Structure of PDB 7fvt Chain A Binding Site BS04

Receptor Information

>7fvt Chain A (length=670) Species: 158879 (Staphylococcus aureus subsp. aureus N315)

KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEK
ARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHI
RTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEH
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYNERNITSEMRE
SFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARI
VGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAA
MRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLAN
GASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPT
AGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNK
ARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNN
LYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYN
LRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEK
QAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVR
DELTEIRDRFGDDRRTEIQL

Ligand information

• Ligand ID: 6I0
• InChI: InChI=1S/C22H23ClN4O4/c23-17-3-1-2-14-8-13(9-16(14)17)10-24-7-6-15-11-27(22(29)31-15)19-5-4-18-21(25-19)26-20(28)12-30-18/h1-5,13,15,24H,6-12H2,(H,25,26,28)
• InChIKey: UEWSGKREJWLMAB-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Clc1cccc2C[C@H](CNCC[C@H]3CN(C(=O)O3)c4ccc5OCC(=O)Nc5n4)Cc12
  OpenEye OEToolkits 2.0.7: c1cc2c(c(c1)Cl)C[C@H](C2)CNCC[C@H]3CN(C(=O)O3)c4ccc5c(n4)NC(=O)CO5
  OpenEye OEToolkits 2.0.7: c1cc2c(c(c1)Cl)CC(C2)CNCCC3CN(C(=O)O3)c4ccc5c(n4)NC(=O)CO5
  ACDLabs 12.01: O=C1COc2ccc(nc2N1)N1CC(CCNCC2Cc3cccc(Cl)c3C2)OC1=O
  CACTVS 3.385: Clc1cccc2C[CH](CNCC[CH]3CN(C(=O)O3)c4ccc5OCC(=O)Nc5n4)Cc12
• Formula: C22 H23 Cl N4 O4
• Name: 6-{(5R)-5-[2-({[(2R)-4-chloro-2,3-dihydro-1H-inden-2-yl]methyl}amino)ethyl]-2-oxo-1,3-oxazolidin-3-yl}-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one
• PDB chain: 7fvt Chain D Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7fvt Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens.
• Resolution: 2.081 Å
• Binding residue (original residue number in PDB): A1068 G1072 M1075 D1083
• Binding residue (residue number reindexed from 1): A248 G252 M255 D263
• Annotation score: 1

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

External links

• PDB: RCSB:7fvt, PDBe:7fvt, PDBj:7fvt
• PDBsum: 7fvt
• PubMed: 37465290
• UniProt: P66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB);
  Q99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)