NP-MRD: Showing NP-Card for Agrocybenine (NP0049855)

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Record Information

Version

2.0

Created at

2022-03-17 21:19:12 UTC

Updated at

2022-03-17 21:19:12 UTC

NP-MRD ID

NP0049855

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Agrocybenine

Description

Agrocybenine belongs to the class of organic compounds known as pyrrolopyridines. Pyrrolopyridines are compounds containing a pyrrolopyridine moiety, which consists of a pyrrole ring fused to a pyridine. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center. Agrocybenine is a very strong basic compound (based on its pKa). Outside of the human body, Agrocybenine has been detected, but not quantified in, mushrooms. Agrocybenine is found in Agrocybe cylindracea and Cyclocybe cylindracea. This could make agrocybenine a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI

  Mrv0541 05061312402D          

 15 16  0  0  0  0            999 V2000
    2.6378    0.9521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0407   -1.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0407   -0.1459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1648   -0.9672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6345   -1.8857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
  9  8  1  0  0  0  0
 10  7  1  0  0  0  0
 11  2  1  0  0  0  0
 11  3  1  0  0  0  0
 11  6  1  0  0  0  0
 12  4  1  0  0  0  0
 12  5  1  0  0  0  0
 12 10  1  0  0  0  0
 13  8  2  0  0  0  0
 13 12  1  0  0  0  0
 14  9  1  0  0  0  0
 14 11  1  0  0  0  0
 15 10  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0049855

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C2NC(C)(C)CC2=NC(C)(C)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H18N2O/c1-7-9-8(6-11(2,3)14-9)13-12(4,5)10(7)15/h14H,6H2,1-5H3

> <INCHI_KEY>
OTBGQBSPIWKINO-UHFFFAOYSA-N

> <FORMULA>
C12H18N2O

> <MOLECULAR_WEIGHT>
206.2841

> <EXACT_MASS>
206.141913208

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
23.569561691677308

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,2,5,5,7-pentamethyl-1H,2H,3H,5H,6H-pyrrolo[3,2-b]pyridin-6-one

> <ALOGPS_LOGP>
1.86

> <JCHEM_LOGP>
1.8653191866666665

> <ALOGPS_LOGS>
-2.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
6.775108234250574

> <JCHEM_POLAR_SURFACE_AREA>
41.46

> <JCHEM_REFRACTIVITY>
61.265

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.54e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,2,5,5,7-pentamethyl-1H,3H-pyrrolo[3,2-b]pyridin-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.924   1.777   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.076  -2.333   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.076  -0.272   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.774  -1.805   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.784  -3.520   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.924  -2.843   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       7.591   0.237   0.000  0.00  0.00           O+0
CONECT    1    7                                                            
CONECT    2   11                                                            
CONECT    3   11                                                            
CONECT    4   12                                                            
CONECT    5   12                                                            
CONECT    6    8   11                                                       
CONECT    7    1    9   10                                                  
CONECT    8    6    9   13                                                  
CONECT    9    7    8   14                                                  
CONECT   10    7   12   15                                                  
CONECT   11    2    3    6   14                                             
CONECT   12    4    5   10   13                                             
CONECT   13    8   12                                                       
CONECT   14    9   11                                                       
CONECT   15   10                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Value	Source
1,2,3,5-Tetrahydro-2,2,5,5,7-pentamethyl-6H-pyrrolo[2,3-b]pyridin-6-one, 9ci	HMDB

Chemical Formula

C₁₂H₁₈N₂O

Average Mass

206.2841 Da

Monoisotopic Mass

206.14191 Da

IUPAC Name

2,2,5,5,7-pentamethyl-1H,2H,3H,5H,6H-pyrrolo[3,2-b]pyridin-6-one

Traditional Name

2,2,5,5,7-pentamethyl-1H,3H-pyrrolo[3,2-b]pyridin-6-one

CAS Registry Number

178764-92-6

SMILES

CC1=C2NC(C)(C)CC2=NC(C)(C)C1=O

InChI Identifier

InChI=1S/C12H18N2O/c1-7-9-8(6-11(2,3)14-9)13-12(4,5)10(7)15/h14H,6H2,1-5H3

InChI Key

OTBGQBSPIWKINO-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Agaricus bisporus	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Agrocybe cylindracea	Fungi	KNApSAcK
Cyclocybe cylindracea	LOTUS Database	35616633
Pleurotus ostreatus	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolopyridines. Pyrrolopyridines are compounds containing a pyrrolopyridine moiety, which consists of a pyrrole ring fused to a pyridine. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolopyridines

Sub Class

Not Available

Direct Parent

Pyrrolopyridines

Alternative Parents

Substituents

Pyrrolopyridine
Pyridine
Pyrrolidine
Vinylogous amide
Ketimine
Ketone
Cyclic ketone
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Azacycle
Secondary amine
Secondary aliphatic amine
Enamine
Hydrocarbon derivative
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Amine
Imine
Organic oxygen compound
Organopnictogen compound
Organic oxide
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	1.86	ALOGPS
logP	1.87	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Basic)	6.78	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	41.46 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	61.26 m³·mol⁻¹	ChemAxon
Polarizability	23.57 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0041445

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB021396

KNApSAcK ID

C00027822

Chemspider ID

10446240

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23278458

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Agrocybenine (NP0049855)

MOL for NP0049855 (Agrocybenine)

3D MOL for NP0049855 (Agrocybenine)

3D SDF for NP0049855 (Agrocybenine)

3D-SDF for NP0049855 (Agrocybenine)

PDB for NP0049855 (Agrocybenine)

3D PDB for NP0049855 (Agrocybenine)

SMILES for NP0049855 (Agrocybenine)

INCHI for NP0049855 (Agrocybenine)

Structure for NP0049855 (Agrocybenine)

3D Structure for NP0049855 (Agrocybenine)