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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 03:07:58 UTC

Update Date

2023-02-21 17:28:42 UTC

HMDB ID

HMDB0041445

Secondary Accession Numbers

HMDB41445

Metabolite 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 has been detected, but not quantified in, a few different foods, such as common mushrooms (Agaricus bisporus), mushrooms, and oyster mushrooms (Pleurotus ostreatus). This could make agrocybenine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Agrocybenine.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0041445
     RDKit          3D
Agrocybenine
 33 34  0  0  0  0  0  0  0  0999 V2000
    0.4772    2.6251   -1.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7442    1.3021   -0.6416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2293    0.4210   -0.3841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6110    0.6316   -0.6663 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3576   -0.4115    0.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9007    0.2399    1.2893 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4691   -0.8537   -0.8923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3743   -1.5003    0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0118   -0.8768    0.2212 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1541   -1.2591    0.5501 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3108   -0.4479    0.3487 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2783   -1.2465   -0.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9789   -0.3130    1.7185 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0778    0.8656   -0.2657 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0408    1.6403   -0.4775 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5050    2.5827   -1.7953 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2356    2.8777   -2.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4032    3.4303   -0.5034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0522    1.3509   -1.2409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680    1.1483    0.9637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0287    0.5889    1.8762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5309   -0.4452    1.8879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4156   -1.9452   -1.0805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4136   -0.3593   -1.8833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4386   -0.5770   -0.4454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4220   -2.3452   -0.4061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4958   -1.8465    1.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0444   -1.1116   -1.6016 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2980   -0.8283   -0.3564 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2979   -2.2982   -0.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3011   -1.3451    1.9887 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8667    0.3163    1.6817 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2151   -0.0102    2.4363 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 11 14  1  0
 14 15  2  0
 14  2  1  0
  9  3  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  4 19  1  0
  6 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 12 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 13 32  1  0
 13 33  1  0
M  END


  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>
HMDB0041445

> <DATABASE_NAME>
hmdb

> <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

$$$$

HMDB0041445
     RDKit          3D
Agrocybenine
 33 34  0  0  0  0  0  0  0  0999 V2000
    0.4772    2.6251   -1.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7442    1.3021   -0.6416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2293    0.4210   -0.3841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6110    0.6316   -0.6663 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3576   -0.4115    0.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9007    0.2399    1.2893 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4691   -0.8537   -0.8923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3743   -1.5003    0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0118   -0.8768    0.2212 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1541   -1.2591    0.5501 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3108   -0.4479    0.3487 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2783   -1.2465   -0.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9789   -0.3130    1.7185 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0778    0.8656   -0.2657 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0408    1.6403   -0.4775 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5050    2.5827   -1.7953 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2356    2.8777   -2.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4032    3.4303   -0.5034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0522    1.3509   -1.2409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680    1.1483    0.9637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0287    0.5889    1.8762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5309   -0.4452    1.8879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4156   -1.9452   -1.0805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4136   -0.3593   -1.8833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4386   -0.5770   -0.4454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4220   -2.3452   -0.4061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4958   -1.8465    1.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0444   -1.1116   -1.6016 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2980   -0.8283   -0.3564 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2979   -2.2982   -0.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3011   -1.3451    1.9887 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8667    0.3163    1.6817 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2151   -0.0102    2.4363 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 11 14  1  0
 14 15  2  0
 14  2  1  0
  9  3  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  4 19  1  0
  6 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 12 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 13 32  1  0
 13 33  1  0
M  END

