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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 17:45:53 UTC

Update Date

2022-09-22 18:34:24 UTC

HMDB ID

HMDB0031842

Secondary Accession Numbers

HMDB31842

Metabolite Identification

Common Name

Rhapontigenin

Description

Rhapontigenin is found in garden rhubarb. Rhapontigenin is isolated from rhizomes of Rheum undulatum (rhubarb) 4-Guanidinobutanoate is a normal metabolite present in low concentrations. Patients with hyperargininemia have an arginase deficiency which leads to blockade of the urea cycle in the last step with several clinical symptoms. Owing to the arginase deficiency this patients accumulate arginine which leads eventually to epileptogenic guanidino compounds (PMID 7752905

Structure

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

HMDB0031842
     RDKit          3D
Rhapontigenin
 33 34  0  0  0  0  0  0  0  0999 V2000
    5.2481    0.6370    1.1376 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9694    1.2182    1.0072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9421    0.6194    0.2886 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0994   -0.5875   -0.3497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0681   -1.1523   -1.0490 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7968   -0.5728   -1.1756 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1625   -1.1717   -2.0563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4226   -1.1489   -1.9245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1821   -0.5610   -0.8751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4562   -0.0403   -1.1191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3039    0.3993   -0.1442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5664    0.9148   -0.3963 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8962    0.3345    1.1780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6524   -0.1701    1.4778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1990   -0.2555    2.7861 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8116   -0.6130    0.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6669    0.6335   -0.5306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7161    1.2223    0.1901 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5310    2.4450    0.8271 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8277    1.1251    1.9427 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1074   -0.4452    1.3527 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8040    0.6891    0.1693 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0613   -1.0732   -0.2801 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2188   -2.1129   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2704   -1.7141   -2.9545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9899   -1.6699   -2.7630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8164    0.0277   -2.1537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7644    1.8838   -0.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5354    0.6726    1.9824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7373    0.0377    3.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8618   -1.0465    0.7780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2357    1.2044   -0.5906 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2662    2.8819    1.3460 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
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
  6 17  1  0
 17 18  2  0
 18 19  1  0
 18  3  1  0
 16  9  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  5 24  1  0
  7 25  1  0
  8 26  1  0
 10 27  1  0
 12 28  1  0
 13 29  1  0
 15 30  1  0
 16 31  1  0
 17 32  1  0
 19 33  1  0
M  END


  Mrv0541 05061306102D          

 19 20  0  0  0  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  5  4  2  0  0  0  0
 10  2  1  0  0  0  0
 10  4  1  0  0  0  0
 10  8  2  0  0  0  0
 11  3  1  0  0  0  0
 11  6  2  0  0  0  0
 11  7  1  0  0  0  0
 12  6  1  0  0  0  0
 12  9  2  0  0  0  0
 13  7  2  0  0  0  0
 13  9  1  0  0  0  0
 14  8  1  0  0  0  0
 15  5  1  0  0  0  0
 15 14  2  0  0  0  0
 16 12  1  0  0  0  0
 17 13  1  0  0  0  0
 18 14  1  0  0  0  0
 19  1  1  0  0  0  0
 19 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031842

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(O)C=C(\C=C/C2=CC(O)=CC(O)=C2)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H14O4/c1-19-15-5-4-10(8-14(15)18)2-3-11-6-12(16)9-13(17)7-11/h2-9,16-18H,1H3/b3-2-

> <INCHI_KEY>
PHMHDRYYFAYWEG-IHWYPQMZSA-N

> <FORMULA>
C15H14O4

> <MOLECULAR_WEIGHT>
258.2693

> <EXACT_MASS>
258.089208936

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
26.44851012916692

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-[(Z)-2-(3-hydroxy-4-methoxyphenyl)ethenyl]benzene-1,3-diol

> <ALOGPS_LOGP>
2.64

> <JCHEM_LOGP>
3.244719620666666

> <ALOGPS_LOGS>
-3.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.855524837796523

