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Record Information
Version2.0
Created at2021-01-06 00:11:39 UTC
Updated at2021-07-15 17:18:58 UTC
NP-MRD IDNP0015075
Secondary Accession NumbersNone
Natural Product Identification
Common NameVineomycin B2
Provided ByNPAtlasNPAtlas Logo
Description Vineomycin B2 is found in Streptomyces. Vineomycin B2 was first documented in 2008 (PMID: 18785743). Based on a literature review very few articles have been published on 4-{1,5-dihydroxy-6-[4-hydroxy-6-methyl-5-({6-methyl-5-[(6-methyl-5-oxo-5,6-dihydro-2H-pyran-2-yl)oxy]oxan-2-yl}oxy)oxan-2-yl]-9,10-dioxo-9,10-dihydroanthracen-2-yl}-3-methyl-3-({6-methyl-5-[(6-methyl-5-oxo-5,6-dihydro-2H-pyran-2-yl)oxy]oxan-2-yl}oxy)butanoic acid (PMID: 28223690) (PMID: 24074200).
Structure
Thumb
Synonyms
ValueSource
4-{1,5-dihydroxy-6-[4-hydroxy-6-methyl-5-({6-methyl-5-[(6-methyl-5-oxo-5,6-dihydro-2H-pyran-2-yl)oxy]oxan-2-yl}oxy)oxan-2-yl]-9,10-dioxo-9,10-dihydroanthracen-2-yl}-3-methyl-3-({6-methyl-5-[(6-methyl-5-oxo-5,6-dihydro-2H-pyran-2-yl)oxy]oxan-2-yl}oxy)butanoateGenerator
Chemical FormulaC49H58O18
Average Mass934.9850 Da
Monoisotopic Mass934.36232 Da
IUPAC Name(3S)-4-{1,5-dihydroxy-6-[(2R,4R,5R,6R)-4-hydroxy-6-methyl-5-{[(2R,5R,6S)-6-methyl-5-{[(2S,6S)-6-methyl-5-oxo-5,6-dihydro-2H-pyran-2-yl]oxy}oxan-2-yl]oxy}oxan-2-yl]-9,10-dioxo-9,10-dihydroanthracen-2-yl}-3-methyl-3-{[(2S,5S,6R)-6-methyl-5-{[(2R,6R)-6-methyl-5-oxo-5,6-dihydro-2H-pyran-2-yl]oxy}oxan-2-yl]oxy}butanoic acid
Traditional Name(3S)-4-{1,5-dihydroxy-6-[(2R,4R,5R,6R)-4-hydroxy-6-methyl-5-{[(2R,5R,6S)-6-methyl-5-{[(2S,6S)-6-methyl-5-oxo-2,6-dihydropyran-2-yl]oxy}oxan-2-yl]oxy}oxan-2-yl]-9,10-dioxoanthracen-2-yl}-3-methyl-3-{[(2S,5S,6R)-6-methyl-5-{[(2R,6R)-6-methyl-5-oxo-2,6-dihydropyran-2-yl]oxy}oxan-2-yl]oxy}butanoic acid
CAS Registry NumberNot Available
SMILES
CC1OC(CCC1OC1OC(C)C(=O)C=C1)OC1C(C)OC(CC1O)C1=C(O)C2=C(C=C1)C(=O)C1=C(C=CC(CC(C)(CC(O)=O)OC3CCC(OC4OC(C)C(=O)C=C4)C(C)O3)=C1O)C2=O
InChI Identifier
InChI=1S/C49H58O18/c1-22-31(50)11-15-38(60-22)64-34-13-17-40(62-24(34)3)66-48-26(5)59-36(19-33(48)52)28-9-10-30-43(45(28)56)47(58)29-8-7-27(44(55)42(29)46(30)57)20-49(6,21-37(53)54)67-41-18-14-35(25(4)63-41)65-39-16-12-32(51)23(2)61-39/h7-12,15-16,22-26,33-36,38-41,48,52,55-56H,13-14,17-21H2,1-6H3,(H,53,54)
InChI KeyNIXHEPPGVVKFMQ-UHFFFAOYSA-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
Chemical Taxonomy
ClassificationNot classified
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
logP3.5ALOGPS
logP7.3ChemAxon
logS-4.9ALOGPS
pKa (Strongest Acidic)3.49ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area249.34 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity236.38 m³·mol⁻¹ChemAxon
Polarizability99.48 ųChemAxon
Number of Rings8ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA010401
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78444165
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound78174182
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Zhu X, Duan Y, Cui Z, Wang Z, Li Z, Zhang Y, Ju J, Huang H: Cytotoxic rearranged angucycline glycosides from deep sea-derived Streptomyces lusitanus SCSIO LR32. J Antibiot (Tokyo). 2017 Jul;70(7):819-822. doi: 10.1038/ja.2017.17. Epub 2017 Feb 22. [PubMed:28223690 ]
  2. Kusumi S, Tomono S, Okuzawa S, Kaneko E, Ueda T, Sasaki K, Takahashi D, Toshima K: Total synthesis of vineomycin B2. J Am Chem Soc. 2013 Oct 23;135(42):15909-12. doi: 10.1021/ja407827n. Epub 2013 Oct 11. [PubMed:24074200 ]
  3. Yu X, O'Doherty GA: De novo asymmetric synthesis and biological evaluation of the trisaccharide portion of PI-080 and vineomycin B2. Org Lett. 2008 Oct 16;10(20):4529-32. doi: 10.1021/ol801817f. Epub 2008 Sep 12. [PubMed:18785743 ]