Structure of PDB 3u2d Chain B Binding Site BS01

Receptor Information
>3u2d Chain B (length=186) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEV
VIEKDNWIKVTDNGRGIPVDIQEGRPAVEVILTSSVVNALSQDLEVYVHR
NETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYET
LQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE
Ligand information
Ligand ID08B
InChIInChI=1S/C16H18BrN5O3/c1-10-12(17)9-13(19-10)16(23)20-11-4-7-21(8-5-11)15-14(22(24)25)3-2-6-18-15/h2-3,6,9,11,19H,4-5,7-8H2,1H3,(H,20,23)
InChIKeyAUXATGQLTJKTRN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Brc1cc(nc1C)C(=O)NC3CCN(c2ncccc2[N+]([O-])=O)CC3
OpenEye OEToolkits 1.7.2Cc1c(cc([nH]1)C(=O)NC2CCN(CC2)c3c(cccn3)[N+](=O)[O-])Br
CACTVS 3.370Cc1[nH]c(cc1Br)C(=O)NC2CCN(CC2)c3ncccc3[N+]([O-])=O
FormulaC16 H18 Br N5 O3
Name4-bromo-5-methyl-N-[1-(3-nitropyridin-2-yl)piperidin-4-yl]-1H-pyrrole-2-carboxamide
ChEMBL
DrugBank
ZINCZINC000098207776
PDB chain3u2d Chain B Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3u2d Pyrrolamide DNA gyrase inhibitors: fragment-based nuclear magnetic resonance screening to identify antibacterial agents.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		N54 E58 D81 R84 G85 I86 P87 I175
Binding residue
(residue number reindexed from 1)		N35 E39 D62 R65 G66 I67 P68 I131
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:0006265 DNA topological change

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Molecular Function
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Biological Process
External links
PDB RCSB:3u2d, PDBe:3u2d, PDBj:3u2d
PDBsum3u2d
PubMed22183167
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB)

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