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.075874343536233

> <JCHEM_PKA_STRONGEST_BASIC>
-4.8888438674983945

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
73.91870000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.82e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(Z)-2-(3-hydroxy-4-methoxyphenyl)ethenyl]benzene-1,3-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0031842
     RDKit          3D
Rhapontigenin
 33 34  0  0  0  0  0  0  0  0999 V2000
    5.2481    0.6370    1.1376 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9694    1.2182    1.0072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9421    0.6194    0.2886 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0994   -0.5875   -0.3497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0681   -1.1523   -1.0490 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7968   -0.5728   -1.1756 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1625   -1.1717   -2.0563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4226   -1.1489   -1.9245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1821   -0.5610   -0.8751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4562   -0.0403   -1.1191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3039    0.3993   -0.1442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5664    0.9148   -0.3963 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8962    0.3345    1.1780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6524   -0.1701    1.4778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1990   -0.2555    2.7861 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8116   -0.6130    0.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6669    0.6335   -0.5306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7161    1.2223    0.1901 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5310    2.4450    0.8271 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8277    1.1251    1.9427 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1074   -0.4452    1.3527 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8040    0.6891    0.1693 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0613   -1.0732   -0.2801 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2188   -2.1129   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2704   -1.7141   -2.9545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9899   -1.6699   -2.7630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8164    0.0277   -2.1537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7644    1.8838   -0.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5354    0.6726    1.9824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7373    0.0377    3.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8618   -1.0465    0.7780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2357    1.2044   -0.5906 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2662    2.8819    1.3460 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
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
  6 17  1  0
 17 18  2  0
 18 19  1  0
 18  3  1  0
 16  9  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  5 24  1  0
  7 25  1  0
  8 26  1  0
 10 27  1  0
 12 28  1  0
 13 29  1  0
 15 30  1  0
 16 31  1  0
 17 32  1  0
 19 33  1  0
M  END

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
CONECT    1   19                                                            
CONECT    2    3   10                                                       
CONECT    3    2   11                                                       
CONECT    4    5   10                                                       
CONECT    5    4   15                                                       
CONECT    6   11   12                                                       
CONECT    7   11   13                                                       
CONECT    8   10   14                                                       
CONECT    9   12   13                                                       
CONECT   10    2    4    8                                                  
CONECT   11    3    6    7                                                  
CONECT   12    6    9   16                                                  
CONECT   13    7    9   17                                                  
CONECT   14    8   15   18                                                  
CONECT   15    5   14   19                                                  
CONECT   16   12                                                            
CONECT   17   13                                                            
CONECT   18   14                                                            
CONECT   19    1   15                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

COMPND    HMDB0031842
HETATM    1  C1  UNL     1       5.248   0.637   1.138  1.00  0.00           C  
HETATM    2  O1  UNL     1       3.969   1.218   1.007  1.00  0.00           O  
HETATM    3  C2  UNL     1       2.942   0.619   0.289  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.099  -0.588  -0.350  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.068  -1.152  -1.049  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.797  -0.573  -1.176  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.162  -1.172  -2.056  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.423  -1.149  -1.924  1.00  0.00           C  
HETATM    9  C8  UNL     1      -2.182  -0.561  -0.875  1.00  0.00           C  
HETATM   10  C9  UNL     1      -3.456  -0.040  -1.119  1.00  0.00           C  
HETATM   11  C10 UNL     1      -4.304   0.399  -0.144  1.00  0.00           C  
HETATM   12  O2  UNL     1      -5.566   0.915  -0.396  1.00  0.00           O  
HETATM   13  C11 UNL     1      -3.896   0.335   1.178  1.00  0.00           C  
HETATM   14  C12 UNL     1      -2.652  -0.170   1.478  1.00  0.00           C  
HETATM   15  O3  UNL     1      -2.199  -0.256   2.786  1.00  0.00           O  
HETATM   16  C13 UNL     1      -1.812  -0.613   0.441  1.00  0.00           C  
HETATM   17  C14 UNL     1       0.667   0.633  -0.531  1.00  0.00           C  
HETATM   18  C15 UNL     1       1.716   1.222   0.190  1.00  0.00           C  
HETATM   19  O4  UNL     1       1.531   2.445   0.827  1.00  0.00           O  
HETATM   20  H1  UNL     1       5.828   1.125   1.943  1.00  0.00           H  
HETATM   21  H2  UNL     1       5.107  -0.445   1.353  1.00  0.00           H  
HETATM   22  H3  UNL     1       5.804   0.689   0.169  1.00  0.00           H  
HETATM   23  H4  UNL     1       4.061  -1.073  -0.280  1.00  0.00           H  
HETATM   24  H5  UNL     1       2.219  -2.113  -1.548  1.00  0.00           H  
HETATM   25  H6  UNL     1       0.270  -1.714  -2.954  1.00  0.00           H  
HETATM   26  H7  UNL     1      -1.990  -1.670  -2.763  1.00  0.00           H  
HETATM   27  H8  UNL     1      -3.816   0.028  -2.154  1.00  0.00           H  
HETATM   28  H9  UNL     1      -5.764   1.884  -0.562  1.00  0.00           H  
HETATM   29  H10 UNL     1      -4.535   0.673   1.982  1.00  0.00           H  
HETATM   30  H11 UNL     1      -2.737   0.038   3.567  1.00  0.00           H  
HETATM   31  H12 UNL     1      -0.862  -1.047   0.778  1.00  0.00           H  
HETATM   32  H13 UNL     1      -0.236   1.204  -0.591  1.00  0.00           H  
HETATM   33  H14 UNL     1       2.266   2.882   1.346  1.00  0.00           H  
CONECT    1    2   20   21   22
CONECT    2    3
CONECT    3    4    4   18
CONECT    4    5   23
CONECT    5    6    6   24
CONECT    6    7   17
CONECT    7    8    8   25
CONECT    8    9   26
CONECT    9   10   10   16
CONECT   10   11   27
CONECT   11   12   13   13
CONECT   12   28
CONECT   13   14   29
CONECT   14   15   16   16
CONECT   15   30
CONECT   16   31
CONECT   17   18   18   32
CONECT   18   19
CONECT   19   33
END

