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Showing metabocard for Pirfenidone (HMDB0256594)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:07:04 UTC
Update Date2021-09-26 23:12:22 UTC
HMDB IDHMDB0256594
Secondary Accession NumbersNone
Metabolite Identification
Common NamePirfenidone
DescriptionPirfenidone, also known as esbriet or AMR 69, belongs to the class of organic compounds known as pyridinones. Pyridinones are compounds containing a pyridine ring, which bears a ketone. Pirfenidone is a drug which is used for the treatment of idiopathic pulmonary fibrosis (ipf). Based on a literature review a significant number of articles have been published on Pirfenidone. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pirfenidone is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pirfenidone 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256594 (Pirfenidone)

  Mrv0541 02231218022D          

 14 15  0  0  0  0            999 V2000
    1.6500    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  6  1  0  0  0  0
  3  9  2  0  0  0  0
  3 10  1  0  0  0  0
  4  5  2  0  0  0  0
  5  7  1  0  0  0  0
  5 11  1  0  0  0  0
  6  8  1  0  0  0  0
  7  8  2  0  0  0  0
  9 12  1  0  0  0  0
 10 13  2  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0256594 (Pirfenidone)

HMDB0256594
     RDKit          3D
Pirfenidone
 25 26  0  0  0  0  0  0  0  0999 V2000
    3.5734    0.9213    0.4666 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4932   -0.0094    0.0653 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7362   -1.2742   -0.4109 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6937   -2.1018   -0.7711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3896   -1.6110   -0.6352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5798   -2.3559   -0.9606 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1508   -0.3827   -0.1729 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1849    0.0755   -0.0508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8694   -0.2459    1.1238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1678    0.1864    1.2684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7964    0.9263    0.2776 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0995    1.2307   -0.8728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8007    0.8128   -1.0466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1650    0.3983    0.1683 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2487    1.9721    0.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4821    0.7975   -0.1573 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8024    0.7425    1.5517 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7658   -1.6248   -0.5040 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8186   -3.1047   -1.1514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4166   -0.8190    1.9179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7228   -0.0485    2.1697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8189    1.2547    0.4155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6104    1.8210   -1.6561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2449    1.0427   -1.9384 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924    1.3964    0.5448 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
  7 14  1  0
 14  2  2  0
 13  8  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  9 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

3D SDF for HMDB0256594 (Pirfenidone)

  Mrv0541 02231218022D          

 14 15  0  0  0  0            999 V2000
    1.6500    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3644   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  6  1  0  0  0  0
  3  9  2  0  0  0  0
  3 10  1  0  0  0  0
  4  5  2  0  0  0  0
  5  7  1  0  0  0  0
  5 11  1  0  0  0  0
  6  8  1  0  0  0  0
  7  8  2  0  0  0  0
  9 12  1  0  0  0  0
 10 13  2  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256594

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN(C(=O)C=C1)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C12H11NO/c1-10-7-8-12(14)13(9-10)11-5-3-2-4-6-11/h2-9H,1H3

> <INCHI_KEY>
ISWRGOKTTBVCFA-UHFFFAOYSA-N

> <FORMULA>
C12H11NO

> <MOLECULAR_WEIGHT>
185.2218

> <EXACT_MASS>
185.084063979

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
20.276823895237797

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-methyl-1-phenyl-1,2-dihydropyridin-2-one

> <ALOGPS_LOGP>
2.00

> <JCHEM_LOGP>
2.1418576873333333

> <ALOGPS_LOGS>
-1.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-1.247993203570275

> <JCHEM_POLAR_SURFACE_AREA>
20.310000000000002

> <JCHEM_REFRACTIVITY>
57.00160000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pirfenidone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256594 (Pirfenidone)

HMDB0256594
     RDKit          3D
Pirfenidone
 25 26  0  0  0  0  0  0  0  0999 V2000
    3.5734    0.9213    0.4666 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4932   -0.0094    0.0653 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7362   -1.2742   -0.4109 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6937   -2.1018   -0.7711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3896   -1.6110   -0.6352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5798   -2.3559   -0.9606 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1508   -0.3827   -0.1729 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1849    0.0755   -0.0508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8694   -0.2459    1.1238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1678    0.1864    1.2684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7964    0.9263    0.2776 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0995    1.2307   -0.8728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8007    0.8128   -1.0466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1650    0.3983    0.1683 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2487    1.9721    0.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4821    0.7975   -0.1573 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8024    0.7425    1.5517 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7658   -1.6248   -0.5040 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8186   -3.1047   -1.1514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4166   -0.8190    1.9179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7228   -0.0485    2.1697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8189    1.2547    0.4155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6104    1.8210   -1.6561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2449    1.0427   -1.9384 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924    1.3964    0.5448 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
  7 14  1  0
 14  2  2  0
 13  8  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  9 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

