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Showing Compound Nigrin B (FDB007040)

Record Information
Version1.0
Creation date2010-04-08 22:07:25 UTC
Update date2019-11-26 03:01:26 UTC
Primary IDFDB007040
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameNigrin B
DescriptionNigrin b, also known as rufocromomycin or nigrin, is a member of the class of compounds known as bipyridines and oligopyridines. Bipyridines and oligopyridines are organic compounds containing two pyridine rings linked to each other. Nigrin b is practically insoluble (in water) and a moderately acidic compound (based on its pKa). Nigrin b can be found in black elderberry, which makes nigrin b a potential biomarker for the consumption of this food product. rRNA N-glycosylase (EC 3.2.2.22, ribosomal ribonucleate N-glycosidase, nigrin b, RNA N-glycosidase, rRNA N-glycosidase, ricin, momorcochin-S, Mirabilis antiviral protein, gelonin, saporins) is an enzyme with systematic name rRNA N-glycohydrolase. This enzyme catalyses the following chemical reaction Hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from eukaryotic ribosomes .
CAS Number3930-19-6
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Predicted Properties
PropertyValueSource
Water Solubility0.04 g/LALOGPS
logP2.4ALOGPS
logP0.26ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)1.17ChemAxon
pKa (Strongest Basic)4.65ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area197.18 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity132.9 m³·mol⁻¹ChemAxon
Polarizability51.14 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC25H22N4O8
IUPAC name5-amino-6-(7-amino-6-methoxy-5,8-dioxo-5,8-dihydroquinolin-2-yl)-4-(2-hydroxy-3,4-dimethoxyphenyl)-3-methylpyridine-2-carboxylic acid
InChI IdentifierInChI=1S/C25H22N4O8/c1-9-14(10-6-8-13(35-2)23(36-3)20(10)30)15(26)19(29-17(9)25(33)34)12-7-5-11-18(28-12)22(32)16(27)24(37-4)21(11)31/h5-8,30H,26-27H2,1-4H3,(H,33,34)
InChI KeyPVYJZLYGTZKPJE-UHFFFAOYSA-N
Isomeric SMILESCOC1=CC=C(C(O)=C1OC)C1=C(N)C(=NC(C(O)=O)=C1C)C1=CC=C2C(=O)C(OC)=C(N)C(=O)C2=N1
Average Molecular Weight506.471
Monoisotopic Molecular Weight506.143763684
Classification
Description Belongs to the class of organic compounds known as bipyridines and oligopyridines. These are organic compounds containing two pyridine rings linked to each other.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassBipyridines and oligopyridines
Direct ParentBipyridines and oligopyridines
Alternative Parents
Substituents
  • 4-phenylpyridine
  • Quinoline quinone
  • Bipyridine
  • Methoxyphenol
  • Dihydroquinoline
  • Dimethoxybenzene
  • O-dimethoxybenzene
  • Pyridine carboxylic acid
  • Pyridine carboxylic acid or derivatives
  • Phenol ether
  • Phenoxy compound
  • Methoxybenzene
  • Anisole
  • Aryl ketone
  • Methylpyridine
  • Phenol
  • 1-hydroxy-4-unsubstituted benzenoid
  • Alkyl aryl ether
  • Aminopyridine
  • Monocyclic benzene moiety
  • Benzenoid
  • Heteroaromatic compound
  • Vinylogous amide
  • Vinylogous ester
  • Ketone
  • Amino acid or derivatives
  • Amino acid
  • Azacycle
  • Carboxylic acid derivative
  • Carboxylic acid
  • Enamine
  • Ether
  • Monocarboxylic acid or derivatives
  • Organopnictogen compound
  • Organic oxygen compound
  • Amine
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
OntologyNo ontology term
Physico-Chemical Properties
Physico-Chemical Properties - Experimental
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSNigrin B, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_2_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_2_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_2_6, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_2_7, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TMS_2_8, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_2_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_2_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_2_6, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_2_7, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSNigrin B, TBDMS_2_8, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-06rf-0000920000-870499c906f05730ab252016-08-02View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-0000900000-1c8a37effe344419c1bd2016-08-02View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01pc-0009400000-c8c623f4ea722fcabb4c2016-08-02View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-1001980000-e16188a5196f513195652016-08-03View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00dr-4000910000-b2810f813cbe8942e6bc2016-08-03View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-4002900000-417b569b19b1e81d662e2016-08-03View Spectrum
NMRNot Available
ChemSpider IDNot Available
ChEMBL IDNot Available
KEGG Compound IDNot Available
Pubchem Compound IDNot Available
Pubchem Substance IDNot Available
ChEBI IDNot Available
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDNot Available
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNIGRIN-B
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
Processing...
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference— Duke, James. 'Dr. Duke's Phytochemical and Ethnobotanical Databases. United States Department of Agriculture.' Agricultural Research Service, Accessed April 27 (2004).