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- ChemComp-84G: Arbekacin -

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Basic information

EntryDatabase: PDB chemical components / ID: 84G
NameName: Arbekacin
Synonyms: (2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide
Commentantibiotic*YM

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Chemical information

Composition
Formula: C22H44N6O10 / Number of atoms: 82 / Formula weight: 552.619 / Formal charge: 0
Others

5u8b
PDB Unreleased entry

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: 84G / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5U8B
History
Create componentDec 23, 2016
Initial releaseApr 11, 2018
Modify synonymsMar 13, 2021
External linksUniChem / ChemSpider / ChEBI / ChEMBL / ChemicalBook / CompTox / DrugBank / HMDB / 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 12.01C(CN)C(C(=O)NC3C(OC1OC(C(C(C1O)N)O)CO)C(O)C(OC2OC(CCC2N)CN)C(C3)N)O
CACTVS 3.385NCC[CH](O)C(=O)N[CH]1C[CH](N)[CH](O[CH]2O[CH](CN)CC[CH]2N)[CH](O)[CH]1O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O
OpenEye OEToolkits 2.0.6C1CC(C(OC1CN)OC2C(CC(C(C2O)OC3C(C(C(C(O3)CO)O)N)O)NC(=O)C(CCN)O)N)N

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SMILES CANONICAL

CACTVS 3.385NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)CC[C@H]2N)[C@H](O)[C@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O
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)NC(=O)[C@H](CCN)O)N)N

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InChI

InChI 1.03InChI=1S/C22H44N6O10/c23-4-3-12(30)20(34)28-11-5-10(26)18(37-21-9(25)2-1-8(6-24)35-21)17(33)19(11)38-22-16(32)14(27)15(31)13(7-29)36-22/h8-19,21-22,29-33H,1-7,23-27H2,(H,28,34)/t8-,9+,10-,11+,12-,13+,14-,15+,16+,17-,18+,19-,21+,22+/m0/s1

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InChIKey

InChI 1.03MKKYBZZTJQGVCD-XTCKQBCOSA-N

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SYSTEMATIC NAME

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

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PDB entries

Showing all 6 items

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

PDB-8ifc:
Arbekacin-bound E.coli 70S ribosome in the PURE system

PDB-8ife:
Arbekacin-added human 80S ribosome

PDB-9b4z:
E. coli 70S ribosome complex (N1-methylated 16S A1408 + arbekacin)

PDB-9b50:
E. coli 70S ribosome complex (unmethylated 16S A1408 + arbekacin)

PDB-9mkk:
Structure of arbekacin bound Escherichia coli 70S ribosome

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