCNCC3)N(C=C(C2=O)C(=O)O)C4CC4
FormulaC17 H18 F N3 O3
Name1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID;
ciprofloxacin
ChEMBLCHEMBL8
DrugBankDB00537
ZINCZINC000000020220
PDB chain2xct Chain G Residue 1020 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2xct Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents.
Resolution3.35 Å
Binding residue
(original residue number in PDB)		R458 S1084
Binding residue
(residue number reindexed from 1)		R42 S262
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.51,IC50=31uM
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:2xct, PDBe:2xct, PDBj:2xct
PDBsum2xct
PubMed20686482
UniProtP66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB);
Q99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)

[Back to BioLiP]