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

COMPND    HMDB0041445
HETATM    1  C1  UNL     1       0.477   2.625  -1.265  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.744   1.302  -0.642  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.229   0.421  -0.384  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.611   0.632  -0.666  1.00  0.00           N  
HETATM    5  C4  UNL     1      -2.358  -0.411   0.041  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.901   0.240   1.289  1.00  0.00           C  
HETATM    7  C6  UNL     1      -3.469  -0.854  -0.892  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.374  -1.500   0.311  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.012  -0.877   0.221  1.00  0.00           C  
HETATM   10  N2  UNL     1       1.154  -1.259   0.550  1.00  0.00           N  
HETATM   11  C9  UNL     1       2.311  -0.448   0.349  1.00  0.00           C  
HETATM   12  C10 UNL     1       3.278  -1.246  -0.533  1.00  0.00           C  
HETATM   13  C11 UNL     1       2.979  -0.313   1.719  1.00  0.00           C  
HETATM   14  C12 UNL     1       2.078   0.866  -0.266  1.00  0.00           C  
HETATM   15  O1  UNL     1       3.041   1.640  -0.477  1.00  0.00           O  
HETATM   16  H1  UNL     1      -0.505   2.583  -1.795  1.00  0.00           H  
HETATM   17  H2  UNL     1       1.236   2.878  -2.047  1.00  0.00           H  
HETATM   18  H3  UNL     1       0.403   3.430  -0.503  1.00  0.00           H  
HETATM   19  H4  UNL     1      -2.052   1.351  -1.241  1.00  0.00           H  
HETATM   20  H5  UNL     1      -3.468   1.148   0.964  1.00  0.00           H  
HETATM   21  H6  UNL     1      -2.029   0.589   1.876  1.00  0.00           H  
HETATM   22  H7  UNL     1      -3.531  -0.445   1.888  1.00  0.00           H  
HETATM   23  H8  UNL     1      -3.416  -1.945  -1.080  1.00  0.00           H  
HETATM   24  H9  UNL     1      -3.414  -0.359  -1.883  1.00  0.00           H  
HETATM   25  H10 UNL     1      -4.439  -0.577  -0.445  1.00  0.00           H  
HETATM   26  H11 UNL     1      -1.422  -2.345  -0.406  1.00  0.00           H  
HETATM   27  H12 UNL     1      -1.496  -1.846   1.374  1.00  0.00           H  
HETATM   28  H13 UNL     1       3.044  -1.112  -1.602  1.00  0.00           H  
HETATM   29  H14 UNL     1       4.298  -0.828  -0.356  1.00  0.00           H  
HETATM   30  H15 UNL     1       3.298  -2.298  -0.203  1.00  0.00           H  
HETATM   31  H16 UNL     1       3.301  -1.345   1.989  1.00  0.00           H  
HETATM   32  H17 UNL     1       3.867   0.316   1.682  1.00  0.00           H  
HETATM   33  H18 UNL     1       2.215  -0.010   2.436  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3    3   14
CONECT    3    4    9
CONECT    4    5   19
CONECT    5    6    7    8
CONECT    6   20   21   22
CONECT    7   23   24   25
CONECT    8    9   26   27
CONECT    9   10   10
CONECT   10   11
CONECT   11   12   13   14
CONECT   12   28   29   30
CONECT   13   31   32   33
CONECT   14   15   15
END

HMDB0041445
     RDKit          3D
Agrocybenine
 33 34  0  0  0  0  0  0  0  0999 V2000
    0.4772    2.6251   -1.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7442    1.3021   -0.6416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2293    0.4210   -0.3841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6110    0.6316   -0.6663 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3576   -0.4115    0.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9007    0.2399    1.2893 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4691   -0.8537   -0.8923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3743   -1.5003    0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0118   -0.8768    0.2212 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1541   -1.2591    0.5501 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3108   -0.4479    0.3487 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2783   -1.2465   -0.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9789   -0.3130    1.7185 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0778    0.8656   -0.2657 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0408    1.6403   -0.4775 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5050    2.5827   -1.7953 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2356    2.8777   -2.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4032    3.4303   -0.5034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0522    1.3509   -1.2409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680    1.1483    0.9637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0287    0.5889    1.8762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5309   -0.4452    1.8879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4156   -1.9452   -1.0805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4136   -0.3593   -1.8833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4386   -0.5770   -0.4454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4220   -2.3452   -0.4061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4958   -1.8465    1.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0444   -1.1116   -1.6016 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2980   -0.8283   -0.3564 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2979   -2.2982   -0.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3011   -1.3451    1.9887 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8667    0.3163    1.6817 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2151   -0.0102    2.4363 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 11 14  1  0
 14 15  2  0
 14  2  1  0
  9  3  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  4 19  1  0
  6 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 12 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 13 32  1  0
 13 33  1  0
M  END

View in JSmol View Stereo Labels

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 Molecular Weight

206.2841

Monoisotopic Molecular Weight

206.141913208

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

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

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0041445)
Cytoplasm (HMDB: HMDB0041445)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0041445)

