Structure of PDB 6iy9 Chain A Binding Site BS01

Receptor Information
>6iy9 Chain A (length=325) Species: 1912 (Streptomyces hygroscopicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QESLLLLDRIDSDDSYASLRNDQEFWEPLARRALEELGLPVPPVLRVPGE
STNPVLVGEPGPVIKLFGEHWCGPESLASESEAYAVLADAPVPVPRLLGR
GELRPGTGAWPWPYLVMSRMTGTTWRSAMDGTTDRNALLALARELGRVLG
RLHRVPLTGNTVLTPHSEVFPELLRERRAATVEDHRGWGYLSPRLLDRLE
DWLPDVDTLLAGREPRFVHGDLHGTNIFVDLAATEVTGIVDFTDVYAGDS
RYSLVQLHLNAFRGDREILAALLDGAQWKRTEDFARELLAFTFLHDFEVF
EETPLDLSGFTDPEELAQFLWGPPD
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 chain6iy9 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6iy9 Structural basis for the substrate recognition of aminoglycoside 7''-phosphotransferase-Ia from Streptomyces hygroscopicus.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
W73 C74 E77 S78 D246 D298 F299 E300
Binding residue
(residue number reindexed from 1)
W71 C72 E75 S76 D244 D296 F297 E298
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.119: hygromycin-B 7''-O-kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008904 hygromycin-B 7''-O-phosphotransferase activity
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:6iy9, PDBe:6iy9, PDBj:6iy9
PDBsum6iy9
PubMed31475927
UniProtP09979|KHYB_STRHY Hygromycin-B 7''-O-kinase (Gene Name=hyg)

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