HMDB0031842
     RDKit          3D
Rhapontigenin
 33 34  0  0  0  0  0  0  0  0999 V2000
    5.2481    0.6370    1.1376 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9694    1.2182    1.0072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9421    0.6194    0.2886 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0994   -0.5875   -0.3497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0681   -1.1523   -1.0490 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7968   -0.5728   -1.1756 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1625   -1.1717   -2.0563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4226   -1.1489   -1.9245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1821   -0.5610   -0.8751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4562   -0.0403   -1.1191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3039    0.3993   -0.1442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5664    0.9148   -0.3963 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8962    0.3345    1.1780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6524   -0.1701    1.4778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1990   -0.2555    2.7861 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8116   -0.6130    0.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6669    0.6335   -0.5306 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7161    1.2223    0.1901 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5310    2.4450    0.8271 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8277    1.1251    1.9427 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1074   -0.4452    1.3527 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8040    0.6891    0.1693 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0613   -1.0732   -0.2801 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2188   -2.1129   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2704   -1.7141   -2.9545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9899   -1.6699   -2.7630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8164    0.0277   -2.1537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7644    1.8838   -0.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5354    0.6726    1.9824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7373    0.0377    3.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8618   -1.0465    0.7780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2357    1.2044   -0.5906 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2662    2.8819    1.3460 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
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
  6 17  1  0
 17 18  2  0
 18 19  1  0
 18  3  1  0
 16  9  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  5 24  1  0
  7 25  1  0
  8 26  1  0
 10 27  1  0
 12 28  1  0
 13 29  1  0
 15 30  1  0
 16 31  1  0
 17 32  1  0
 19 33  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-(3,5-Dihydroxyphenyl)-2-(3-hydroxy-4-methoxyphenyl)ethylene	HMDB
3,3',5-Trihydroxy-4'-methoxystilbene	HMDB
4'-Methoxy-3,3',5-trihydroxystilbene	HMDB
4-Guanidinobutanoic acid	HMDB
Pontigenin	HMDB

Chemical Formula

C₁₅H₁₄O₄

Average Molecular Weight

258.2693

Monoisotopic Molecular Weight

258.089208936

IUPAC Name

5-[(Z)-2-(3-hydroxy-4-methoxyphenyl)ethenyl]benzene-1,3-diol

Traditional Name

5-[(Z)-2-(3-hydroxy-4-methoxyphenyl)ethenyl]benzene-1,3-diol

CAS Registry Number

500-65-2

SMILES

COC1=C(O)C=C(\C=C/C2=CC(O)=CC(O)=C2)C=C1

InChI Identifier

InChI=1S/C15H14O4/c1-19-15-5-4-10(8-14(15)18)2-3-11-6-12(16)9-13(17)7-11/h2-9,16-18H,1H3/b3-2-

