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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 17:07:48 UTC

Update Date

2021-09-26 23:12:23 UTC

HMDB ID

HMDB0256606

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Pirmagrel

Description

Pirmagrel, also known as CGS 13080, belongs to the class of organic compounds known as imidazopyridines. These are organic polycyclic compounds containing an imidazole ring fused to a pyridine ring. Imidazole is 5-membered ring consisting of three carbon atoms, and two nitrogen centers at the 1- and 3-positions. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center. Based on a literature review a significant number of articles have been published on Pirmagrel. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pirmagrel is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pirmagrel is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0256606
     RDKit          3D
Pirmagrel
 33 34  0  0  0  0  0  0  0  0999 V2000
    5.3044   -0.3434   -1.1841 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7410    0.6280   -0.6254 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3628    1.8659   -0.7364 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4835    0.4125    0.0999 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0940   -1.0233    0.0250 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8288   -1.3912    0.7264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6853   -0.6275    0.1476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6379   -0.9482    0.8034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6746   -0.1181    0.1287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3805    0.7589   -0.8992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3492    1.5320   -1.5274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6558    1.4281   -1.1175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9382    0.5510   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1215    0.2440    0.5125 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8952   -0.6649    1.4576 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5755   -0.9152    1.4332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9768   -0.1803    0.4919 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8768    2.6946   -0.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6641    1.0689   -0.3171 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6158    0.7776    1.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9648   -1.6294    0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0521   -1.2927   -1.0635 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6604   -2.4828    0.5663 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9423   -1.2625    1.8165 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6108   -0.8800   -0.9179 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8439    0.4680    0.3354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8723   -2.0143    0.5494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6361   -0.8062    1.8866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3703    0.8691   -1.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0713    2.2031   -2.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4362    2.0078   -1.5762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0870    0.6865    0.2461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0525   -1.6160    2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17  9  1  0
 17 13  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
 10 29  1  0
 11 30  1  0
 12 31  1  0
 14 32  1  0
 16 33  1  0
M  END

  Mrv1652309112119082D          

 17 18  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    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
   -0.6131    1.3770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2775    2.1307    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5429    2.0445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
    2.1434    1.2375    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
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    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
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  1  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256606

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CCCCCC1=CC=CC2=CN=CN12

> <INCHI_IDENTIFIER>
InChI=1S/C13H16N2O2/c16-13(17)8-3-1-2-5-11-6-4-7-12-9-14-10-15(11)12/h4,6-7,9-10H,1-3,5,8H2,(H,16,17)

> <INCHI_KEY>
LIFOFTJHFFTNRV-UHFFFAOYSA-N

> <FORMULA>
C13H16N2O2

> <MOLECULAR_WEIGHT>
232.283

> <EXACT_MASS>
232.121177763

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.36289621946442

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-{imidazo[1,5-a]pyridin-5-yl}hexanoic acid

> <ALOGPS_LOGP>
1.95

> <JCHEM_LOGP>
0.7729009269099039

> <ALOGPS_LOGS>
-3.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.306106115574068

