ChemFOnt: Showing chemical card for Nigrin B (CFc000334564)

Record Information

Version

1.0

Creation Date

Update Date

2022-09-14 05:26:32 UTC

Chemfont ID

CFc000334564

Molecule Identification

Common Name

Nigrin B

Definition

Nigrin 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 .

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
5-Amino-6-(7-amino-5,8-dihydro-6-methoxy-5,8-dioxo-2-quinolyl)-4-(2-hydroxy-3,4-dimethoxyphenyl)-3-methylpicolinic acid	ChEBI
Rufocromomicina	ChEBI
Rufocromomycin	ChEBI
Rufocromomycine	ChEBI
Rufocromomycinum	ChEBI
Streptonigran	ChEBI
Nigrin	Kegg
5-Amino-6-(7-amino-5,8-dihydro-6-methoxy-5,8-dioxo-2-quinolyl)-4-(2-hydroxy-3,4-dimethoxyphenyl)-3-methylpicolinate	Generator
Brunemycin	MeSH
Bruneomycin	MeSH

Chemical Formula

C₂₅H₂₂N₄O₈

Average Molecular Weight

506.471

Monoisotopic Molecular Weight

506.143763684

IUPAC Name

5-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

Traditional Name

nigrin

CAS Registry Number

3930-19-6

SMILES

COC1=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

InChI Identifier

InChI=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 Key

PVYJZLYGTZKPJE-UHFFFAOYSA-N

Chemical Taxonomy

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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Bipyridines and oligopyridines

Direct Parent

Bipyridines 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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

pyridines (CHEBI:9287 )
quinolone (CHEBI:9287 )

Functional Ontology

Not Available

Exogenous (FooDB: )

Food

Fruit

Berry

Black elderberry (FooDB: FOOD00166)

Process

Not Available

Role

Not Available

Physical Properties

Predicted Properties

Property	Value	Source
Water Solubility	0.04 g/L	ALOGPS
logP	2.4	ALOGPS
logP	0.26	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	1.17	ChemAxon
pKa (Strongest Basic)	4.65	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	197.18 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	132.9 m³·mol⁻¹	ChemAxon
Polarizability	51.14 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0258512

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

9287

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

Showing chemical card for Nigrin B (CFc000334564)

MOL for CFc000334564 (Nigrin B)

3D MOL for CFc000334564 (Nigrin B)

3D SDF for CFc000334564 (Nigrin B)

3D-SDF for CFc000334564 (Nigrin B)

PDB for CFc000334564 (Nigrin B)

3D PDB for CFc000334564 (Nigrin B)

SMILES for CFc000334564 (Nigrin B)

INCHI for CFc000334564 (Nigrin B)

Structure for CFc000334564 (Nigrin B)

3D Structure for CFc000334564 (Nigrin B)