Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:39:10 UTC

Update Date

2022-03-07 02:52:42 UTC

HMDB ID

HMDB0030808

Secondary Accession Numbers

HMDB30808

Metabolite Identification

Common Name

Pinocembrin

Description

(S)-Pinocembrin, also known as dihydrochrysin, belongs to the class of organic compounds known as flavanones. Flavanones are compounds containing a flavan-3-one moiety, with a structure characterized by a 2-phenyl-3,4-dihydro-2H-1-benzopyran bearing a ketone at the carbon C3. Thus, (S)-pinocembrin is considered to be a flavonoid lipid molecule (S)-Pinocembrin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Outside of the human body, (S)-Pinocembrin is found, on average, in the highest concentration within mexican oregano (S)-Pinocembrin has also been detected, but not quantified in, pine nuts and prunus (cherry, plum). This could make (S)-pinocembrin a potential biomarker for the consumption of these foods. A dihydroxyflavanone in which the two hydroxy groups are located at positions 5 and 7.

Structure

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

HMDB0030808
     RDKit          3D
Pinocembrin
 31 33  0  0  0  0  0  0  0  0999 V2000
   -1.6890   -2.9189    0.0149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1452   -1.7715   -0.0045 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3168   -1.6203   -0.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7510   -0.2783    0.4969 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1894   -0.0561    0.2467 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0083   -1.0991   -0.1125 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3447   -0.8629   -0.3395 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9229    0.3905   -0.2243 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0788    1.4317    0.1396 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7442    1.2079    0.3685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0131    0.7500   -0.1492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4030    0.6652   -0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2286    1.7619   -0.1003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6072    1.6600   -0.0410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4358    2.7613   -0.0512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1286    0.3868    0.0300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3573   -0.7534    0.0440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9149   -2.0206    0.1163 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9811   -0.5854   -0.0177 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7548   -1.7672   -1.0364 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7292   -2.3997    0.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5634   -0.2059    1.5961 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6567   -2.1159   -0.2297 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0176   -1.6760   -0.6265 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9771    0.5511   -0.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4932    2.4279    0.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1108    2.0588    0.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8077    2.7508   -0.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8115    3.1818   -0.9084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2122    0.2233    0.0798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9238   -2.0779    0.1589 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  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
  4 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 16 17  1  0
 17 18  1  0
 17 19  2  0
 19  2  1  0
 10  5  1  0
 19 12  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  1
  6 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 13 28  1  0
 15 29  1  0
 16 30  1  0
 18 31  1  0
M  END


  Mrv1652309272007322D          

 19 21  0  0  0  0            999 V2000
10000.0175 9998.1294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5927 9998.1294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.165910000.6151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.592810000.6104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.878210000.1979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8782 9999.3729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5927 9998.9604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.017910000.6105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.303410000.1980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3034 9999.3729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0179 9998.9605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7324 9999.3729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.732410000.1980    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10002.874310001.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.159810001.8519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.445310001.4393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.445210000.6144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.159710000.2019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.874310000.6144    0.0000 C   0  0  0  0  0  0  0  0  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
  9 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
  8  9  1  0  0  0  0
  8 13  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 14  1  0  0  0  0
  5  3  1  0  0  0  0
  7  2  1  0  0  0  0
  1 11  2  0  0  0  0
 13 17  1  6  0  0  0
  9  4  2  0  0  0  0
  7 10  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0030808

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC(O)=C2C(=O)C[C@H](OC2=C1)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H12O4/c16-10-6-11(17)15-12(18)8-13(19-14(15)7-10)9-4-2-1-3-5-9/h1-7,13,16-17H,8H2/t13-/m0/s1

> <INCHI_KEY>
URFCJEUYXNAHFI-ZDUSSCGKSA-N

> <FORMULA>
C15H12O4

> <MOLECULAR_WEIGHT>
256.2534

> <EXACT_MASS>
256.073558872

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
26.272466547500862

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-5,7-dihydroxy-2-phenyl-3,4-dihydro-2H-1-benzopyran-4-one