> <JCHEM_PKA_STRONGEST_BASIC>
7.888283043146562

> <JCHEM_POLAR_SURFACE_AREA>
54.60000000000001

> <JCHEM_REFRACTIVITY>
66.0798

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pirmagrel

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0256606
     RDKit          3D
Pirmagrel
 33 34  0  0  0  0  0  0  0  0999 V2000
    5.3044   -0.3434   -1.1841 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7410    0.6280   -0.6254 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3628    1.8659   -0.7364 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4835    0.4125    0.0999 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0940   -1.0233    0.0250 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8288   -1.3912    0.7264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6853   -0.6275    0.1476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6379   -0.9482    0.8034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6746   -0.1181    0.1287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3805    0.7589   -0.8992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3492    1.5320   -1.5274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6558    1.4281   -1.1175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9382    0.5510   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1215    0.2440    0.5125 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8952   -0.6649    1.4576 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5755   -0.9152    1.4332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9768   -0.1803    0.4919 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8768    2.6946   -0.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6641    1.0689   -0.3171 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6158    0.7776    1.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9648   -1.6294    0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0521   -1.2927   -1.0635 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6604   -2.4828    0.5663 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9423   -1.2625    1.8165 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6108   -0.8800   -0.9179 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8439    0.4680    0.3354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8723   -2.0143    0.5494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6361   -0.8062    1.8866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3703    0.8691   -1.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0713    2.2031   -2.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4362    2.0078   -1.5762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0870    0.6865    0.2461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0525   -1.6160    2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17  9  1  0
 17 13  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
 10 29  1  0
 11 30  1  0
 12 31  1  0
 14 32  1  0
 16 33  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.144   2.570   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.518   3.977   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.013   3.816   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.003   2.310   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      10.669   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    1                                                       
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0256606
HETATM    1  O1  UNL     1       5.304  -0.343  -1.184  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.741   0.628  -0.625  1.00  0.00           C  
HETATM    3  O2  UNL     1       5.363   1.866  -0.736  1.00  0.00           O  
HETATM    4  C2  UNL     1       3.484   0.413   0.100  1.00  0.00           C  
HETATM    5  C3  UNL     1       3.094  -1.023   0.025  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.829  -1.391   0.726  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.685  -0.627   0.148  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.638  -0.948   0.803  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.675  -0.118   0.129  1.00  0.00           C  
HETATM   10  C8  UNL     1      -1.381   0.759  -0.899  1.00  0.00           C  
HETATM   11  C9  UNL     1      -2.349   1.532  -1.527  1.00  0.00           C  
HETATM   12  C10 UNL     1      -3.656   1.428  -1.118  1.00  0.00           C  
HETATM   13  C11 UNL     1      -3.938   0.551  -0.092  1.00  0.00           C  
HETATM   14  C12 UNL     1      -5.121   0.244   0.513  1.00  0.00           C  
HETATM   15  N1  UNL     1      -4.895  -0.665   1.458  1.00  0.00           N  
HETATM   16  C13 UNL     1      -3.576  -0.915   1.433  1.00  0.00           C  
HETATM   17  N2  UNL     1      -2.977  -0.180   0.492  1.00  0.00           N  
HETATM   18  H1  UNL     1       4.877   2.695  -0.433  1.00  0.00           H  
HETATM   19  H2  UNL     1       2.664   1.069  -0.317  1.00  0.00           H  
HETATM   20  H3  UNL     1       3.616   0.778   1.148  1.00  0.00           H  
HETATM   21  H4  UNL     1       3.965  -1.629   0.414  1.00  0.00           H  
HETATM   22  H5  UNL     1       3.052  -1.293  -1.064  1.00  0.00           H  
HETATM   23  H6  UNL     1       1.660  -2.483   0.566  1.00  0.00           H  
HETATM   24  H7  UNL     1       1.942  -1.263   1.817  1.00  0.00           H  
HETATM   25  H8  UNL     1       0.611  -0.880  -0.918  1.00  0.00           H  
HETATM   26  H9  UNL     1       0.844   0.468   0.335  1.00  0.00           H  
HETATM   27  H10 UNL     1      -0.872  -2.014   0.549  1.00  0.00           H  
HETATM   28  H11 UNL     1      -0.636  -0.806   1.887  1.00  0.00           H  
HETATM   29  H12 UNL     1      -0.370   0.869  -1.248  1.00  0.00           H  
HETATM   30  H13 UNL     1      -2.071   2.203  -2.326  1.00  0.00           H  
HETATM   31  H14 UNL     1      -4.436   2.008  -1.576  1.00  0.00           H  
HETATM   32  H15 UNL     1      -6.087   0.687   0.246  1.00  0.00           H  
HETATM   33  H16 UNL     1      -3.052  -1.616   2.083  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   18
CONECT    4    5   19   20
CONECT    5    6   21   22
CONECT    6    7   23   24
CONECT    7    8   25   26
CONECT    8    9   27   28
CONECT    9   10   10   17
CONECT   10   11   29
CONECT   11   12   12   30
CONECT   12   13   31
CONECT   13   14   14   17
CONECT   14   15   32
CONECT   15   16   16
CONECT   16   17   33
END