PDB for HMDB0256594 (Pirfenidone)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       3.080   0.770   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0       5.747   0.770   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.747  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.081   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.081   3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.414   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.747   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.414   3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.081  -1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.414  -1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.415   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.081  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.414  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.747  -3.850   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    3    4    6                                                  
CONECT    3    2    9   10                                                  
CONECT    4    2    5                                                       
CONECT    5    4    7   11                                                  
CONECT    6    1    2    8                                                  
CONECT    7    5    8                                                       
CONECT    8    6    7                                                       
CONECT    9    3   12                                                       
CONECT   10    3   13                                                       
CONECT   11    5                                                            
CONECT   12    9   14                                                       
CONECT   13   10   14                                                       
CONECT   14   12   13                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END
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3D PDB for HMDB0256594 (Pirfenidone)

COMPND    HMDB0256594
HETATM    1  C1  UNL     1       3.573   0.921   0.467  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.493  -0.009   0.065  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.736  -1.274  -0.411  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.694  -2.102  -0.771  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.390  -1.611  -0.635  1.00  0.00           C  
HETATM    6  O1  UNL     1      -0.580  -2.356  -0.961  1.00  0.00           O  
HETATM    7  N1  UNL     1       0.151  -0.383  -0.173  1.00  0.00           N  
HETATM    8  C6  UNL     1      -1.185   0.075  -0.051  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.869  -0.246   1.124  1.00  0.00           C  
HETATM   10  C8  UNL     1      -3.168   0.186   1.268  1.00  0.00           C  
HETATM   11  C9  UNL     1      -3.796   0.926   0.278  1.00  0.00           C  
HETATM   12  C10 UNL     1      -3.099   1.231  -0.873  1.00  0.00           C  
HETATM   13  C11 UNL     1      -1.801   0.813  -1.047  1.00  0.00           C  
HETATM   14  C12 UNL     1       1.165   0.398   0.168  1.00  0.00           C  
HETATM   15  H1  UNL     1       3.249   1.972   0.358  1.00  0.00           H  
HETATM   16  H2  UNL     1       4.482   0.797  -0.157  1.00  0.00           H  
HETATM   17  H3  UNL     1       3.802   0.742   1.552  1.00  0.00           H  
HETATM   18  H4  UNL     1       3.766  -1.625  -0.504  1.00  0.00           H  
HETATM   19  H5  UNL     1       1.819  -3.105  -1.151  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.417  -0.819   1.918  1.00  0.00           H  
HETATM   21  H7  UNL     1      -3.723  -0.049   2.170  1.00  0.00           H  
HETATM   22  H8  UNL     1      -4.819   1.255   0.416  1.00  0.00           H  
HETATM   23  H9  UNL     1      -3.610   1.821  -1.656  1.00  0.00           H  
HETATM   24  H10 UNL     1      -1.245   1.043  -1.938  1.00  0.00           H  
HETATM   25  H11 UNL     1       0.992   1.396   0.545  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3   14   14
CONECT    3    4    4   18
CONECT    4    5   19
CONECT    5    6    6    7
CONECT    7    8   14
CONECT    8    9    9   13
CONECT    9   10   20
CONECT   10   11   11   21
CONECT   11   12   22
CONECT   12   13   13   23
CONECT   13   24
CONECT   14   25
END
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SMILES for HMDB0256594 (Pirfenidone)

CC1=CN(C(=O)C=C1)C1=CC=CC=C1
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INCHI for HMDB0256594 (Pirfenidone)

InChI=1S/C12H11NO/c1-10-7-8-12(14)13(9-10)11-5-3-2-4-6-11/h2-9H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
AMR 69ChEBI
AMR-69ChEBI
EsbrietChEBI
PirfenidonaChEBI
PirfenidonumChEBI
5-Methyl-1-phenyl-2-(1H)-pyridoneMeSH
DeskarMeSH
Chemical FormulaC12H11NO
Average Molecular Weight185.2218
Monoisotopic Molecular Weight185.084063979
IUPAC Name5-methyl-1-phenyl-1,2-dihydropyridin-2-one
Traditional Namepirfenidone
CAS Registry NumberNot Available
SMILES
CC1=CN(C(=O)C=C1)C1=CC=CC=C1
InChI Identifier
InChI=1S/C12H11NO/c1-10-7-8-12(14)13(9-10)11-5-3-2-4-6-11/h2-9H,1H3
InChI KeyISWRGOKTTBVCFA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridinones. Pyridinones are compounds containing a pyridine ring, which bears a ketone.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHydropyridines
Direct ParentPyridinones
Alternative Parents
Substituents
  • Dihydropyridine
  • Pyridinone
  • Methylpyridine
  • Monocyclic benzene moiety
  • Benzenoid
  • Heteroaromatic compound
  • Lactam
  • Azacycle
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB04951
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID37115
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPirfenidone
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID32016
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]