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Record Information
Version2.0
Created at2021-01-06 06:49:13 UTC
Updated at2021-07-15 17:36:35 UTC
NP-MRD IDNP0021527
Secondary Accession NumbersNone
Natural Product Identification
Common NameLividomycin A
Provided ByNPAtlasNPAtlas Logo
DescriptionLividomycin A is also known as antibiotic 503-2 or lividomicina. Lividomycin A is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Lividomycin A is found in Streptomyces and Streptomyces lividus. Lividomycin A was first documented in 1971 (PMID: 5091208). Based on a literature review a small amount of articles have been published on Lividomycin A (PMID: 1047630) (PMID: 1052072) (PMID: 4142798) (PMID: 4203572).
Structure
Thumb
Synonyms
ValueSource
Antibiotic 503-2ChEBI
Antibiotic SF 767 aChEBI
LividomicinaChEBI
LividomycinChEBI
LividomycineChEBI
LividomycinumChEBI
MannosyldeoxyparomomycinChEBI
O-2-Amino-2,3-dideoxy-alpha-D-ribo-hexopyranosyl-(1-4)-O-(O-alpha-D-mannopyranosyl-(1-4)-O-2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl-(1-3)-beta-D-ribofuranosyl-(1-5))-2-deoxy-D-streptamineChEBI
Quintomycin bChEBI
SF 767 aChEBI
O-2-Amino-2,3-dideoxy-a-D-ribo-hexopyranosyl-(1-4)-O-(O-a-D-mannopyranosyl-(1-4)-O-2,6-diamino-2,6-dideoxy-b-L-idopyranosyl-(1-3)-b-D-ribofuranosyl-(1-5))-2-deoxy-D-streptamineGenerator
O-2-Amino-2,3-dideoxy-α-D-ribo-hexopyranosyl-(1-4)-O-(O-α-D-mannopyranosyl-(1-4)-O-2,6-diamino-2,6-dideoxy-β-L-idopyranosyl-(1-3)-β-D-ribofuranosyl-(1-5))-2-deoxy-D-streptamineGenerator
Chemical FormulaC29H55N5O18
Average Mass761.7697 Da
Monoisotopic Mass761.35421 Da
IUPAC 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,5S,6R)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-hydroxycyclohexyl]oxy}-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}-4-hydroxyoxan-3-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Namelividomycin A
CAS Registry NumberNot Available
SMILES
NC[C@@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O[C@@H]3[C@@H](O)[C@H](N)C[C@H](N)[C@H]3O[C@H]3O[C@H](CO)[C@@H](O)C[C@H]3N)[C@@H]2O)[C@H](N)[C@@H](O)[C@@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O
InChI Identifier
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
InChI KeyDBLVDAUGBTYDFR-SWMBIRFSSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
StreptomycesNPAtlas
Streptomyces lividusLOTUS Database
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a glycosidically linked to a pyranose of furanose unit at the C4- and C5-positions.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct Parent4,5-disubstituted 2-deoxystreptamines
Alternative Parents
Substituents
  • 4,5-disubstituted 2-deoxystreptamine
  • Disaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Aminocyclitol or derivatives
  • Cyclohexanol
  • Cyclohexylamine
  • Cyclitol or derivatives
  • Oxane
  • Tetrahydrofuran
  • Cyclic alcohol
  • Secondary alcohol
  • 1,2-aminoalcohol
  • Polyol
  • Acetal
  • Organoheterocyclic compound
  • Oxacycle
  • Primary alcohol
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organonitrogen compound
  • Organic nitrogen compound
  • Amine
  • Alcohol
  • Primary amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.9ALOGPS
logP-9.4ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)12.02ChemAxon
pKa (Strongest Basic)9.77ChemAxon
Physiological Charge5ChemAxon
Hydrogen Acceptor Count23ChemAxon
Hydrogen Donor Count15ChemAxon
Polar Surface Area406.24 ŲChemAxon
Rotatable Bond Count12ChemAxon
Refractivity165.56 m³·mol⁻¹ChemAxon
Polarizability74.39 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA021204
HMDB IDNot Available
DrugBank IDDB04728
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID65327
KEGG Compound IDC17707
BioCyc IDCPD-14175
BiGG IDNot Available
Wikipedia LinkLividomycin
METLIN IDNot Available
PubChem Compound72394
PDB IDNot Available
ChEBI ID71961
Good Scents IDNot Available
References
General References
  1. Oda T, Mori T, Ito H, Kunieda T, Munakata K: Studies on new antibiotic lividomycins. I. Taxonomic studies on the lividomycin-producing strain Streptomyces lividus nov. sp. J Antibiot (Tokyo). 1971 Jun;24(6):333-8. [PubMed:5091208 ]
  2. Marmo E, Cazzola M, Brita G, Paciello C: [In-vitro antibacterial activity of an aminoglucoside antibiotic: lividomycin A]. Arch Monaldi. 1975 Jul-Aug;30(4):287-310. [PubMed:1047630 ]
  3. Leroy A, Humbert G, Oksenhendler G, Fillastre JP: Comparative pharmacokinetics of lividomycin, amikacin and sisomicin in normal subjects and in uraemic patients. J Antimicrob Chemother. 1976 Dec;2(4):373-81. doi: 10.1093/jac/2.4.373. [PubMed:1052072 ]
  4. Shimizu T: Studies on lividomycin. I. In vitro antibacterial activities of LVDM against clinical isolates of Mycobacterium tuberculosis. Jpn J Antibiot. 1974 Dec;27(6):766-74. [PubMed:4142798 ]
  5. Kumazawa J, Momose S: Clinical effectiveness of lividomycin on urinary tract infections: evaluation with double-blind method. Curr Ther Res Clin Exp. 1973 Dec;15(12):873-901. [PubMed:4203572 ]