Structure of PDB 5npk Chain B Binding Site BS05

Receptor Information
>5npk Chain B (length=673) 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
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANNERNITSEM
RESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSA
RIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGA
AAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLL
ANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDF
PTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQV
NKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVIL
NNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQ
YNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLS
EKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQL
VRDELTEIRDRFGDDRRTEIQLG
Ligand information
Ligand ID94H
InChIInChI=1S/C20H18N4OS/c21-10-17(13-5-2-1-3-6-13)24-20(25)18-9-14(12-26-18)16-11-23-19-15(16)7-4-8-22-19/h1-9,11-12,17H,10,21H2,(H,22,23)(H,24,25)/t17-/m0/s1
InChIKeyZNBOMXQVNVLXCZ-KRWDZBQOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)[C@H](CN)NC(=O)c2cc(cs2)c3c[nH]c4c3cccn4
CACTVS 3.385NC[CH](NC(=O)c1scc(c1)c2c[nH]c3ncccc23)c4ccccc4
CACTVS 3.385NC[C@H](NC(=O)c1scc(c1)c2c[nH]c3ncccc23)c4ccccc4
OpenEye OEToolkits 2.0.6c1ccc(cc1)C(CN)NC(=O)c2cc(cs2)c3c[nH]c4c3cccn4
FormulaC20 H18 N4 O S
Name~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide
ChEMBL
DrugBank
ZINCZINC000040395520
PDB chain5npk Chain B Residue 1506 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5npk Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		I1386 D1389 H1390 E1393 R1414 F1415
Binding residue
(residue number reindexed from 1)		I568 D571 H572 E575 R596 F597
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5npk, PDBe:5npk, PDBj:5npk
PDBsum5npk
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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