Structure of PDB 5npk Chain D Binding Site BS04

Receptor Information
>5npk Chain D (length=674) 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
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLNERNITSE
MRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKS
ARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDG
AAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNL
LANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPD
FPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQ
VNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVI
LNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRT
QYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKL
SEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQ
LVRDELTEIRDRFGDDRRTEIQLG
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 D Residue 1503 [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)		R630 I633 E634 A637 M1027 M1179 R1342 P1343
Binding residue
(residue number reindexed from 1)		R180 I183 E184 A187 M210 M362 R525 P526
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
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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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