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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:35:34 UTC
Update Date2022-03-07 02:52:28 UTC
HMDB IDHMDB0030228
Secondary Accession Numbers
  • HMDB30228
Metabolite Identification
Common NameNigakinone
DescriptionNigakinone, also known as methyl nigakinone, belongs to the class of organic compounds known as indolonaphthyridine alkaloids. These are a numerous and relatively straightforward subgroup of the b-carbolines, e.g. Canthin-6-one, in which an additional C3 unit is attached between C-1 and the indole nitrogen to form an additional ring. The group includes a few dimeric examples, such as Haplophytine. Nigakinone is a moderately basic compound (based on its pKa). Alkaloid from the wood of Picrasma excelsa (Jamaican quassiawood).
Structure
Data?1563861956
Synonyms
ValueSource
4,5-Dimethoxy-6H-indolo(3,2,1-de)(1,5)naphthyridin-6-oneHMDB
4,5-Dimethoxy-6H-indolo[3,2,1-de]-1,5-naphthyridin-6-oneHMDB
4,5-Dimethoxy-6H-indolo[3,2,1-de][1,5]naphthyridin-6-oneHMDB
5-Hydroxy-4-methoxy-6H-indolo[3,2,1-de][1,5]naphthyridin-6-one, 9ciHMDB
5-Hydroxy-4-methoxycanthin-6-oneHMDB
Methyl nigakinoneHMDB
Chemical FormulaC14H8N2O3
Average Molecular Weight252.2249
Monoisotopic Molecular Weight252.053492132
IUPAC Name3,4-dihydroxy-1,6-diazatetracyclo[7.6.1.0⁵,¹⁶.0¹⁰,¹⁵]hexadeca-3,5,7,9(16),10,12,14-heptaen-2-one
Traditional Name3,4-dihydroxy-1,6-diazatetracyclo[7.6.1.0⁵,¹⁶.0¹⁰,¹⁵]hexadeca-3,5,7,9(16),10,12,14-heptaen-2-one
CAS Registry Number18110-86-6
SMILES
OC1=C(O)C2=NC=CC3=C2N(C2=CC=CC=C32)C1=O
InChI Identifier
InChI=1S/C14H8N2O3/c17-12-10-11-8(5-6-15-10)7-3-1-2-4-9(7)16(11)14(19)13(12)18/h1-6,17-18H
InChI KeyXPMYKCPEDQIDCM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indolonaphthyridine alkaloids. These are a numerous and relatively straightforward subgroup of the b-carbolines, e.G. Canthin-6-one, in which an additional C3 unit is attached between C-1 and the indole nitrogen to form an additional ring. The group includes a few dimeric examples, such as Haplophytine.
KingdomOrganic compounds
Super ClassAlkaloids and derivatives
ClassIndolonaphthyridine alkaloids
Sub ClassNot Available
Direct ParentIndolonaphthyridine alkaloids
Alternative Parents
Substituents
  • Indolo[3,2-1de][1,5]naphthyridine
  • Beta-carboline
  • Pyridoindole
  • Diazanaphthalene
  • Naphthyridine
  • Indole
  • Indole or derivatives
  • Indolizine
  • Pyrrolopyridine
  • Hydroxypyridine
  • Pyridinone
  • Benzenoid
  • Pyridine
  • Vinylogous acid
  • Heteroaromatic compound
  • Pyrrole
  • Lactam
  • Organoheterocyclic compound
  • Azacycle
  • Organic oxide
  • Organonitrogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organopnictogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point223 - 224 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.59 g/LALOGPS
logP1.08ALOGPS
logP0.96ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)5.48ChemAxon
pKa (Strongest Basic)1.44ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area75.35 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity68.43 m³·mol⁻¹ChemAxon
Polarizability24.77 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-190.25630932474
DeepCCS[M+Na]+165.65530932474
AllCCS[M+H]+154.532859911
AllCCS[M+H-H2O]+150.432859911
AllCCS[M+NH4]+158.332859911
AllCCS[M+Na]+159.432859911
AllCCS[M-H]-157.132859911
AllCCS[M+Na-2H]-156.132859911
AllCCS[M+HCOO]-155.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
NigakinoneOC1=C(O)C2=NC=CC3=C2N(C2=CC=CC=C32)C1=O3455.8Standard polar33892256
NigakinoneOC1=C(O)C2=NC=CC3=C2N(C2=CC=CC=C32)C1=O2612.5Standard non polar33892256
NigakinoneOC1=C(O)C2=NC=CC3=C2N(C2=CC=CC=C32)C1=O2602.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Nigakinone,1TMS,isomer #1C[Si](C)(C)OC1=C(O)C2=NC=CC3=C2N(C1=O)C1=CC=CC=C312978.2Semi standard non polar33892256
Nigakinone,1TMS,isomer #2C[Si](C)(C)OC1=C(O)C(=O)N2C3=CC=CC=C3C3=C2C1=NC=C32910.1Semi standard non polar33892256
Nigakinone,2TMS,isomer #1C[Si](C)(C)OC1=C(O[Si](C)(C)C)C2=NC=CC3=C2N(C1=O)C1=CC=CC=C312928.9Semi standard non polar33892256
Nigakinone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=C(O)C2=NC=CC3=C2N(C1=O)C1=CC=CC=C313153.9Semi standard non polar33892256
Nigakinone,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC1=C(O)C(=O)N2C3=CC=CC=C3C3=C2C1=NC=C33118.2Semi standard non polar33892256
Nigakinone,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)C2=NC=CC3=C2N(C1=O)C1=CC=CC=C313327.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Nigakinone GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-0390000000-310c3ad20c019421e7032017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nigakinone GC-MS (2 TMS) - 70eV, Positivesplash10-00e9-3119000000-2f52b75ab4ef56a40c112017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nigakinone GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 10V, Positive-QTOFsplash10-0udi-0090000000-ffd4ff1b19deb16890a42016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 20V, Positive-QTOFsplash10-0udi-0090000000-c87f98c9d0149a1aa4de2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 40V, Positive-QTOFsplash10-014i-0900000000-d5b59f6be190aca23a652016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 10V, Negative-QTOFsplash10-0udi-0290000000-3a9284f6f8845f17905e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 20V, Negative-QTOFsplash10-0udi-0590000000-8650ba377405918ee49f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 40V, Negative-QTOFsplash10-014i-0900000000-46d0ce11b863d98113482016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 10V, Negative-QTOFsplash10-0udi-0090000000-eb7c2ff7d3762b310f842021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 20V, Negative-QTOFsplash10-0udi-0190000000-c3a3700c91cde77e4c6c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 40V, Negative-QTOFsplash10-014l-0900000000-fc190407fe92bb1193ec2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 10V, Positive-QTOFsplash10-0udi-0090000000-bff44a744dc6d7c2d8652021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 20V, Positive-QTOFsplash10-0udi-0090000000-bff44a744dc6d7c2d8652021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nigakinone 40V, Positive-QTOFsplash10-00kb-0930000000-6b3731402c27a24cf8142021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB002047
KNApSAcK IDNot Available
Chemspider ID30776821
KEGG Compound IDC16996
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound137185901
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .