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Showing metabocard for Pyrene (HMDB0042002)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-13 11:52:31 UTC
Update Date2021-10-13 08:41:42 UTC
HMDB IDHMDB0042002
Secondary Accession Numbers
  • HMDB42002
Metabolite Identification
Common NamePyrene
DescriptionPyrene, also known as beta-pyrene or β-pyrene, belongs to the class of organic compounds known as pyrenes. Pyrenes are compounds containing a pyrene moiety, which consists four fused benzene rings, resulting in a flat aromatic system. Pyrene is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Pyrene.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0042002 (Pyrene)

  Mrv1652304272019052D          

 16 19  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
  3 11  1  0  0  0  0
  4 12  2  0  0  0  0
  5 13  1  0  0  0  0
  6 14  2  0  0  0  0
  7  9  1  0  0  0  0
  7 11  2  0  0  0  0
  8 10  2  0  0  0  0
  8 12  1  0  0  0  0
  9 13  2  0  0  0  0
 10 14  1  0  0  0  0
 11 15  1  0  0  0  0
 12 15  1  0  0  0  0
 13 16  1  0  0  0  0
 14 16  1  0  0  0  0
 15 16  2  0  0  0  0
M  END
Download

3D MOL for HMDB0042002 (Pyrene)

HMDB0042002
     RDKit          3D
Pyrene
 26 29  0  0  0  0  0  0  0  0999 V2000
    3.2961    1.1863    0.3385 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0099   -0.1624    0.3361 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7155   -0.6379    0.2034 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4278   -1.9873    0.2009 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1269   -2.4549    0.0673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355   -1.5857   -0.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2360   -2.0317   -0.2030 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3030   -1.1681   -0.3397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0065    0.1799   -0.3361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7092    0.6377   -0.2027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4121    1.9854   -0.1991 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1149    2.4542   -0.0659 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9478    1.5844    0.0704 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2467    2.0579    0.2037 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6542    0.2352    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6474   -0.2356   -0.0664 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3270    1.4887    0.4459 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7924   -0.9159    0.4389 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2533   -2.6765    0.3071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0800   -3.5070    0.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4600   -3.1054   -0.2045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3206   -1.5197   -0.4445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8372    0.8723   -0.4430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2537    2.6658   -0.3069 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0662    3.5194   -0.0690 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4523    3.1210    0.2033 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  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
 13 15  1  0
 15 16  2  0
 14  1  1  0
 15  3  1  0
 16  6  1  0
 16 10  1  0
  1 17  1  0
  2 18  1  0
  4 19  1  0
  5 20  1  0
  7 21  1  0
  8 22  1  0
  9 23  1  0
 11 24  1  0
 12 25  1  0
 14 26  1  0
M  END
Download

3D SDF for HMDB0042002 (Pyrene)

  Mrv1652304272019052D          

 16 19  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
  3 11  1  0  0  0  0
  4 12  2  0  0  0  0
  5 13  1  0  0  0  0
  6 14  2  0  0  0  0
  7  9  1  0  0  0  0
  7 11  2  0  0  0  0
  8 10  2  0  0  0  0
  8 12  1  0  0  0  0
  9 13  2  0  0  0  0
 10 14  1  0  0  0  0
 11 15  1  0  0  0  0
 12 15  1  0  0  0  0
 13 16  1  0  0  0  0
 14 16  1  0  0  0  0
 15 16  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0042002

> <DATABASE_NAME>
hmdb

> <SMILES>
C1=CC2=CC=C3C=CC=C4C=CC(=C1)C2=C34

> <INCHI_IDENTIFIER>
InChI=1S/C16H10/c1-3-11-7-9-13-5-2-6-14-10-8-12(4-1)15(11)16(13)14/h1-10H

> <INCHI_KEY>
BBEAQIROQSPTKN-UHFFFAOYSA-N

> <FORMULA>
C16H10

> <MOLECULAR_WEIGHT>
202.2506

> <EXACT_MASS>
202.07825032

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
22.858462966797536

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
pyrene

> <ALOGPS_LOGP>
5.19

> <JCHEM_LOGP>
4.283927480666667

> <ALOGPS_LOGS>
-6.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
66.72260000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.31e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0042002 (Pyrene)

HMDB0042002
     RDKit          3D
Pyrene
 26 29  0  0  0  0  0  0  0  0999 V2000
    3.2961    1.1863    0.3385 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0099   -0.1624    0.3361 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7155   -0.6379    0.2034 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4278   -1.9873    0.2009 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1269   -2.4549    0.0673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355   -1.5857   -0.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2360   -2.0317   -0.2030 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3030   -1.1681   -0.3397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0065    0.1799   -0.3361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7092    0.6377   -0.2027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4121    1.9854   -0.1991 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1149    2.4542   -0.0659 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9478    1.5844    0.0704 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2467    2.0579    0.2037 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6542    0.2352    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6474   -0.2356   -0.0664 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3270    1.4887    0.4459 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7924   -0.9159    0.4389 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2533   -2.6765    0.3071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0800   -3.5070    0.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4600   -3.1054   -0.2045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3206   -1.5197   -0.4445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8372    0.8723   -0.4430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2537    2.6658   -0.3069 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0662    3.5194   -0.0690 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4523    3.1210    0.2033 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  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
 13 15  1  0
 15 16  2  0
 14  1  1  0
 15  3  1  0
 16  6  1  0
 16 10  1  0
  1 17  1  0
  2 18  1  0
  4 19  1  0
  5 20  1  0
  7 21  1  0
  8 22  1  0
  9 23  1  0
 11 24  1  0
 12 25  1  0
 14 26  1  0
M  END
Download

PDB for HMDB0042002 (Pyrene)

HEADER    PROTEIN                                 27-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-20         0                                  
HETATM    1  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.160   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.770   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.390  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.390   1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.540  -2.667   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.540   2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.080   2.667   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.850  -1.334   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.850   1.334   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.540   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.080   0.000   0.000  0.00  0.00           C+0
CONECT    1    3    4                                                       
CONECT    2    5    6                                                       
CONECT    3    1   11                                                       
CONECT    4    1   12                                                       
CONECT    5    2   13                                                       
CONECT    6    2   14                                                       
CONECT    7    9   11                                                       
CONECT    8   10   12                                                       
CONECT    9    7   13                                                       
CONECT   10    8   14                                                       
CONECT   11    3    7   15                                                  
CONECT   12    4    8   15                                                  
CONECT   13    5    9   16                                                  
CONECT   14    6   10   16                                                  
CONECT   15   11   12   16                                                  
CONECT   16   13   14   15                                                  
MASTER        0    0    0    0    0    0    0    0   16    0   38    0
END
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3D PDB for HMDB0042002 (Pyrene)