> <ALOGPS_LOGP>
2.85

> <JCHEM_LOGP>
3.1386733719999995

> <ALOGPS_LOGS>
-3.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.508211062918406

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.866811828409287

> <JCHEM_PKA_STRONGEST_BASIC>
-4.950227971056941

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
69.30890000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.88e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pinocembrin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0030808
     RDKit          3D
Pinocembrin
 31 33  0  0  0  0  0  0  0  0999 V2000
   -1.6890   -2.9189    0.0149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1452   -1.7715   -0.0045 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3168   -1.6203   -0.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7510   -0.2783    0.4969 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1894   -0.0561    0.2467 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0083   -1.0991   -0.1125 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3447   -0.8629   -0.3395 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9229    0.3905   -0.2243 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0788    1.4317    0.1396 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7442    1.2079    0.3685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0131    0.7500   -0.1492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4030    0.6652   -0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2286    1.7619   -0.1003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6072    1.6600   -0.0410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4358    2.7613   -0.0512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1286    0.3868    0.0300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3573   -0.7534    0.0440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9149   -2.0206    0.1163 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9811   -0.5854   -0.0177 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7548   -1.7672   -1.0364 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7292   -2.3997    0.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5634   -0.2059    1.5961 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6567   -2.1159   -0.2297 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0176   -1.6760   -0.6265 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9771    0.5511   -0.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4932    2.4279    0.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1108    2.0588    0.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8077    2.7508   -0.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8115    3.1818   -0.9084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2122    0.2233    0.0798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9238   -2.0779    0.1589 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  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
  4 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 16 17  1  0
 17 18  1  0
 17 19  2  0
 19  2  1  0
 10  5  1  0
 19 12  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  1
  6 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 13 28  1  0
 15 29  1  0
 16 30  1  0
 18 31  1  0
M  END