InChI Key

PHMHDRYYFAYWEG-IHWYPQMZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as stilbenes. These are organic compounds containing a 1,2-diphenylethylene moiety. Stilbenes (C6-C2-C6 ) are derived from the common phenylpropene (C6-C3) skeleton building block. The introduction of one or more hydroxyl groups to a phenyl ring lead to stilbenoids.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Stilbenes

Sub Class

Not Available

Direct Parent

Stilbenes

Alternative Parents

Substituents

Stilbene
Methoxyphenol
Anisole
Phenoxy compound
Phenol ether
Resorcinol
Styrene
Methoxybenzene
1-hydroxy-4-unsubstituted benzenoid
Phenol
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Monocyclic benzene moiety
Benzenoid
Ether
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0031842)
Cell membrane (HMDB: HMDB0031842)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0031842)

Source

Endogenous

Endogenous (HMDB: HMDB0031842)

Plant

Plant (HMDB: HMDB0031842)

Exogenous

Food

Food (HMDB: HMDB0031842)

Vegetable

Stalk vegetable

Garden rhubarb (FooDB: FOOD00154)

Leaf vegetable

Green vegetables (FooDB: FOOD00872)

Exogenous (HMDB: HMDB0031842)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	186 - 187 °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	0.048 g/L	ALOGPS
logP	2.64	ALOGPS
logP	3.24	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	9.08	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.92 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	73.92 m³·mol⁻¹	ChemAxon
Polarizability	26.45 Å³	ChemAxon
Number of Rings	2	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
DeepCCS	[M+H]+	165.21	30932474
DeepCCS	[M-H]-	162.852	30932474
DeepCCS	[M-2H]-	195.738	30932474
DeepCCS	[M+Na]+	171.303	30932474
AllCCS	[M+H]+	159.3	32859911
AllCCS	[M+H-H2O]+	155.3	32859911
AllCCS	[M+NH4]+	163.0	32859911
AllCCS	[M+Na]+	164.0	32859911
AllCCS	[M-H]-	159.8	32859911
AllCCS	[M+Na-2H]-	159.4	32859911
AllCCS	[M+HCOO]-	159.1	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.	6.11 minutes	32390414
Predicted by Siyang on May 30, 2022	11.3696 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.37 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	25.3 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1631.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	271.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	145.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	159.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	229.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	595.1 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	408.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	122.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1020.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	385.3 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	1167.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	318.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	349.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	385.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	215.9 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	47.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Rhapontigenin	COC1=C(O)C=C(\C=C/C2=CC(O)=CC(O)=C2)C=C1	4601.9	Standard polar	33892256
Rhapontigenin	COC1=C(O)C=C(\C=C/C2=CC(O)=CC(O)=C2)C=C1	2708.6	Standard non polar	33892256
Rhapontigenin	COC1=C(O)C=C(\C=C/C2=CC(O)=CC(O)=C2)C=C1	2902.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Rhapontigenin,1TMS,isomer #1	COC1=CC=C(/C=C\C2=CC(O)=CC(O)=C2)C=C1O[Si](C)(C)C	2766.9	Semi standard non polar	33892256
Rhapontigenin,1TMS,isomer #2	COC1=CC=C(/C=C\C2=CC(O)=CC(O[Si](C)(C)C)=C2)C=C1O	2781.3	Semi standard non polar	33892256
Rhapontigenin,2TMS,isomer #1	COC1=CC=C(/C=C\C2=CC(O)=CC(O[Si](C)(C)C)=C2)C=C1O[Si](C)(C)C	2724.0	Semi standard non polar	33892256
Rhapontigenin,2TMS,isomer #2	COC1=CC=C(/C=C\C2=CC(O[Si](C)(C)C)=CC(O[Si](C)(C)C)=C2)C=C1O	2739.5	Semi standard non polar	33892256
Rhapontigenin,3TMS,isomer #1	COC1=CC=C(/C=C\C2=CC(O[Si](C)(C)C)=CC(O[Si](C)(C)C)=C2)C=C1O[Si](C)(C)C	2756.7	Semi standard non polar	33892256
Rhapontigenin,1TBDMS,isomer #1	COC1=CC=C(/C=C\C2=CC(O)=CC(O)=C2)C=C1O[Si](C)(C)C(C)(C)C	3074.9	Semi standard non polar	33892256
Rhapontigenin,1TBDMS,isomer #2	COC1=CC=C(/C=C\C2=CC(O)=CC(O[Si](C)(C)C(C)(C)C)=C2)C=C1O	3074.9	Semi standard non polar	33892256
Rhapontigenin,2TBDMS,isomer #1	COC1=CC=C(/C=C\C2=CC(O)=CC(O[Si](C)(C)C(C)(C)C)=C2)C=C1O[Si](C)(C)C(C)(C)C	3287.1	Semi standard non polar	33892256
Rhapontigenin,2TBDMS,isomer #2	COC1=CC=C(/C=C\C2=CC(O[Si](C)(C)C(C)(C)C)=CC(O[Si](C)(C)C(C)(C)C)=C2)C=C1O	3299.0	Semi standard non polar	33892256
Rhapontigenin,3TBDMS,isomer #1	COC1=CC=C(/C=C\C2=CC(O[Si](C)(C)C(C)(C)C)=CC(O[Si](C)(C)C(C)(C)C)=C2)C=C1O[Si](C)(C)C(C)(C)C	3538.0	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 - Rhapontigenin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4l-0490000000-0c7e3c1cc1544fd01557	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rhapontigenin GC-MS (3 TMS) - 70eV, Positive	splash10-0bt9-1001900000-036b5d08a976c1505736	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rhapontigenin 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 - Rhapontigenin 10V, Positive-QTOF	splash10-0a4i-0190000000-cc3e35bd8d646ecf9ddd	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 20V, Positive-QTOF	splash10-0a4i-0590000000-fb36ae977a4e36814287	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 40V, Positive-QTOF	splash10-0fkl-3920000000-c70ef1d9e39f8d23d409	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 10V, Negative-QTOF	splash10-0a4i-0090000000-326dbc7596b8abc29f7c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 20V, Negative-QTOF	splash10-0a4i-0090000000-2c9ea4e757e72cb68c00	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 40V, Negative-QTOF	splash10-0006-2890000000-e1781ac257911d64c7ac	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 10V, Negative-QTOF	splash10-0a4i-0090000000-c2a50a42dfada53572a9	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 20V, Negative-QTOF	splash10-0a4i-0190000000-96cc8797cb39e482f4e4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 40V, Negative-QTOF	splash10-0ab9-0950000000-a841efaa4f3f27296400	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 10V, Positive-QTOF	splash10-0a4i-0090000000-5436edd338e0c37ed496	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 20V, Positive-QTOF	splash10-052r-0960000000-b790cc1b715a020f8232	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rhapontigenin 40V, Positive-QTOF	splash10-05g0-0910000000-d0d4c5ff03d7f0ca5185	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

