Structure of PDB 3tyk Chain A Binding Site BS01

Receptor Information
>3tyk 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]
TATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRGYVLRVNSCADG
FYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLPET
ELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIAD
PHVYHWQTVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLT
DNGRITAVIDWSEAMFGDSQYEVANIFFWRPWLACMEQQTRYFERRHPEL
AGSPRLRAYMLRIGLDQLYQSLVDGNFDDAAWAQGRCDAIVRSGAG
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 chain3tyk Chain A Residue 342 [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]
PDB3tyk Structure and function of APH(4)-Ia, a hygromycin B resistance enzyme.
Resolution1.95 Å
Binding residue
(original residue number in PDB)
Q101 D198 S201 N231 W235 W238 L239 D285
Binding residue
(residue number reindexed from 1)
Q95 D192 S195 N225 W229 W232 L233 D279
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:3tyk, PDBe:3tyk, PDBj:3tyk
PDBsum3tyk
PubMed21084294
UniProtP00557|KHYB_ECOLX Hygromycin-B 4-O-kinase (Gene Name=hph)

[Back to BioLiP]