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  O   UNK     0    8666.6998663.175   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8664.0408663.175   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8661.3768667.815   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0    8664.0408667.806   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8662.7068667.036   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8662.7068665.496   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8664.0408664.726   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8666.7008667.806   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0    8665.3668667.036   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8665.3668665.496   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8666.7008664.726   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8668.0348665.496   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8668.0348667.036   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8672.0328669.354   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8670.6988670.124   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8669.3658669.353   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8669.3648667.814   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8670.6988667.044   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8672.0328667.814   0.000  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2    7                                                            
CONECT    3    5                                                            
CONECT    4    5    9                                                       
CONECT    5    4    6    3                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2   10                                                  
CONECT    8    9   13                                                       
CONECT    9   10    8    4                                                  
CONECT   10    9   11    7                                                  
CONECT   11   10   12    1                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8   17                                                  
CONECT   14   15   19                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   13                                                  
CONECT   18   17   19                                                       
CONECT   19   18   14                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0030808
HETATM    1  O1  UNL     1      -1.689  -2.919   0.015  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.145  -1.771  -0.005  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.317  -1.620  -0.014  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.751  -0.278   0.497  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.189  -0.056   0.247  1.00  0.00           C  
HETATM    6  C5  UNL     1       3.008  -1.099  -0.113  1.00  0.00           C  
HETATM    7  C6  UNL     1       4.345  -0.863  -0.339  1.00  0.00           C  
HETATM    8  C7  UNL     1       4.923   0.390  -0.224  1.00  0.00           C  
HETATM    9  C8  UNL     1       4.079   1.432   0.140  1.00  0.00           C  
HETATM   10  C9  UNL     1       2.744   1.208   0.369  1.00  0.00           C  
HETATM   11  O2  UNL     1      -0.013   0.750  -0.149  1.00  0.00           O  
HETATM   12  C10 UNL     1      -1.403   0.665  -0.090  1.00  0.00           C  
HETATM   13  C11 UNL     1      -2.229   1.762  -0.100  1.00  0.00           C  
HETATM   14  C12 UNL     1      -3.607   1.660  -0.041  1.00  0.00           C  
HETATM   15  O3  UNL     1      -4.436   2.761  -0.051  1.00  0.00           O  
HETATM   16  C13 UNL     1      -4.129   0.387   0.030  1.00  0.00           C  
HETATM   17  C14 UNL     1      -3.357  -0.753   0.044  1.00  0.00           C  
HETATM   18  O4  UNL     1      -3.915  -2.021   0.116  1.00  0.00           O  
HETATM   19  C15 UNL     1      -1.981  -0.585  -0.018  1.00  0.00           C  
HETATM   20  H1  UNL     1       0.755  -1.767  -1.036  1.00  0.00           H  
HETATM   21  H2  UNL     1       0.729  -2.400   0.676  1.00  0.00           H  
HETATM   22  H3  UNL     1       0.563  -0.206   1.596  1.00  0.00           H  
HETATM   23  H4  UNL     1       2.657  -2.116  -0.230  1.00  0.00           H  
HETATM   24  H5  UNL     1       5.018  -1.676  -0.627  1.00  0.00           H  
HETATM   25  H6  UNL     1       5.977   0.551  -0.408  1.00  0.00           H  
HETATM   26  H7  UNL     1       4.493   2.428   0.240  1.00  0.00           H  
HETATM   27  H8  UNL     1       2.111   2.059   0.655  1.00  0.00           H  
HETATM   28  H9  UNL     1      -1.808   2.751  -0.156  1.00  0.00           H  
HETATM   29  H10 UNL     1      -4.812   3.182  -0.908  1.00  0.00           H  
HETATM   30  H11 UNL     1      -5.212   0.223   0.080  1.00  0.00           H  
HETATM   31  H12 UNL     1      -4.924  -2.078   0.159  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   19
CONECT    3    4   20   21
CONECT    4    5   11   22
CONECT    5    6    6   10
CONECT    6    7   23
CONECT    7    8    8   24
CONECT    8    9   25
CONECT    9   10   10   26
CONECT   10   27
CONECT   11   12
CONECT   12   13   13   19
CONECT   13   14   28
CONECT   14   15   16   16
CONECT   15   29
CONECT   16   17   30
CONECT   17   18   19   19
CONECT   18   31
END

HMDB0030808
     RDKit          3D
Pinocembrin
 31 33  0  0  0  0  0  0  0  0999 V2000
   -1.6890   -2.9189    0.0149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1452   -1.7715   -0.0045 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3168   -1.6203   -0.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7510   -0.2783    0.4969 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1894   -0.0561    0.2467 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0083   -1.0991   -0.1125 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3447   -0.8629   -0.3395 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9229    0.3905   -0.2243 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0788    1.4317    0.1396 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7442    1.2079    0.3685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0131    0.7500   -0.1492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4030    0.6652   -0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2286    1.7619   -0.1003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6072    1.6600   -0.0410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4358    2.7613   -0.0512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1286    0.3868    0.0300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3573   -0.7534    0.0440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9149   -2.0206    0.1163 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9811   -0.5854   -0.0177 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7548   -1.7672   -1.0364 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7292   -2.3997    0.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5634   -0.2059    1.5961 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6567   -2.1159   -0.2297 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0176   -1.6760   -0.6265 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9771    0.5511   -0.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4932    2.4279    0.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1108    2.0588    0.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8077    2.7508   -0.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8115    3.1818   -0.9084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2122    0.2233    0.0798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9238   -2.0779    0.1589 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  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
  4 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 16 17  1  0
 17 18  1  0
 17 19  2  0
 19  2  1  0
 10  5  1  0
 19 12  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  1
  6 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 13 28  1  0
 15 29  1  0
 16 30  1  0
 18 31  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(2S)-Pinocembrin	ChEBI
(S)-2,3-Dihydro-5,7-dihydroxy-2-phenyl-4H-1-benzopyran-4-one	ChEBI
(S)-5,7-Dihydroxyflavanone	ChEBI
5,7-Dihydroxyflavanone	ChEBI
Dihydrochrysin	ChEBI
Galangin flavanone	ChEBI
Pinocembrine	MeSH, HMDB
(S)-Pinocembrin	ChEBI
(+)-Pinocoembrin	MeSH
(+)-Pinocembrin	PhytoBank

