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- ChemComp-84D: Dibekacin -

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Basic information

EntryDatabase: PDB chemical components / ID: 84D
NameName: Dibekacin
Synonyms: (1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside
Commentantibiotic*YM

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Chemical information

Composition
Formula: C18H37N5O8 / Number of atoms: 68 / Formula weight: 451.515 / Formal charge: 0
Others

5u7y
PDB Unreleased entry

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: 84D / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5U7Y
History
Create componentDec 23, 2016
Initial releaseApr 11, 2018
Modify synonymsMar 13, 2021
External linksUniChem / ChemSpider / Brenda / ChEBI / ChEMBL / CompTox / DrugBank / Nikkaji / PubChem / PubChem_TPharma / SureChEMBL / ZINC / Wikipedia search / Google search

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Details

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SMILES

ACDLabs 12.01C3C(N)C(OC2C(N)CC(C(OC1OC(C(O)C(C1O)N)CO)C2O)N)OC(C3)CN
CACTVS 3.385NC[CH]1CC[CH](N)[CH](O1)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O
OpenEye OEToolkits 2.0.6C1CC(C(OC1CN)OC2C(CC(C(C2O)OC3C(C(C(C(O3)CO)O)N)O)N)N)N

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SMILES CANONICAL

CACTVS 3.385NC[C@@H]1CC[C@@H](N)[C@H](O1)O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O
OpenEye OEToolkits 2.0.6C1C[C@H]([C@H](O[C@@H]1CN)O[C@@H]2[C@H](C[C@H]([C@@H]([C@H]2O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)N)O)N)N)N

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InChI

InChI 1.03InChI=1S/C18H37N5O8/c19-4-6-1-2-7(20)17(28-6)30-15-8(21)3-9(22)16(14(15)27)31-18-13(26)11(23)12(25)10(5-24)29-18/h6-18,24-27H,1-5,19-23H2/t6-,7+,8-,9+,10+,11-,12+,13+,14-,15+,16-,17+,18+/m0/s1

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InChIKey

InChI 1.03JJCQSGDBDPYCEO-XVZSLQNASA-N

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SYSTEMATIC NAME

ACDLabs 12.01(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside
OpenEye OEToolkits 2.0.6(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},6~{S})-6-(aminomethyl)-3-azanyl-oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-4-azanyl-6-(hydroxymethyl)oxane-3,5-diol

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PDB entries

Showing all 3 items

PDB-6cav:
Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Dibekacin

PDB-8ifb:
Dibekacin-bound E.coli 70S ribosome in the PURE system

PDB-8ifd:
Dibekacin-added human 80S ribosome

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