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Showing metabocard for 5-Phenylvaleric acid (HMDB0002043)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-05-22 14:17:33 UTC
Update Date2023-02-21 17:16:06 UTC
HMDB IDHMDB0002043
Secondary Accession Numbers
  • HMDB02043
Metabolite Identification
Common Name5-Phenylvaleric acid
Description5-Phenylvaleric acid, also known as delta-phenylvalerate or benzenepentanoic-acid, is a monocarboxylic acid that is valeric acid substituted by a phenyl group at the delta-position. It is a monocarboxylic acid and a member of benzenes. It derives from a valeric acid. 5-Phenylvaleric acid belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002043 (5-Phenylvaleric acid)

5PV
  Mrv1652305271900002D          

 13 13  0  0  0  0            999 V2000
   -1.0563   -0.0459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7708   -0.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4853   -0.0459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4853    0.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7708    1.1916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0563    0.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3419   -0.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3726   -0.0459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0871   -0.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8015   -0.0459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5160   -0.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2305   -0.0459    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5160   -1.2834    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  1  7  1  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
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3D MOL for HMDB0002043 (5-Phenylvaleric acid)

HMDB0002043
     RDKit          3D
5-Phenylvaleric acid
 27 27  0  0  0  0  0  0  0  0999 V2000
    3.8060   -1.3832    0.4943 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6257   -0.1609    0.2393 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5435    0.4335   -0.6494 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5350    0.6644    0.8041 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3132    0.5390   -0.0701 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8970   -0.8845   -0.1100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3279   -1.1419   -0.9507 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5112   -0.4150   -0.4889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8085    0.8362   -0.9473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9375    1.4769   -0.4785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7721    0.8690    0.4494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4832   -0.3944    0.9202 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3414   -1.0187    0.4334 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4347   -0.0009   -0.8656 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3035    0.2866    1.8207 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8850    1.7245    0.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5420    1.2304    0.3208 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6334    0.8818   -1.0972 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7532   -1.4674   -0.5536 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7840   -1.2658    0.9250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4898   -2.2457   -0.9716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0808   -0.8532   -1.9994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1823    1.3647   -1.6829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1975    2.4785   -0.8287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6639    1.3491    0.8332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1299   -0.8809    1.6471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1305   -2.0223    0.8204 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  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13  8  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  0
 12 26  1  0
 13 27  1  0
M  END
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3D SDF for HMDB0002043 (5-Phenylvaleric acid)

5PV
  Mrv1652305271900002D          

 13 13  0  0  0  0            999 V2000
   -1.0563   -0.0459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7708   -0.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4853   -0.0459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4853    0.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7708    1.1916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0563    0.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3419   -0.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3726   -0.0459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0871   -0.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8015   -0.0459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5160   -0.4584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2305   -0.0459    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5160   -1.2834    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  1  7  1  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002043

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CCCCC1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O2/c12-11(13)9-5-4-8-10-6-2-1-3-7-10/h1-3,6-7H,4-5,8-9H2,(H,12,13)

> <INCHI_KEY>
BYHDDXPKOZIZRV-UHFFFAOYSA-N

> <FORMULA>
C11H14O2

> <MOLECULAR_WEIGHT>
178.2277

> <EXACT_MASS>
178.099379692

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
20.112580185383067

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-phenylpentanoic acid

> <ALOGPS_LOGP>
2.81

> <JCHEM_LOGP>
2.944700100333333

> <ALOGPS_LOGS>
-2.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.9403773022308055

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
51.1686

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.04e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-phenylvaleric acid

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0002043 (5-Phenylvaleric acid)

HMDB0002043
     RDKit          3D
5-Phenylvaleric acid
 27 27  0  0  0  0  0  0  0  0999 V2000
    3.8060   -1.3832    0.4943 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6257   -0.1609    0.2393 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5435    0.4335   -0.6494 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5350    0.6644    0.8041 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3132    0.5390   -0.0701 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8970   -0.8845   -0.1100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3279   -1.1419   -0.9507 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5112   -0.4150   -0.4889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8085    0.8362   -0.9473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9375    1.4769   -0.4785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7721    0.8690    0.4494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4832   -0.3944    0.9202 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3414   -1.0187    0.4334 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4347   -0.0009   -0.8656 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3035    0.2866    1.8207 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8850    1.7245    0.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5420    1.2304    0.3208 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6334    0.8818   -1.0972 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7532   -1.4674   -0.5536 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7840   -1.2658    0.9250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4898   -2.2457   -0.9716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0808   -0.8532   -1.9994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1823    1.3647   -1.6829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1975    2.4785   -0.8287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6639    1.3491    0.8332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1299   -0.8809    1.6471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1305   -2.0223    0.8204 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  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13  8  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  0
 12 26  1  0
 13 27  1  0
M  END
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PDB for HMDB0002043 (5-Phenylvaleric acid)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 5PV                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      -1.972  -0.086   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.305  -0.856   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.639  -0.086   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.639   1.454   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.305   2.224   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.972   1.454   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.638  -0.856   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.696  -0.086   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.029  -0.856   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.363  -0.086   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.697  -0.856   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.030  -0.086   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.697  -2.396   0.000  0.00  0.00           O+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5                                                       
CONECT    7    1    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0002043 (5-Phenylvaleric acid)

