Structure of PDB 3w0q Chain A Binding Site BS02

Receptor Information
>3w0q Chain A (length=296) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATSVEKFLIEKFGSVSDLMQLSEGEESRAFSFDVGGRGYVLRVNSCADGF
YKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLPETE
LPAVLQPVAEVMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADP
HVYHWQTVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNAVLTD
NGRITAVIDWSEAMFGDPLYEVANIFFWRPWLACMEQQARYFERRHPELA
GSPRLRAYMLRIGLDQLYQSLVDGNFDDAAWAQGRCDAIVRSGAGT
Ligand information
Ligand IDHY0
InChIInChI=1S/C20H37N3O13/c1-23-7-2-5(21)9(26)15(10(7)27)33-19-17-16(11(28)8(4-25)32-19)35-20(36-17)18(31)13(30)12(29)14(34-20)6(22)3-24/h5-19,23-31H,2-4,21-22H2,1H3/t5-,6+,7+,8-,9+,10-,11+,12-,13+,14-,15-,16+,17+,18-,19+,20-/m1/s1
InChIKeyGRRNUXAQVGOGFE-XFOBNZBXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CNC1CC(C(C(C1O)OC2C3C(C(C(O2)CO)O)OC4(O3)C(C(C(C(O4)C(CO)N)O)O)O)O)N
OpenEye OEToolkits 1.7.0CN[C@H]1C[C@H]([C@@H]([C@H]([C@@H]1O)O[C@H]2[C@@H]3[C@H]([C@H]([C@H](O2)CO)O)O[C@@]4(O3)[C@@H]([C@H]([C@H]([C@H](O4)[C@H](CO)N)O)O)O)O)N
ACDLabs 12.01O1C4C(OC12OC(C(O)C(O)C2O)C(N)CO)C(O)C(OC4OC3C(O)C(N)CC(NC)C3O)CO
CACTVS 3.370CN[CH]1C[CH](N)[CH](O)[CH](O[CH]2O[CH](CO)[CH](O)[CH]3O[C]4(O[CH]([CH](N)CO)[CH](O)[CH](O)[CH]4O)O[CH]23)[CH]1O
CACTVS 3.370CN[C@H]1C[C@@H](N)[C@H](O)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@@H]3O[C@@]4(O[C@H]([C@@H](N)CO)[C@H](O)[C@H](O)[C@H]4O)O[C@H]23)[C@@H]1O
FormulaC20 H37 N3 O13
NameHYGROMYCIN B VARIANT;
(2R,3'R,3aS,4S,4'S,5'R,6R,6'R,7S,7aS)-4-[(1R,2S,3R,5S,6R)-3-azanyl-2,6-dihydroxy-5-(methylamino)cyclohexyl]oxy-6'-[(1S) -1-azanyl-2-hydroxy-ethyl]-6-(hydroxymethyl)spiro[4,6,7,7a-tetrahydro-3aH-[1,3]dioxolo[4,5-c]pyran-2,2'-oxane]-3',4',5', 7-tetrol
ChEMBL
DrugBank
ZINCZINC000043860491
PDB chain3w0q Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3w0q Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant.
Resolution1.8 Å
Binding residue
(original residue number in PDB)
Q101 D198 S201 N202 N231 W235 W238 L239 D285
Binding residue
(residue number reindexed from 1)
Q94 D191 S194 N195 N224 W228 W231 L232 D278
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.163: hygromycin B 4-O-kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
Biological Process
GO:0016310 phosphorylation
GO:0046677 response to antibiotic

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:3w0q, PDBe:3w0q, PDBj:3w0q
PDBsum3w0q
PubMed23747390
UniProtP00557|KHYB_ECOLX Hygromycin-B 4-O-kinase (Gene Name=hph)

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