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Showing metabocard for Phenanthrene (HMDB0256390)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:48:09 UTC
Update Date2021-09-26 23:12:01 UTC
HMDB IDHMDB0256390
Secondary Accession NumbersNone
Metabolite Identification
Common NamePhenanthrene
DescriptionPhenanthrene belongs to the class of organic compounds known as phenanthrenes and derivatives. These are polycyclic compounds containing a phenanthrene moiety, which is a tricyclic aromatic compound with three non-linearly fused benzene. Phenanthrene exists in all living organisms, ranging from bacteria to humans. Phenanthrene 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 small amount of articles have been published on Phenanthrene. This compound has been identified in human blood as reported by (PMID: 31557052 ). Phenanthrene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Phenanthrene 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 HMDB0256390 (Phenanthrene)

  Mrv1652304272019042D          

 14 16  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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.7145    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
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    0.7145    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  5  1  0  0  0  0
  2  4  2  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5 11  2  0  0  0  0
  6 12  2  0  0  0  0
  7 13  2  0  0  0  0
  8 14  2  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0256390 (Phenanthrene)

HMDB0256390
     RDKit          3D
Phenanthrene
 24 26  0  0  0  0  0  0  0  0999 V2000
    3.4068   -0.8021    0.0006 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5481   -1.7959    0.4020 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1661   -1.6098    0.4485 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6372   -0.3956    0.0826 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5253    0.6081   -0.3244 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8932    0.4201   -0.3692 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9659    1.8182   -0.6865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3860    2.0361   -0.6531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2570    1.0499   -0.2533 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6230    1.2477   -0.2120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5002    0.2628    0.1878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9728   -0.9555    0.5552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5926   -1.1813    0.5222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7207   -0.1940    0.1220 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4898   -0.9794   -0.0253 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9232   -2.7628    0.6970 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5882   -2.4246    0.7676 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5388    1.2333   -0.6931 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6237    2.6313   -1.0114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8264    3.0020   -0.9426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0041    2.2141   -0.5064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5606    0.4719    0.2012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6044   -1.7672    0.8774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2587   -2.1272    0.8133 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
  5  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
  6  1  1  0
 14  9  1  0
 14  4  1  0
  1 15  1  0
  2 16  1  0
  3 17  1  0
  6 18  1  0
  7 19  1  0
  8 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
 13 24  1  0
M  END
Download

3D SDF for HMDB0256390 (Phenanthrene)

  Mrv1652304272019042D          

 14 16  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   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.7145    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
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    0.7145    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  5  1  0  0  0  0
  2  4  2  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5 11  2  0  0  0  0
  6 12  2  0  0  0  0
  7 13  2  0  0  0  0
  8 14  2  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256390

> <DATABASE_NAME>
hmdb

> <SMILES>
C1=CC=C2C(C=CC3=CC=CC=C23)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H

> <INCHI_KEY>
YNPNZTXNASCQKK-UHFFFAOYSA-N

> <FORMULA>
C14H10

> <MOLECULAR_WEIGHT>
178.2292

> <EXACT_MASS>
178.07825032

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
20.430342365126172

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
phenanthrene

> <ALOGPS_LOGP>
4.55

> <JCHEM_LOGP>
3.9521993293333337

> <ALOGPS_LOGS>
-5.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
58.95840000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.41e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
phenanthrene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256390 (Phenanthrene)

HMDB0256390
     RDKit          3D
Phenanthrene
 24 26  0  0  0  0  0  0  0  0999 V2000
    3.4068   -0.8021    0.0006 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5481   -1.7959    0.4020 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1661   -1.6098    0.4485 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6372   -0.3956    0.0826 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5253    0.6081   -0.3244 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8932    0.4201   -0.3692 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9659    1.8182   -0.6865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3860    2.0361   -0.6531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2570    1.0499   -0.2533 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6230    1.2477   -0.2120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5002    0.2628    0.1878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9728   -0.9555    0.5552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5926   -1.1813    0.5222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7207   -0.1940    0.1220 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4898   -0.9794   -0.0253 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9232   -2.7628    0.6970 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5882   -2.4246    0.7676 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5388    1.2333   -0.6931 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6237    2.6313   -1.0114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8264    3.0020   -0.9426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0041    2.2141   -0.5064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5606    0.4719    0.2012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6044   -1.7672    0.8774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2587   -2.1272    0.8133 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
  5  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
  6  1  1  0
 14  9  1  0
 14  4  1  0
  1 15  1  0
  2 16  1  0
  3 17  1  0
  6 18  1  0
  7 19  1  0
  8 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
 13 24  1  0
M  END
Download