COMPND    HMDB0042002
HETATM    1  C1  UNL     1       3.296   1.186   0.339  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.010  -0.162   0.336  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.716  -0.638   0.203  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.428  -1.987   0.201  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.127  -2.455   0.067  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.935  -1.586  -0.069  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.236  -2.032  -0.203  1.00  0.00           C  
HETATM    8  C8  UNL     1      -3.303  -1.168  -0.340  1.00  0.00           C  
HETATM    9  C9  UNL     1      -3.006   0.180  -0.336  1.00  0.00           C  
HETATM   10  C10 UNL     1      -1.709   0.638  -0.203  1.00  0.00           C  
HETATM   11  C11 UNL     1      -1.412   1.985  -0.199  1.00  0.00           C  
HETATM   12  C12 UNL     1      -0.115   2.454  -0.066  1.00  0.00           C  
HETATM   13  C13 UNL     1       0.948   1.584   0.070  1.00  0.00           C  
HETATM   14  C14 UNL     1       2.247   2.058   0.204  1.00  0.00           C  
HETATM   15  C15 UNL     1       0.654   0.235   0.067  1.00  0.00           C  
HETATM   16  C16 UNL     1      -0.647  -0.236  -0.066  1.00  0.00           C  
HETATM   17  H1  UNL     1       4.327   1.489   0.446  1.00  0.00           H  
HETATM   18  H2  UNL     1       3.792  -0.916   0.439  1.00  0.00           H  
HETATM   19  H3  UNL     1       2.253  -2.676   0.307  1.00  0.00           H  
HETATM   20  H4  UNL     1      -0.080  -3.507   0.067  1.00  0.00           H  
HETATM   21  H5  UNL     1      -2.460  -3.105  -0.205  1.00  0.00           H  
HETATM   22  H6  UNL     1      -4.321  -1.520  -0.444  1.00  0.00           H  
HETATM   23  H7  UNL     1      -3.837   0.872  -0.443  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.254   2.666  -0.307  1.00  0.00           H  
HETATM   25  H9  UNL     1       0.066   3.519  -0.069  1.00  0.00           H  
HETATM   26  H10 UNL     1       2.452   3.121   0.203  1.00  0.00           H  
CONECT    1    2    2   14   17
CONECT    2    3   18
CONECT    3    4    4   15
CONECT    4    5   19
CONECT    5    6    6   20
CONECT    6    7   16
CONECT    7    8    8   21
CONECT    8    9   22
CONECT    9   10   10   23
CONECT   10   11   16
CONECT   11   12   12   24
CONECT   12   13   25
CONECT   13   14   14   15
CONECT   14   26
CONECT   15   16   16
END
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SMILES for HMDB0042002 (Pyrene)

C1=CC2=CC=C3C=CC=C4C=CC(=C1)C2=C34
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INCHI for HMDB0042002 (Pyrene)

InChI=1S/C16H10/c1-3-11-7-9-13-5-2-6-14-10-8-12(4-1)15(11)16(13)14/h1-10H
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Synonyms
ValueSource
Benzo[def]phenanthreneChEBI
beta-PyreneChEBI
PyrenChEBI
b-PyreneGenerator
Β-pyreneGenerator
BenzpyreneHMDB
Coal tar pitch volatiles:pyreneHMDB
Pyrene (acd/name 4.0)HMDB
{Benzo[def]phenanthrene}HMDB
Chemical FormulaC16H10
Average Molecular Weight202.2506
Monoisotopic Molecular Weight202.07825032
IUPAC Namepyrene
Traditional Namepyrene
CAS Registry Number129-00-0
SMILES
C1=CC2=C3C(C=CC4=CC=CC(C=C2)=C34)=C1
InChI Identifier
InChI=1S/C16H10/c1-3-11-7-9-13-5-2-6-14-10-8-12(4-1)15(11)16(13)14/h1-10H
InChI KeyBBEAQIROQSPTKN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrenes. Pyrenes are compounds containing a pyrene moiety, which consists four fused benzene rings, resulting in a flat aromatic system.
KingdomOrganic compounds
Super ClassBenzenoids
ClassPyrenes
Sub ClassNot Available
Direct ParentPyrenes
Alternative Parents
Substituents
  • Pyrene
  • Phenanthrene
  • Naphthalene
  • Aromatic hydrocarbon
  • Polycyclic hydrocarbon
  • Unsaturated hydrocarbon
  • Hydrocarbon
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point151.2 °CNot Available
Boiling Point404.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility0.00014 mg/mL at 25 °CNot Available
LogP4.88Not Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available137.971http://allccs.zhulab.cn/database/detail?ID=AllCCS00002028
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00014864
Chemspider ID29153
KEGG Compound IDC14335
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyrene
METLIN IDNot Available
PubChem Compound31423
PDB IDNot Available
ChEBI ID39106
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1279441
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available