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Record Information
Version2.0
Created at2020-12-09 01:32:50 UTC
Updated at2021-07-15 16:48:03 UTC
NP-MRD IDNP0004036
Secondary Accession NumbersNone
Natural Product Identification
Common NameApicidin D3
Provided ByNPAtlasNPAtlas Logo
Description(3S,6S,9S,15aR)-9-(butan-2-yl)-1,4,7-trihydroxy-3-(7-hydroxyoctyl)-6-[(1-methoxy-1H-indol-3-yl)methyl]-3H,6H,9H,10H,12H,13H,14H,15H,15aH-pyrido[1,2-a]1,4,7,10-tetraazacyclododecan-10-one belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. Apicidin D3 is found in Fusarium sp., Fusarium sp.ATCC74289 and Fusarium sp.ATCC74322. Based on a literature review very few articles have been published on (3S,6S,9S,15aR)-9-(butan-2-yl)-1,4,7-trihydroxy-3-(7-hydroxyoctyl)-6-[(1-methoxy-1H-indol-3-yl)methyl]-3H,6H,9H,10H,12H,13H,14H,15H,15aH-pyrido[1,2-a]1,4,7,10-tetraazacyclododecan-10-one.
Structure
Thumb
SynonymsNot Available
Chemical FormulaC34H51N5O6
Average Mass625.8110 Da
Monoisotopic Mass625.38393 Da
IUPAC Name(3S,6S,9S,15aR)-9-[(2R)-butan-2-yl]-3-[(7R)-7-hydroxyoctyl]-6-[(1-methoxy-1H-indol-3-yl)methyl]-tetradecahydro-1H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone
Traditional Name(3S,6S,9S,15aR)-9-[(2R)-butan-2-yl]-3-[(7R)-7-hydroxyoctyl]-6-[(1-methoxyindol-3-yl)methyl]-decahydro-2H-pyrido[1,2-a]1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrone
CAS Registry NumberNot Available
SMILES
CCC(C)[C@@H]1NC(=O)[C@H](CC2=CN(OC)C3=CC=CC=C23)NC(=O)[C@H](CCCCCCC(C)O)NC(=O)[C@H]2CCCCN2C1=O
InChI Identifier
InChI=1S/C34H51N5O6/c1-5-22(2)30-34(44)38-19-13-12-18-29(38)33(43)35-26(16-9-7-6-8-14-23(3)40)31(41)36-27(32(42)37-30)20-24-21-39(45-4)28-17-11-10-15-25(24)28/h10-11,15,17,21-23,26-27,29-30,40H,5-9,12-14,16,18-20H2,1-4H3,(H,35,43)(H,36,41)(H,37,42)/t22?,23?,26-,27-,29+,30-/m0/s1
InChI KeyPCPGDKJMCJKQBE-KUAULRTKSA-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
Fusarium sp.NPAtlas
Fusarium sp.ATCC74289Fungi
Fusarium sp.ATCC74322Fungi
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentOligopeptides
Alternative Parents
Substituents
  • Alpha-oligopeptide
  • Cyclic alpha peptide
  • Macrolactam
  • Alpha-amino acid or derivatives
  • 3-alkylindole
  • Indole
  • Indole or derivatives
  • Piperidine
  • Benzenoid
  • Substituted pyrrole
  • Heteroaromatic compound
  • Tertiary carboxylic acid amide
  • Pyrrole
  • Carboxamide group
  • Lactam
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Azacycle
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Alcohol
  • Organooxygen compound
  • Carbonyl group
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
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
logP3.38ALOGPS
logP3.09ChemAxon
logS-4.6ALOGPS
pKa (Strongest Acidic)10.85ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area142 ŲChemAxon
Rotatable Bond Count12ChemAxon
Refractivity172.32 m³·mol⁻¹ChemAxon
Polarizability69.94 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA009777
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID9127508
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10952288
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References