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

FDB008524

KNApSAcK ID

C00015562

Chemspider ID

9055029

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Rhapontigenin

METLIN ID

Not Available

PubChem Compound

10879760

PDB ID

Not Available

ChEBI ID

Not Available

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

Marescau B, De Deyn PP, Holvoet J, Possemiers I, Nagels G, Saxena V, Mahler C: Guanidino compounds in serum and urine of cirrhotic patients. Metabolism. 1995 May;44(5):584-8. [PubMed:7752905 ]
Jung DB, Lee HJ, Jeong SJ, Lee HJ, Lee EO, Kim YC, Ahn KS, Chen CY, Kim SH: Rhapontigenin inhibited hypoxia inducible factor 1 alpha accumulation and angiogenesis in hypoxic PC-3 prostate cancer cells. Biol Pharm Bull. 2011;34(6):850-5. [PubMed:21628883 ]
Kim JK, Kim N, Lim YH: Evaluation of the antibacterial activity of rhapontigenin produced from rhapontin by biotransformation against Propionibacterium acnes. J Microbiol Biotechnol. 2010 Jan;20(1):82-7. [PubMed:20134237 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Rhapontigenin (HMDB0031842)

MOL for HMDB0031842 (Rhapontigenin)

3D MOL for HMDB0031842 (Rhapontigenin)

3D SDF for HMDB0031842 (Rhapontigenin)

3D-SDF for HMDB0031842 (Rhapontigenin)

PDB for HMDB0031842 (Rhapontigenin)

3D PDB for HMDB0031842 (Rhapontigenin)

SMILES for HMDB0031842 (Rhapontigenin)

INCHI for HMDB0031842 (Rhapontigenin)

Structure for HMDB0031842 (Rhapontigenin)

3D Structure for HMDB0031842 (Rhapontigenin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra