Structure of PDB 3u2d Chain A Binding Site BS01

Receptor Information
>3u2d Chain A (length=194) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGY
ANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQ
DLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTE
TTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE
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 A Residue 1 [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]
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
Binding residue
(residue number reindexed from 1)		N41 E45 D68 R71 G72 I73 P74
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

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

[Back to BioLiP]