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- ChemComp-EDS: (2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-{[... -

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Basic information

EntryDatabase: PDB chemical components / ID: EDS
NameName: (2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-{[(2-hydroxyethyl)amino]methyl}-3,4-dihydro-2H-pyran-2-y
Synonyms: plazomicin
Commentantibiotic*YM

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Chemical information

Composition
Formula: C25H48N6O10 / Number of atoms: 89 / Formula weight: 592.683 / Formal charge: 0
Others

6c0c
PDB Unreleased entry

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: EDS / Ideal coordinates details: Corina / Model coordinates PDB-ID: 6C0C
History
Create componentJan 2, 2018
Initial releaseJan 31, 2018
Modify synonymsJun 5, 2020
External linksUniChem / ChemSpider / DailyMed / DrugBank / GtoPharmacology / Nikkaji / PubChem / PubChem_TPharma / 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 12.01C1(C(NC(=O)C(CCN)O)CC(C(C1O)OC2C(CC=C(O2)CNCCO)N)N)OC3C(C(NC)C(O)(CO3)C)O
CACTVS 3.385CN[CH]1[CH](O)[CH](OC[C]1(C)O)O[CH]2[CH](O)[CH](O[CH]3OC(=CC[CH]3N)CNCCO)[CH](N)C[CH]2NC(=O)[CH](O)CCN
OpenEye OEToolkits 2.0.6CC1(COC(C(C1NC)O)OC2C(CC(C(C2O)OC3C(CC=C(O3)CNCCO)N)N)NC(=O)C(CCN)O)O

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SMILES CANONICAL

CACTVS 3.385CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@@H]2[C@@H](O)[C@H](O[C@H]3OC(=CC[C@H]3N)CNCCO)[C@@H](N)C[C@H]2NC(=O)[C@@H](O)CCN
OpenEye OEToolkits 2.0.6C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H](CC=C(O3)CNCCO)N)N)NC(=O)[C@H](CCN)O)O

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InChI

InChI 1.03InChI=1S/C25H48N6O10/c1-25(37)11-38-24(18(35)21(25)29-2)41-20-15(31-22(36)16(33)5-6-26)9-14(28)19(17(20)34)40-23-13(27)4-3-12(39-23)10-30-7-8-32/h3,13-21,23-24,29-30,32-35,37H,4-11,26-28H2,1-2H3,(H,31,36)/t13-,14+,15-,16+,17+,18-,19-,20+,21-,23-,24-,25+/m1/s1

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InChIKey

InChI 1.03IYDYFVUFSPQPPV-PEXOCOHZSA-N

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SYSTEMATIC NAME

ACDLabs 12.01(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-{[(2-hydroxyethyl)amino]methyl}-3,4-dihydro-2H-pyran-2-yl]oxy}-2-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide
OpenEye OEToolkits 2.0.6(2~{S})-4-azanyl-~{N}-[(1~{R},2~{S},3~{S},4~{R},5~{S})-5-azanyl-4-[[(2~{S},3~{R})-3-azanyl-6-[(2-hydroxyethylamino)methyl]-3,4-dihydro-2~{H}-pyran-2-yl]oxy]-2-[(2~{R},3~{R},4~{R},5~{R})-5-methyl-4-(methylamino)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-2-oxidanyl-butanamide

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PDB entries

Showing all 2 items

PDB-6cd7:
Crystal structure of APH(2")-IVa in complex with plazomicin

PDB-7lh5:
Crystal structure of the Thermus thermophilus 70S ribosome in complex with plazomicin, mRNA and tRNAs

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