Structure of PDB 5npp Chain B Binding Site BS05

Receptor Information
>5npp Chain B (length=672) 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
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYINERNITSEMR
ESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSAR
IVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAA
AMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLA
NGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFP
TAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVN
KARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILN
NLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQY
NLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSE
KQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLV
RDELTEIRDRFGDDRRTEIQLG
Ligand information
Ligand ID94K
InChIInChI=1S/C20H19ClN2OS/c1-13-16(11-19(25-13)15-9-5-6-10-17(15)21)20(24)23-18(12-22)14-7-3-2-4-8-14/h2-11,18H,12,22H2,1H3,(H,23,24)/t18-/m0/s1
InChIKeyGEDDMFGBKRREEU-SFHVURJKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c(cc(s1)c2ccccc2Cl)C(=O)NC(CN)c3ccccc3
CACTVS 3.385Cc1sc(cc1C(=O)N[CH](CN)c2ccccc2)c3ccccc3Cl
OpenEye OEToolkits 2.0.6Cc1c(cc(s1)c2ccccc2Cl)C(=O)N[C@@H](CN)c3ccccc3
CACTVS 3.385Cc1sc(cc1C(=O)N[C@@H](CN)c2ccccc2)c3ccccc3Cl
FormulaC20 H19 Cl N2 O S
Name~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
ChEMBLCHEMBL4443422
DrugBank
ZINC
PDB chain5npp Chain B Residue 1502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5npp Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Resolution2.22 Å
Binding residue
(original residue number in PDB)		R630 I633 E634 A637 M1179 R1342 P1343
Binding residue
(residue number reindexed from 1)		R180 I183 E184 A187 M360 R523 P524
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:5npp, PDBe:5npp, PDBj:5npp
PDBsum5npp
PubMed28507124
UniProtP66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB);
Q99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)

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