Structure of PDB 7fvs Chain B Binding Site BS05

Receptor Information
>7fvs Chain B (length=671) 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
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYNERNITSEMRE
SFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARI
VGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAA
MRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLAN
GASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPT
AGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNK
ARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNN
LYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYN
LRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEK
QAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVR
DELTEIRDRFGDDRRTEIQLG
Ligand information
Ligand ID61I
InChIInChI=1S/C22H21ClFN3O2/c23-22-17-6-13(5-15(17)3-4-25-22)10-27-11-14(12-27)9-26-19-8-21(28)29-20-2-1-16(24)7-18(19)20/h1-4,7-8,13-14,26H,5-6,9-12H2
InChIKeyHCXCXUYRFPJWRR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc2c(cc1F)C(=CC(=O)O2)NCC3CN(C3)CC4Cc5ccnc(c5C4)Cl
OpenEye OEToolkits 2.0.7c1cc2c(cc1F)C(=CC(=O)O2)NCC3CN(C3)C[C@@H]4Cc5ccnc(c5C4)Cl
CACTVS 3.385Fc1ccc2OC(=O)C=C(NCC3CN(C3)C[CH]4Cc5ccnc(Cl)c5C4)c2c1
ACDLabs 12.01Clc1nccc2CC(Cc21)CN1CC(C1)CNC1=CC(=O)Oc2ccc(F)cc21
CACTVS 3.385Fc1ccc2OC(=O)C=C(NCC3CN(C3)C[C@@H]4Cc5ccnc(Cl)c5C4)c2c1
FormulaC22 H21 Cl F N3 O2
Name4-{[(1-{[(6R)-1-chloro-6,7-dihydro-5H-cyclopenta[c]pyridin-6-yl]methyl}azetidin-3-yl)methyl]amino}-6-fluoro-2H-1-benzopyran-2-one
ChEMBL
DrugBank
ZINC
PDB chain7fvs Chain B Residue 1504 [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]
PDB7fvs Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens.
Resolution2.16 Å
Binding residue
(original residue number in PDB)		A1068 M1075 D1083
Binding residue
(residue number reindexed from 1)		A248 M255 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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7fvs, PDBe:7fvs, PDBj:7fvs
PDBsum7fvs
PubMed37465290
UniProtP66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB);
Q99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)

[Back to BioLiP]