Chemical Formula

C₁₅H₁₂O₄

Average Molecular Weight

256.2534

Monoisotopic Molecular Weight

256.073558872

IUPAC Name

(2S)-5,7-dihydroxy-2-phenyl-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

pinocembrin

CAS Registry Number

480-39-7

SMILES

OC1=CC(O)=C2C(=O)C[C@H](OC2=C1)C1=CC=CC=C1

InChI Identifier

InChI=1S/C15H12O4/c16-10-6-11(17)15-12(18)8-13(19-14(15)7-10)9-4-2-1-3-5-9/h1-7,13,16-17H,8H2/t13-/m0/s1

InChI Key

URFCJEUYXNAHFI-ZDUSSCGKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavanones. Flavanones are compounds containing a flavan-3-one moiety, with a structure characterized by a 2-phenyl-3,4-dihydro-2H-1-benzopyran bearing a ketone at the carbon C3.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavans

Direct Parent

Flavanones

Alternative Parents

Substituents

Flavanone
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Chromone
Benzopyran
Chromane
1-benzopyran
Aryl ketone
Aryl alkyl ketone
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Vinylogous acid
Ketone
Oxacycle
Organoheterocyclic compound
Ether
Organic oxygen compound
Organic oxide
Organooxygen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dihydroxyflavanone (CHEBI:28157 )
flavanones (C09827 )
Flavanones (LMPK12140214 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	192 - 193 °C	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
Water Solubility	0.19 g/L	ALOGPS
logP	2.85	ALOGPS
logP	3.14	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	7.87	ChemAxon
pKa (Strongest Basic)	-5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.31 m³·mol⁻¹	ChemAxon
Polarizability	26.27 Å³	ChemAxon
Number of Rings	3	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
DarkChem	[M+H]+	159.024	31661259
DarkChem	[M-H]-	157.387	31661259
DeepCCS	[M+H]+	158.17	30932474
DeepCCS	[M-H]-	155.799	30932474
DeepCCS	[M-2H]-	188.887	30932474
DeepCCS	[M+Na]+	164.25	30932474
AllCCS	[M+H]+	159.2	32859911
AllCCS	[M+H-H2O]+	155.2	32859911
AllCCS	[M+NH4]+	163.0	32859911
AllCCS	[M+Na]+	164.0	32859911
AllCCS	[M-H]-	160.0	32859911
AllCCS	[M+Na-2H]-	159.4	32859911
AllCCS	[M+HCOO]-	158.8	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	7.53 minutes	32390414
Predicted by Siyang on May 30, 2022	13.5449 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.42 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2364.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	374.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	165.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	212.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	324.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	643.0 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	673.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	70.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1215.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	470.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1415.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	397.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	416.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	406.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	201.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	84.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pinocembrin	OC1=CC(O)=C2C(=O)C[C@H](OC2=C1)C1=CC=CC=C1	3483.3	Standard polar	33892256
Pinocembrin	OC1=CC(O)=C2C(=O)C[C@H](OC2=C1)C1=CC=CC=C1	2564.2	Standard non polar	33892256
Pinocembrin	OC1=CC(O)=C2C(=O)C[C@H](OC2=C1)C1=CC=CC=C1	2507.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Pinocembrin,1TMS,isomer #1	C[Si](C)(C)OC1=CC(O)=C2C(=O)C[C@@H](C3=CC=CC=C3)OC2=C1	2439.0	Semi standard non polar	33892256
Pinocembrin,1TMS,isomer #2	C[Si](C)(C)OC1=CC(O)=CC2=C1C(=O)C[C@@H](C1=CC=CC=C1)O2	2424.6	Semi standard non polar	33892256
Pinocembrin,2TMS,isomer #1	C[Si](C)(C)OC1=CC2=C(C(=O)C[C@@H](C3=CC=CC=C3)O2)C(O[Si](C)(C)C)=C1	2470.9	Semi standard non polar	33892256
Pinocembrin,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC(O)=C2C(=O)C[C@@H](C3=CC=CC=C3)OC2=C1	2696.9	Semi standard non polar	33892256
Pinocembrin,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=CC(O)=CC2=C1C(=O)C[C@@H](C1=CC=CC=C1)O2	2675.5	Semi standard non polar	33892256
Pinocembrin,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC2=C(C(=O)C[C@@H](C3=CC=CC=C3)O2)C(O[Si](C)(C)C(C)(C)C)=C1	2895.9	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 - Pinocembrin GC-MS (2 TMS) - 70eV, Positive	splash10-024i-7359000000-bbe602140f5eb8e64c35	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pinocembrin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0553-2490000000-ab0d5fb04a17ac900f46	2017-11-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pinocembrin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pinocembrin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pinocembrin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 10V, Positive-QTOF	splash10-0a4i-0290000000-da83748cebaf2aff41e7	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 20V, Positive-QTOF	splash10-0pbi-0970000000-4da94433e475e4b0655c	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 40V, Positive-QTOF	splash10-0udi-4900000000-2027700d1a9013d79861	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 10V, Negative-QTOF	splash10-0a4i-0090000000-3e50055087cb60de2aa7	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 20V, Negative-QTOF	splash10-0a4i-0290000000-047a6df1cc7ac9b1ae05	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 40V, Negative-QTOF	splash10-0ufr-5910000000-bfc1ff4fa9dc8cd944c8	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 10V, Negative-QTOF	splash10-0a4i-0090000000-74e7833e04a924835b1e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 20V, Negative-QTOF	splash10-0pb9-0980000000-884390bd07a6c6de61c4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 40V, Negative-QTOF	splash10-0udi-0900000000-2e4404a2a08d29364139	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 10V, Positive-QTOF	splash10-0a4i-0090000000-95fde3556f3ac1e6ef94	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 20V, Positive-QTOF	splash10-0zfs-0940000000-6587ef358d202da97874	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pinocembrin 40V, Positive-QTOF	splash10-0udi-0900000000-fc81a674baf331f83b9b	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

FDB002759

KNApSAcK ID

C00000992

Chemspider ID

Not Available

KEGG Compound ID

C09827

BioCyc ID

CPD-6991

BiGG ID

Not Available

Wikipedia Link

Pinocembrin

METLIN ID

Not Available

PubChem Compound

68071

PDB ID

Not Available

ChEBI ID

28157

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

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details

1. UDP-glucuronosyltransferase 1-1

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:: UGT1A1
Uniprot ID:: P22309
Molecular weight:: 59590.91

Reactions

Pinocembrin → 3,4,5-trihydroxy-6-[(7-hydroxy-4-oxo-2-phenyl-3,4-dihydro-2H-1-benzopyran-5-yl)oxy]oxane-2-carboxylic acid	details
Pinocembrin → 3,4,5-trihydroxy-6-[(5-hydroxy-4-oxo-2-phenyl-3,4-dihydro-2H-1-benzopyran-7-yl)oxy]oxane-2-carboxylic acid	details

Showing metabocard for Pinocembrin (HMDB0030808)

MOL for HMDB0030808 (Pinocembrin)

3D MOL for HMDB0030808 (Pinocembrin)

3D SDF for HMDB0030808 (Pinocembrin)

3D-SDF for HMDB0030808 (Pinocembrin)

PDB for HMDB0030808 (Pinocembrin)

3D PDB for HMDB0030808 (Pinocembrin)

SMILES for HMDB0030808 (Pinocembrin)

INCHI for HMDB0030808 (Pinocembrin)

Structure for HMDB0030808 (Pinocembrin)

3D Structure for HMDB0030808 (Pinocembrin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

Reactions