PDB for HMDB0256390 (Phenanthrene)

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      -5.390  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.770   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      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.540   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      -3.850   1.334   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.540   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.080   0.000   0.000  0.00  0.00           C+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    1   11                                                       
CONECT    6    2   12                                                       
CONECT    7    3   13                                                       
CONECT    8    4   14                                                       
CONECT    9   10   11                                                       
CONECT   10    9   12                                                       
CONECT   11    5    9   13                                                  
CONECT   12    6   10   14                                                  
CONECT   13    7   11   14                                                  
CONECT   14    8   12   13                                                  
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END
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3D PDB for HMDB0256390 (Phenanthrene)

COMPND    HMDB0256390
HETATM    1  C1  UNL     1       3.407  -0.802   0.001  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.548  -1.796   0.402  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.166  -1.610   0.448  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.637  -0.396   0.083  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.525   0.608  -0.324  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.893   0.420  -0.369  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.966   1.818  -0.687  1.00  0.00           C  
HETATM    8  C8  UNL     1      -0.386   2.036  -0.653  1.00  0.00           C  
HETATM    9  C9  UNL     1      -1.257   1.050  -0.253  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.623   1.248  -0.212  1.00  0.00           C  
HETATM   11  C11 UNL     1      -3.500   0.263   0.188  1.00  0.00           C  
HETATM   12  C12 UNL     1      -2.973  -0.956   0.555  1.00  0.00           C  
HETATM   13  C13 UNL     1      -1.593  -1.181   0.522  1.00  0.00           C  
HETATM   14  C14 UNL     1      -0.721  -0.194   0.122  1.00  0.00           C  
HETATM   15  H1  UNL     1       4.490  -0.979  -0.025  1.00  0.00           H  
HETATM   16  H2  UNL     1       2.923  -2.763   0.697  1.00  0.00           H  
HETATM   17  H3  UNL     1       0.588  -2.425   0.768  1.00  0.00           H  
HETATM   18  H4  UNL     1       3.539   1.233  -0.693  1.00  0.00           H  
HETATM   19  H5  UNL     1       1.624   2.631  -1.011  1.00  0.00           H  
HETATM   20  H6  UNL     1      -0.826   3.002  -0.943  1.00  0.00           H  
HETATM   21  H7  UNL     1      -3.004   2.214  -0.506  1.00  0.00           H  
HETATM   22  H8  UNL     1      -4.561   0.472   0.201  1.00  0.00           H  
HETATM   23  H9  UNL     1      -3.604  -1.767   0.877  1.00  0.00           H  
HETATM   24  H10 UNL     1      -1.259  -2.127   0.813  1.00  0.00           H  
CONECT    1    2    2    6   15
CONECT    2    3   16
CONECT    3    4    4   17
CONECT    4    5   14
CONECT    5    6    6    7
CONECT    6   18
CONECT    7    8    8   19
CONECT    8    9   20
CONECT    9   10   10   14
CONECT   10   11   21
CONECT   11   12   12   22
CONECT   12   13   23
CONECT   13   14   14   24
END
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SMILES for HMDB0256390 (Phenanthrene)

C1=CC=C2C(C=CC3=CC=CC=C23)=C1
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INCHI for HMDB0256390 (Phenanthrene)

InChI=1S/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
PhenanthraceneChEBI
PhenanthrenChEBI
Chemical FormulaC14H10
Average Molecular Weight178.2292
Monoisotopic Molecular Weight178.07825032
IUPAC Namephenanthrene
Traditional Namephenanthrene
CAS Registry NumberNot Available
SMILES
C1=CC=C2C(C=CC3=CC=CC=C23)=C1
InChI Identifier
InChI=1S/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H
InChI KeyYNPNZTXNASCQKK-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phenanthrenes and derivatives. These are polycyclic compounds containing a phenanthrene moiety, which is a tricyclic aromatic compound with three non-linearly fused benzene.
KingdomOrganic compounds
Super ClassBenzenoids
ClassPhenanthrenes and derivatives
Sub ClassNot Available
Direct ParentPhenanthrenes and derivatives
Alternative Parents
Substituents
  • 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
Role
Environmental role
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
PropertyValueSource
logP4.55ALOGPS
logP3.95ChemAxon
logS-5.7ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity58.96 m³·mol⁻¹ChemAxon
Polarizability20.43 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
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 IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00000325
Chemspider ID970
KEGG Compound IDC11422
BioCyc IDCPD-13485
BiGG IDNot Available
Wikipedia LinkPhenanthrene
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID28851
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 ]