COMPND    HMDB0002043
HETATM    1  O1  UNL     1       3.806  -1.383   0.494  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.626  -0.161   0.239  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.543   0.434  -0.649  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.535   0.664   0.804  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.313   0.539  -0.070  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.897  -0.885  -0.110  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.328  -1.142  -0.951  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.511  -0.415  -0.489  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.808   0.836  -0.947  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.937   1.477  -0.478  1.00  0.00           C  
HETATM   11  C9  UNL     1      -3.772   0.869   0.449  1.00  0.00           C  
HETATM   12  C10 UNL     1      -3.483  -0.394   0.920  1.00  0.00           C  
HETATM   13  C11 UNL     1      -2.341  -1.019   0.433  1.00  0.00           C  
HETATM   14  H1  UNL     1       5.435  -0.001  -0.866  1.00  0.00           H  
HETATM   15  H2  UNL     1       2.303   0.287   1.821  1.00  0.00           H  
HETATM   16  H3  UNL     1       2.885   1.724   0.837  1.00  0.00           H  
HETATM   17  H4  UNL     1       0.542   1.230   0.321  1.00  0.00           H  
HETATM   18  H5  UNL     1       1.633   0.882  -1.097  1.00  0.00           H  
HETATM   19  H6  UNL     1       1.753  -1.467  -0.554  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.784  -1.266   0.925  1.00  0.00           H  
HETATM   21  H8  UNL     1      -0.490  -2.246  -0.972  1.00  0.00           H  
HETATM   22  H9  UNL     1      -0.081  -0.853  -1.999  1.00  0.00           H  
HETATM   23  H10 UNL     1      -1.182   1.365  -1.683  1.00  0.00           H  
HETATM   24  H11 UNL     1      -3.197   2.479  -0.829  1.00  0.00           H  
HETATM   25  H12 UNL     1      -4.664   1.349   0.833  1.00  0.00           H  
HETATM   26  H13 UNL     1      -4.130  -0.881   1.647  1.00  0.00           H  
HETATM   27  H14 UNL     1      -2.130  -2.022   0.820  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8    9    9   13
CONECT    9   10   23
CONECT   10   11   11   24
CONECT   11   12   25
CONECT   12   13   13   26
CONECT   13   27
END
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SMILES for HMDB0002043 (5-Phenylvaleric acid)

OC(=O)CCCCC1=CC=CC=C1
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INCHI for HMDB0002043 (5-Phenylvaleric acid)

InChI=1S/C11H14O2/c12-11(13)9-5-4-8-10-6-2-1-3-7-10/h1-3,6-7H,4-5,8-9H2,(H,12,13)
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC11H14O2
Average Molecular Weight178.2277
Monoisotopic Molecular Weight178.099379692
IUPAC Name5-phenylpentanoic acid
Traditional Name5-phenylvaleric acid
CAS Registry Number2270-20-4
SMILES
OC(=O)CCCCC1=CC=CC=C1
InChI Identifier
InChI=1S/C11H14O2/c12-11(13)9-5-4-8-10-6-2-1-3-7-10/h1-3,6-7H,4-5,8-9H2,(H,12,13)
InChI KeyBYHDDXPKOZIZRV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Benzenoid
  • Monocyclic benzene moiety
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point57.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.61 mg/mL at 25 °CNot Available
LogP2.94AUSTIN,RP ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB04051
Phenol Explorer Compound IDNot Available
FooDB IDFDB022814
KNApSAcK IDNot Available
Chemspider ID15886
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6456
PubChem Compound16757
PDB IDNot Available
ChEBI ID40131
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. Kim KR, Kim JH, Jeong DH, Paek DJ, Liebich HM: Gas chromatographic profiling analysis of urinary organic acids from nonsmokers and smokers. J Chromatogr B Biomed Sci Appl. 1997 Nov 7;701(1):1-8. [PubMed:9389332 ]