Source

Exogenous

Food

Food (HMDB: HMDB0041445)

Plant (HMDB: HMDB0041445)

Process

Not Available

Role

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0041445)

Biological role

Nutrient (HMDB: HMDB0041445)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	567.3 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.55 g/L	ALOGPS
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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	149.479	31661259
DarkChem	[M-H]-	146.008	31661259
DeepCCS	[M+H]+	150.924	30932474
DeepCCS	[M-H]-	148.566	30932474
DeepCCS	[M-2H]-	183.046	30932474
DeepCCS	[M+Na]+	157.646	30932474
AllCCS	[M+H]+	144.2	32859911
AllCCS	[M+H-H2O]+	140.2	32859911
AllCCS	[M+NH4]+	148.0	32859911
AllCCS	[M+Na]+	149.1	32859911
AllCCS	[M-H]-	153.4	32859911
AllCCS	[M+Na-2H]-	154.0	32859911
AllCCS	[M+HCOO]-	154.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Agrocybenine	CC1=C2NC(C)(C)CC2=NC(C)(C)C1=O	2260.3	Standard polar	33892256
Agrocybenine	CC1=C2NC(C)(C)CC2=NC(C)(C)C1=O	1572.5	Standard non polar	33892256
Agrocybenine	CC1=C2NC(C)(C)CC2=NC(C)(C)C1=O	1647.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Agrocybenine,1TMS,isomer #1	CC1=C2C(=NC(C)(C)C1=O)CC(C)(C)N2[Si](C)(C)C	1803.1	Semi standard non polar	33892256
Agrocybenine,1TMS,isomer #1	CC1=C2C(=NC(C)(C)C1=O)CC(C)(C)N2[Si](C)(C)C	1718.9	Standard non polar	33892256
Agrocybenine,1TBDMS,isomer #1	CC1=C2C(=NC(C)(C)C1=O)CC(C)(C)N2[Si](C)(C)C(C)(C)C	2015.2	Semi standard non polar	33892256
Agrocybenine,1TBDMS,isomer #1	CC1=C2C(=NC(C)(C)C1=O)CC(C)(C)N2[Si](C)(C)C(C)(C)C	1980.8	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Agrocybenine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0udl-3900000000-004e49894baea0339d29	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agrocybenine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 10V, Positive-QTOF	splash10-0a4i-0190000000-f3fe2bf3a97beeacc5dd	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 20V, Positive-QTOF	splash10-0a4i-1960000000-3e3b9550493822128da3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 40V, Positive-QTOF	splash10-014i-9000000000-596872f3a3aa3a8fffe7	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 10V, Negative-QTOF	splash10-0a4i-0090000000-b901ce8e24e79a027638	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 20V, Negative-QTOF	splash10-052b-9040000000-a5f283dd20be5a0335e5	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 40V, Negative-QTOF	splash10-03ki-2900000000-2dbc0df0e5f2d4fe189e	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 10V, Negative-QTOF	splash10-0a4i-0090000000-f986a2b5346dd94f331a	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 20V, Negative-QTOF	splash10-0a4i-0090000000-d01987e2e2a1ffcb3f4e	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 40V, Negative-QTOF	splash10-0fdp-5920000000-8f98f4b4afa2fc8fb5a8	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 10V, Positive-QTOF	splash10-0a4i-0090000000-3e5ae49add9b8a734651	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 20V, Positive-QTOF	splash10-0a4i-1970000000-daf84e5cdc2ad39ca18f	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agrocybenine 40V, Positive-QTOF	splash10-0006-9500000000-e9bdb2b5e5d5db8fcd82	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1892531

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Agrocybenine (HMDB0041445)

MOL for HMDB0041445 (Agrocybenine)

3D MOL for HMDB0041445 (Agrocybenine)

3D SDF for HMDB0041445 (Agrocybenine)

3D-SDF for HMDB0041445 (Agrocybenine)

PDB for HMDB0041445 (Agrocybenine)

3D PDB for HMDB0041445 (Agrocybenine)

SMILES for HMDB0041445 (Agrocybenine)

INCHI for HMDB0041445 (Agrocybenine)

Structure for HMDB0041445 (Agrocybenine)

3D Structure for HMDB0041445 (Agrocybenine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra