MiMeDB: Showing metabocard for Nygerone A (MMDBc0003327)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 21:24:58 UTC

Update Date

2022-08-31 06:20:47 UTC

Metabolite ID

MMDBc0003327

Metabolite Identification

Common Name

Nygerone A

Description

Nygerone A belongs to the class of organic compounds known as nicotinamides. These are heterocyclic aromatic compounds containing a pyridine ring substituted at position 3 by a carboxamide group. Nygerone A is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a small amount of articles have been published on Nygerone A.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305142123242D          

 32 34  0  0  1  0            999 V2000
   -6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  2  0  0  0  0
 16  1  1  6  0  0  0
 16 12  1  0  0  0  0
 17  8  2  0  0  0  0
 17  9  1  0  0  0  0
 17 13  1  0  0  0  0
 18 10  2  0  0  0  0
 18 11  1  0  0  0  0
 19 13  1  0  0  0  0
 19 14  2  0  0  0  0
 20 15  2  0  0  0  0
 21 14  1  0  0  0  0
 21 20  1  0  0  0  0
 22 12  1  0  0  0  0
 23 20  1  0  0  0  0
 24 16  1  0  0  0  0
 25 22  2  0  0  0  0
 25 23  1  4  0  0  0
 26 15  1  0  0  0  0
 26 18  1  0  0  0  0
 26 19  1  0  0  0  0
 27 21  2  0  0  0  0
 28 22  1  0  0  0  0
 29 23  2  0  0  0  0
 30 24  2  0  0  0  0
 31 24  1  0  0  0  0
 16 32  1  1  0  0  0
M  END


  Mrv1652305142123242D          

 32 34  0  0  1  0            999 V2000
   -6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  2  0  0  0  0
 16  1  1  6  0  0  0
 16 12  1  0  0  0  0
 17  8  2  0  0  0  0
 17  9  1  0  0  0  0
 17 13  1  0  0  0  0
 18 10  2  0  0  0  0
 18 11  1  0  0  0  0
 19 13  1  0  0  0  0
 19 14  2  0  0  0  0
 20 15  2  0  0  0  0
 21 14  1  0  0  0  0
 21 20  1  0  0  0  0
 22 12  1  0  0  0  0
 23 20  1  0  0  0  0
 24 16  1  0  0  0  0
 25 22  2  0  0  0  0
 25 23  1  4  0  0  0
 26 15  1  0  0  0  0
 26 18  1  0  0  0  0
 26 19  1  0  0  0  0
 27 21  2  0  0  0  0
 28 22  1  0  0  0  0
 29 23  2  0  0  0  0
 30 24  2  0  0  0  0
 31 24  1  0  0  0  0
 16 32  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0003327

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](C)(CC(O)=NC(=O)C1=CN(C(CC2=CC=CC=C2)=CC1=O)C1=CC=CC=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H22N2O5/c1-16(24(30)31)12-22(28)25-23(29)20-15-26(18-10-6-3-7-11-18)19(14-21(20)27)13-17-8-4-2-5-9-17/h2-11,14-16H,12-13H2,1H3,(H,30,31)(H,25,28,29)/t16-/m0/s1

> <INCHI_KEY>
NTTJVIQCCNYXRP-INIZCTEOSA-N

> <FORMULA>
C24H22N2O5

> <MOLECULAR_WEIGHT>
418.449

> <EXACT_MASS>
418.152871816

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
43.36896060258921

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-3-[(6-benzyl-4-oxo-1-phenyl-1,4-dihydropyridine-3-carbonyl)-C-hydroxycarbonimidoyl]-2-methylpropanoic acid

