ChemComp-LIV: (2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((...

Basic information

• Entry: Database: PDB chemical components / ID: LIV
• Name: Name: (2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-diamino-2-((2S,3R; Synonyms: LIVIDOMYCIN A
• Comment: antibiotic*YM

Chemical information

Composition

Formula: C₂₉H₅₅N₅O₁₈ / Number of atoms: 107 / Formula weight: 761.77 / Formal charge: 0

Others

2esj

Type: NON-POLYMER / PDB classification: HETAD / Three letter code: LIV / Model coordinates PDB-ID: 2ESJ

History

Create component	Nov 16, 2005
Modify descriptor	Jun 4, 2011
Modify synonyms	Jun 5, 2020

• External links: UniChem / ChemSpider / BindingDB / Brenda / ChEBI / ChEMBL / ChemicalBook / CompTox / DrugBank / KEGG_Ligand / Metabolights / NMRShiftDB / Nikkaji / PubChem / PubChem_TPharma / SureChEMBL / ZINC / Wikipedia search / Google search

Details

SMILES

• ACDLabs 10.04: O(C2C(OC1OC(CO)C(O)CC1N)C(N)CC(N)C2O)C5OC(C(OC4OC(CN)C(OC3OC(CO)C(O)C(O)C3O)C(O)C4N)C5O)CO
• CACTVS 3.341: NC[CH]1O[CH](O[CH]2[CH](O)[CH](O[CH]2CO)O[CH]3[CH](O)[CH](N)C[CH](N)[CH]3O[CH]4O[CH](CO)[CH](O)C[CH]4N)[CH](N)[CH](O)[CH]1O[CH]5O[CH](CO)[CH](O)[CH](O)[CH]5O
• OpenEye OEToolkits 1.5.0: C1C(C(C(C(C1N)OC2C(CC(C(O2)CO)O)N)OC3C(C(C(O3)CO)OC4C(C(C(C(O4)CN)OC5C(C(C(C(O5)CO)O)O)O)O)N)O)O)N

SMILES CANONICAL

• CACTVS 3.341: NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO)O[C@@H]3[C@@H](O)[C@H](N)C[C@H](N)[C@H]3O[C@H]4O[C@H](CO)[C@@H](O)C[C@H]4N)[C@H](N)[C@@H](O)[C@@H]1O[C@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]5O
• OpenEye OEToolkits 1.5.0: C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@@H](C[C@@H]([C@H](O2)CO)O)N)O[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O[C@@H]4[C@@H]([C@H]([C@@H]([C@@H](O4)CN)O[C@@H]5[C@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O)O)N)O)O)N

InChI

• InChI 1.03: InChI=1S/C29H55N5O18/c30-3-11-23(51-28-20(43)19(42)17(40)13(5-36)47-28)18(41)15(34)27(45-11)50-24-14(6-37)48-29(21(24)44)52-25-16(39)7(31)1-8(32)22(25)49-26-9(33)2-10(38)12(4-35)46-26/h7-29,35-44H,1-6,30-34H2/t7-,8+,9-,10+,11+,12-,13-,14-,15-,16+,17-,18-,19+,20+,21-,22-,23-,24-,25-,26-,27-,28-,29+/m1/s1

InChIKey

• InChI 1.03: DBLVDAUGBTYDFR-SWMBIRFSSA-N

SYSTEMATIC NAME

• ACDLabs 10.04: (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-{[alpha-D-mannopyranosyl-(1->4)-2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl-(1->3)-beta-D-ribofuranosyl]oxy}cyclohexyl 2-amino-2,3-dideoxy-alpha-D-ribo-hexopyranoside
• OpenEye OEToolkits 1.5.0: (2R,3S,4S,5S,6R)-2-[(2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(2R,3S,4R,5S)-5-[(1R,2R,3S,5R,6S)-3,5-diamino-2-[(2S,3R,5S,6R)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxy-cyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxy-oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol

PDB entries

Showing all 4 items

PDB-2esj:
Complex between Lividomycin A and the 16S-Rrna A Site

PDB-2fd0:
HIV-1 DIS kissing-loop in complex with lividomycin

PDB-3c5d:
Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycin

PDB-6cey:
Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Lividomycin moieties