Structure of PDB 7mvs Chain A Binding Site BS04

Receptor Information
>7mvs Chain A (length=674) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVE
KARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAH
IRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPE
HRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYARINERNITS
EMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKK
SARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGD
GAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPN
LLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGP
DFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPF
QVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASV
ILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRR
TQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFK
LSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLL
QLVRDELTEIRDRFGDDRRTEIQL
Ligand information
Ligand IDY1W
InChIInChI=1S/C25H27FN2O6/c1-30-17-3-4-20-18(9-17)25(19(26)12-28-20)21(29)10-24-33-13-16(14-34-24)27-11-15-2-5-22-23(8-15)32-7-6-31-22/h2-5,8-9,12,16,21,24,27,29H,6-7,10-11,13-14H2,1H3/t16-,21-,24-/m0/s1
InChIKeyOWUGLCKBNARAPP-SWDVRCMSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COc1ccc2c(c1)c(c(cn2)F)C(CC3OCC(CO3)NCc4ccc5c(c4)OCCO5)O
CACTVS 3.385COc1ccc2ncc(F)c([C@@H](O)C[C@@H]3OC[C@H](CO3)NCc4ccc5OCCOc5c4)c2c1
ACDLabs 12.01OC(CC1OCC(CO1)NCc1ccc2OCCOc2c1)c1c2cc(OC)ccc2ncc1F
CACTVS 3.385COc1ccc2ncc(F)c([CH](O)C[CH]3OC[CH](CO3)NCc4ccc5OCCOc5c4)c2c1
OpenEye OEToolkits 2.0.7COc1ccc2c(c1)c(c(cn2)F)[C@H](CC3OCC(CO3)NCc4ccc5c(c4)OCCO5)O
FormulaC25 H27 F N2 O6
Name(1S)-2-[(2r,5S)-5-{[(2,3-dihydro-1,4-benzodioxin-6-yl)methyl]amino}-1,3-dioxan-2-yl]-1-(3-fluoro-6-methoxyquinolin-4-yl)ethan-1-ol
ChEMBL
DrugBank
ZINC
PDB chain7mvs Chain D Residue 101 [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]
PDB7mvs Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA.
Resolution2.60137 Å
Binding residue
(original residue number in PDB)		D284 M322
Binding residue
(residue number reindexed from 1)		D267 M305
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:7mvs, PDBe:7mvs, PDBj:7mvs
PDBsum7mvs
PubMed34614347
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB);
P20831

[Back to BioLiP]