> <ALOGPS_LOGP>
2.99

> <JCHEM_LOGP>
3.4752754121472056

> <ALOGPS_LOGS>
-4.96

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.380736946980984

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9311975039975446

> <JCHEM_PKA_STRONGEST_BASIC>
2.70264561810458

> <JCHEM_POLAR_SURFACE_AREA>
107.27

> <JCHEM_REFRACTIVITY>
117.09959999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.61e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-[(6-benzyl-4-oxo-1-phenylpyridine-3-carbonyl)-C-hydroxycarbonimidoyl]-2-methylpropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-21         0                                  
HETATM    1  C   UNK     0     -12.003   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.000   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -9.336   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -10.669   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -9.336   2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -10.669   6.160   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0      -8.002   1.540   0.000  0.00  0.00           N+0
HETATM   26  N   UNK     0      -2.667   1.540   0.000  0.00  0.00           N+0
HETATM   27  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0     -10.669   1.540   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -6.668   3.850   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -9.336   6.930   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0     -12.003   6.930   0.000  0.00  0.00           O+0
HETATM   32  H   UNK     0     -10.669   3.080   0.000  0.00  0.00           H+0
CONECT    1   16                                                            
CONECT    2    4    5                                                       
CONECT    3    6    7                                                       
CONECT    4    2    8                                                       
CONECT    5    2    9                                                       
CONECT    6    3   10                                                       
CONECT    7    3   11                                                       
CONECT    8    4   17                                                       
CONECT    9    5   17                                                       
CONECT   10    6   18                                                       
CONECT   11    7   18                                                       
CONECT   12   16   22                                                       
CONECT   13   17   19                                                       
CONECT   14   19   21                                                       
CONECT   15   20   26                                                       
CONECT   16    1   12   24   32                                             
CONECT   17    8    9   13                                                  
CONECT   18   10   11   26                                                  
CONECT   19   13   14   26                                                  
CONECT   20   15   21   23                                                  
CONECT   21   14   20   27                                                  
CONECT   22   12   25   28                                                  
CONECT   23   20   25   29                                                  
CONECT   24   16   30   31                                                  
CONECT   25   22   23                                                       
CONECT   26   15   18   19                                                  
CONECT   27   21                                                            
CONECT   28   22                                                            
CONECT   29   23                                                            
CONECT   30   24                                                            
CONECT   31   24                                                            
CONECT   32   16                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

Synonyms

Not Available

Molecular Formula

C₂₄H₂₂N₂O₅

Average Mass

418.449

Monoisotopic Mass

418.152871816

IUPAC Name

(2S)-3-[(6-benzyl-4-oxo-1-phenyl-1,4-dihydropyridine-3-carbonyl)-C-hydroxycarbonimidoyl]-2-methylpropanoic acid

Traditional Name

(2S)-3-[(6-benzyl-4-oxo-1-phenylpyridine-3-carbonyl)-C-hydroxycarbonimidoyl]-2-methylpropanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@](C)(CC(O)=NC(=O)C1=CN(C(CC2=CC=CC=C2)=CC1=O)C1=CC=CC=C1)C(O)=O

InChI Identifier

InChI=1S/C24H22N2O5/c1-16(24(30)31)12-22(28)25-23(29)20-15-26(18-10-6-3-7-11-18)19(14-21(20)27)13-17-8-4-2-5-9-17/h2-11,14-16H,12-13H2,1H3,(H,30,31)(H,25,28,29)/t16-/m0/s1

InChI Key

NTTJVIQCCNYXRP-INIZCTEOSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as nicotinamides. These are heterocyclic aromatic compounds containing a pyridine ring substituted at position 3 by a carboxamide group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridinecarboxylic acids and derivatives

Direct Parent

Nicotinamides

Alternative Parents

Substituents

Nicotinamide
Dihydropyridine
Monocyclic benzene moiety
Hydropyridine
N-acyl-amine
Benzenoid
Carboxylic acid imide
Dicarboximide
Carboxylic acid imide, n-unsubstituted
Heteroaromatic compound
Vinylogous amide
Cyclic ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Azacycle
Organonitrogen compound
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

dicarboximide (CHEBI:69408 )
monocarboxylic acid (CHEBI:69408 )
dihydropyridine (CHEBI:69408 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0046 g/L	ALOGPS
logP	2.99	ALOGPS
logP	3.48	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	3.93	ChemAxon
pKa (Strongest Basic)	2.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	107.27 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	117.1 m³·mol⁻¹	ChemAxon
Polarizability	43.37 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

28285959

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25209072

PDB ID

Not Available

ChEBI ID

69408

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Nygerone A (MMDBc0003327)

MOL for #<Metabolite:0x00007f923c881488>

3D MOL for #<Metabolite:0x00007f923c881488>

3D SDF for #<Metabolite:0x00007f923c881488>

3D-SDF for #<Metabolite:0x00007f923c881488>

PDB for #<Metabolite:0x00007f923c881488>

3D PDB for #<Metabolite:0x00007f923c881488>

SMILES for #<Metabolite:0x00007f923c881488>

INCHI for #<Metabolite:0x00007f923c881488>

Structure for #<Metabolite:0x00007f923c881488>

3D Structure for #<Metabolite:0x00007f923c881488>