HMDB0256606
     RDKit          3D
Pirmagrel
 33 34  0  0  0  0  0  0  0  0999 V2000
    5.3044   -0.3434   -1.1841 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7410    0.6280   -0.6254 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3628    1.8659   -0.7364 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4835    0.4125    0.0999 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0940   -1.0233    0.0250 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8288   -1.3912    0.7264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6853   -0.6275    0.1476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6379   -0.9482    0.8034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6746   -0.1181    0.1287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3805    0.7589   -0.8992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3492    1.5320   -1.5274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6558    1.4281   -1.1175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9382    0.5510   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1215    0.2440    0.5125 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8952   -0.6649    1.4576 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5755   -0.9152    1.4332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9768   -0.1803    0.4919 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8768    2.6946   -0.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6641    1.0689   -0.3171 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6158    0.7776    1.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9648   -1.6294    0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0521   -1.2927   -1.0635 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6604   -2.4828    0.5663 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9423   -1.2625    1.8165 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6108   -0.8800   -0.9179 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8439    0.4680    0.3354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8723   -2.0143    0.5494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6361   -0.8062    1.8866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3703    0.8691   -1.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0713    2.2031   -2.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4362    2.0078   -1.5762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0870    0.6865    0.2461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0525   -1.6160    2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17  9  1  0
 17 13  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
 10 29  1  0
 11 30  1  0
 12 31  1  0
 14 32  1  0
 16 33  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
CGS 13080	Kegg
6-{imidazo[1,5-a]pyridin-5-yl}hexanoate	HMDB
Imidazol(1,5-a)pyridine-5-hexanoic acid	HMDB

Chemical Formula

C₁₃H₁₆N₂O₂

Average Molecular Weight

232.283

Monoisotopic Molecular Weight

232.121177763

IUPAC Name

6-{imidazo[1,5-a]pyridin-5-yl}hexanoic acid

Traditional Name

pirmagrel

CAS Registry Number

Not Available

SMILES

OC(=O)CCCCCC1=CC=CC2=CN=CN12

InChI Identifier

InChI=1S/C13H16N2O2/c16-13(17)8-3-1-2-5-11-6-4-7-12-9-14-10-15(11)12/h4,6-7,9-10H,1-3,5,8H2,(H,16,17)

InChI Key

LIFOFTJHFFTNRV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as imidazopyridines. These are organic polycyclic compounds containing an imidazole ring fused to a pyridine ring. Imidazole is 5-membered ring consisting of three carbon atoms, and two nitrogen centers at the 1- and 3-positions. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyridines

Sub Class

Not Available

Direct Parent

Imidazopyridines

Alternative Parents

Substituents

Imidazopyridine
Medium-chain fatty acid
Amino fatty acid
Heterocyclic fatty acid
N-substituted imidazole
Pyridine
Fatty acid
Fatty acyl
Azole
Imidazole
Heteroaromatic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Azacycle
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

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	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	1.95	ALOGPS
logP	0.77	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	4.31	ChemAxon
pKa (Strongest Basic)	7.89	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.6 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	66.08 m³·mol⁻¹	ChemAxon
Polarizability	25.36 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
DeepCCS	[M-2H]-	182.86	30932474
DeepCCS	[M+Na]+	158.398	30932474
AllCCS	[M+H]+	154.1	32859911
AllCCS	[M+H-H2O]+	150.2	32859911
AllCCS	[M+NH4]+	157.8	32859911
AllCCS	[M+Na]+	158.8	32859911
AllCCS	[M-H]-	158.9	32859911
AllCCS	[M+Na-2H]-	159.0	32859911
AllCCS	[M+HCOO]-	159.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pirmagrel	OC(=O)CCCCCC1=CC=CC2=CN=CN12	3364.2	Standard polar	33892256
Pirmagrel	OC(=O)CCCCCC1=CC=CC2=CN=CN12	2111.5	Standard non polar	33892256
Pirmagrel	OC(=O)CCCCCC1=CC=CC2=CN=CN12	2279.3	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Pirmagrel GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a6r-6940000000-26a083e628c8df2055ea	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pirmagrel GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pirmagrel GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pirmagrel GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

50016

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

55390

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Pirmagrel (HMDB0256606)

MOL for HMDB0256606 (Pirmagrel)

3D MOL for HMDB0256606 (Pirmagrel)

3D SDF for HMDB0256606 (Pirmagrel)

3D-SDF for HMDB0256606 (Pirmagrel)

PDB for HMDB0256606 (Pirmagrel)

3D PDB for HMDB0256606 (Pirmagrel)

SMILES for HMDB0256606 (Pirmagrel)

INCHI for HMDB0256606 (Pirmagrel)

Structure for HMDB0256606 (Pirmagrel)

3D Structure for HMDB0256606 (Pirmagrel)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra