Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:49:37 UTC

Update Date

2022-03-07 02:53:58 UTC

HMDB ID

HMDB0034049

Secondary Accession Numbers

HMDB34049

Metabolite Identification

Common Name

Pachyrrhizin

Description

Pachyrrhizin belongs to the class of organic compounds known as isoflav-3-enones. These are flavonoids with a structure based on an isoflav-3-ene skeleton bearing an oxo-group at position C2. Thus, pachyrrhizin is considered to be a flavonoid. Pachyrrhizin has been detected, but not quantified in, jicamas (Pachyrhizus erosus) and pulses. This could make pachyrrhizin a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Pachyrrhizin.

Structure

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

  Mrv0541 05061307322D          

 25 29  0  0  0  0            999 V2000
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6005   -2.4570    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4209   -2.5432    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    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
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4130    1.6500    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
    0.7145   -0.4125    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
    0.0000    0.8250    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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
   -2.1434    2.0625    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
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7565   -1.7895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9280    0.9826    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9280    2.3174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
 10  2  1  0  0  0  0
 10  4  2  0  0  0  0
 11  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  5  2  0  0  0  0
 13 12  1  0  0  0  0
 14  7  2  0  0  0  0
 14 10  1  0  0  0  0
 15  7  1  0  0  0  0
 15 11  2  0  0  0  0
 16  8  2  0  0  0  0
 16 12  1  0  0  0  0
 17  6  1  0  0  0  0
 18  8  1  0  0  0  0
 18 17  2  0  0  0  0
 19 13  1  0  0  0  0
 20 19  2  0  0  0  0
 21  1  1  0  0  0  0
 21 16  1  0  0  0  0
 22  3  1  0  0  0  0
 22 14  1  0  0  0  0
 23  9  1  0  0  0  0
 23 17  1  0  0  0  0
 24  9  1  0  0  0  0
 24 18  1  0  0  0  0
 25 15  1  0  0  0  0
 25 19  1  0  0  0  0
M  END

HMDB0034049
     RDKit          3D
Pachyrrhizin
 37 41  0  0  0  0  0  0  0  0999 V2000
    1.3233    0.1577    3.4251 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0459    0.2584    2.0447 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0209    0.2761    1.0682 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3644    0.1959    1.3638 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3364    0.2150    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9403    0.3169   -0.9445 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5814    0.3986   -1.2530 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6304    0.3778   -0.2465 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2215    0.4617   -0.5498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7448   -0.3307   -0.0143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0590   -0.1594   -0.3794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0820   -0.9391    0.1354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3979   -0.7594   -0.2376 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5942   -1.3608    0.0930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6153   -0.7529   -0.6064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0478    0.1797   -1.3298 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7500    0.2221   -1.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7182    0.9903   -1.6576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4020    0.8207   -1.2936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4343    1.5717   -1.7926 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1760    1.4291   -1.4619 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6995    2.1887   -1.9835 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0702    0.3166   -1.7503 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1590   -0.0192   -0.9128 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7143    0.1495    0.4132 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3534   -0.0025    3.9406 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7790    1.0803    3.8273 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9361   -0.7551    3.6494 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7031    0.1156    2.3750 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3022    0.4779   -2.3001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4637   -1.0932    0.6994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8375   -1.7089    0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7118   -2.1889    0.7984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6878   -1.0011   -0.5648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9445    1.7678   -2.3750 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4553   -1.0857   -1.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0303    0.6689   -1.1191 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  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
  6 23  1  0
 23 24  1  0
 24 25  1  0
  8  3  1  0
 21  9  1  0
 25  5  1  0
 19 11  1  0
 17 13  2  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  7 30  1  0
 10 31  1  0
 12 32  1  0
 14 33  1  0
 15 34  1  0
 18 35  1  0
 24 36  1  0
 24 37  1  0
M  END

  Mrv0541 05061307322D          

 25 29  0  0  0  0            999 V2000
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6005   -2.4570    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4209   -2.5432    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    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
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4130    1.6500    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
    0.7145   -0.4125    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
    0.0000    0.8250    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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
   -2.1434    2.0625    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
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7565   -1.7895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9280    0.9826    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9280    2.3174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
 10  2  1  0  0  0  0
 10  4  2  0  0  0  0
 11  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  5  2  0  0  0  0
 13 12  1  0  0  0  0
 14  7  2  0  0  0  0
 14 10  1  0  0  0  0
 15  7  1  0  0  0  0
 15 11  2  0  0  0  0
 16  8  2  0  0  0  0
 16 12  1  0  0  0  0
 17  6  1  0  0  0  0
 18  8  1  0  0  0  0
 18 17  2  0  0  0  0
 19 13  1  0  0  0  0
 20 19  2  0  0  0  0
 21  1  1  0  0  0  0
 21 16  1  0  0  0  0
 22  3  1  0  0  0  0
 22 14  1  0  0  0  0
 23  9  1  0  0  0  0
 23 17  1  0  0  0  0
 24  9  1  0  0  0  0
 24 18  1  0  0  0  0
 25 15  1  0  0  0  0
 25 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034049

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC2=C(OCO2)C=C1C1=CC2=C(OC1=O)C=C1OC=CC1=C2

> <INCHI_IDENTIFIER>
InChI=1S/C19H12O6/c1-21-16-8-18-17(23-9-24-18)6-12(16)13-5-11-4-10-2-3-22-14(10)7-15(11)25-19(13)20/h2-8H,9H2,1H3

> <INCHI_KEY>
PENSQRMNZZWMGV-UHFFFAOYSA-N

> <FORMULA>
C19H12O6

> <MOLECULAR_WEIGHT>
336.295

> <EXACT_MASS>
336.063388116

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
33.911084921879485

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-(6-methoxy-2H-1,3-benzodioxol-5-yl)-7H-furo[3,2-g]chromen-7-one

> <ALOGPS_LOGP>
3.15

> <JCHEM_LOGP>
3.076133013333333

> <ALOGPS_LOGS>
-3.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2005140954355773

> <JCHEM_POLAR_SURFACE_AREA>
67.13000000000001

> <JCHEM_REFRACTIVITY>
87.07189999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.72e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pachyrrhizin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0034049
     RDKit          3D
Pachyrrhizin
 37 41  0  0  0  0  0  0  0  0999 V2000
    1.3233    0.1577    3.4251 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0459    0.2584    2.0447 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0209    0.2761    1.0682 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3644    0.1959    1.3638 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3364    0.2150    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9403    0.3169   -0.9445 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5814    0.3986   -1.2530 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6304    0.3778   -0.2465 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2215    0.4617   -0.5498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7448   -0.3307   -0.0143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0590   -0.1594   -0.3794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0820   -0.9391    0.1354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3979   -0.7594   -0.2376 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5942   -1.3608    0.0930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6153   -0.7529   -0.6064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0478    0.1797   -1.3298 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7500    0.2221   -1.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7182    0.9903   -1.6576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4020    0.8207   -1.2936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4343    1.5717   -1.7926 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1760    1.4291   -1.4619 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6995    2.1887   -1.9835 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0702    0.3166   -1.7503 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1590   -0.0192   -0.9128 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7143    0.1495    0.4132 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3534   -0.0025    3.9406 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7790    1.0803    3.8273 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9361   -0.7551    3.6494 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7031    0.1156    2.3750 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3022    0.4779   -2.3001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4637   -1.0932    0.6994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8375   -1.7089    0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7118   -2.1889    0.7984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6878   -1.0011   -0.5648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9445    1.7678   -2.3750 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4553   -1.0857   -1.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0303    0.6689   -1.1191 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  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
  6 23  1  0
 23 24  1  0
 24 25  1  0
  8  3  1  0
 21  9  1  0
 25  5  1  0
 19 11  1  0
 17 13  2  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  7 30  1  0
 10 31  1  0
 12 32  1  0
 14 33  1  0
 15 34  1  0
 18 35  1  0
 24 36  1  0
 24 37  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       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.988  -4.586   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.519  -4.747   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.371   3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       5.145  -3.340   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -5.466   1.834   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -5.466   4.326   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
CONECT    1   21                                                            
CONECT    2    3   10                                                       
CONECT    3    2   22                                                       
CONECT    4   10   11                                                       
CONECT    5   11   13                                                       
CONECT    6   12   17                                                       
CONECT    7   14   15                                                       
CONECT    8   16   18                                                       
CONECT    9   23   24                                                       
CONECT   10    2    4   14                                                  
CONECT   11    4    5   15                                                  
CONECT   12    6   13   16                                                  
CONECT   13    5   12   19                                                  
CONECT   14    7   10   22                                                  
CONECT   15    7   11   25                                                  
CONECT   16    8   12   21                                                  
CONECT   17    6   18   23                                                  
CONECT   18    8   17   24                                                  
CONECT   19   13   20   25                                                  
CONECT   20   19                                                            
CONECT   21    1   16                                                       
CONECT   22    3   14                                                       
CONECT   23    9   17                                                       
CONECT   24    9   18                                                       
CONECT   25   15   19                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   58    0
END

COMPND    HMDB0034049
HETATM    1  C1  UNL     1       1.323   0.158   3.425  1.00  0.00           C  
HETATM    2  O1  UNL     1       1.046   0.258   2.045  1.00  0.00           O  
HETATM    3  C2  UNL     1       2.021   0.276   1.068  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.364   0.196   1.364  1.00  0.00           C  
HETATM    5  C4  UNL     1       4.336   0.215   0.369  1.00  0.00           C  
HETATM    6  C5  UNL     1       3.940   0.317  -0.945  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.581   0.399  -1.253  1.00  0.00           C  
HETATM    8  C7  UNL     1       1.630   0.378  -0.247  1.00  0.00           C  
HETATM    9  C8  UNL     1       0.221   0.462  -0.550  1.00  0.00           C  
HETATM   10  C9  UNL     1      -0.745  -0.331  -0.014  1.00  0.00           C  
HETATM   11  C10 UNL     1      -2.059  -0.159  -0.379  1.00  0.00           C  
HETATM   12  C11 UNL     1      -3.082  -0.939   0.135  1.00  0.00           C  
HETATM   13  C12 UNL     1      -4.398  -0.759  -0.238  1.00  0.00           C  
HETATM   14  C13 UNL     1      -5.594  -1.361   0.093  1.00  0.00           C  
HETATM   15  C14 UNL     1      -6.615  -0.753  -0.606  1.00  0.00           C  
HETATM   16  O2  UNL     1      -6.048   0.180  -1.330  1.00  0.00           O  
HETATM   17  C15 UNL     1      -4.750   0.222  -1.154  1.00  0.00           C  
HETATM   18  C16 UNL     1      -3.718   0.990  -1.658  1.00  0.00           C  
HETATM   19  C17 UNL     1      -2.402   0.821  -1.294  1.00  0.00           C  
HETATM   20  O3  UNL     1      -1.434   1.572  -1.793  1.00  0.00           O  
HETATM   21  C18 UNL     1      -0.176   1.429  -1.462  1.00  0.00           C  
HETATM   22  O4  UNL     1       0.700   2.189  -1.984  1.00  0.00           O  
HETATM   23  O5  UNL     1       5.070   0.317  -1.750  1.00  0.00           O  
HETATM   24  C19 UNL     1       6.159  -0.019  -0.913  1.00  0.00           C  
HETATM   25  O6  UNL     1       5.714   0.149   0.413  1.00  0.00           O  
HETATM   26  H1  UNL     1       0.353  -0.002   3.941  1.00  0.00           H  
HETATM   27  H2  UNL     1       1.779   1.080   3.827  1.00  0.00           H  
HETATM   28  H3  UNL     1       1.936  -0.755   3.649  1.00  0.00           H  
HETATM   29  H4  UNL     1       3.703   0.116   2.375  1.00  0.00           H  
HETATM   30  H5  UNL     1       2.302   0.478  -2.300  1.00  0.00           H  
HETATM   31  H6  UNL     1      -0.464  -1.093   0.699  1.00  0.00           H  
HETATM   32  H7  UNL     1      -2.838  -1.709   0.849  1.00  0.00           H  
HETATM   33  H8  UNL     1      -5.712  -2.189   0.798  1.00  0.00           H  
HETATM   34  H9  UNL     1      -7.688  -1.001  -0.565  1.00  0.00           H  
HETATM   35  H10 UNL     1      -3.944   1.768  -2.375  1.00  0.00           H  
HETATM   36  H11 UNL     1       6.455  -1.086  -1.125  1.00  0.00           H  
HETATM   37  H12 UNL     1       7.030   0.669  -1.119  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5   29
CONECT    5    6    6   25
CONECT    6    7   23
CONECT    7    8    8   30
CONECT    8    9
CONECT    9   10   10   21
CONECT   10   11   31
CONECT   11   12   12   19
CONECT   12   13   32
CONECT   13   14   17   17
CONECT   14   15   15   33
CONECT   15   16   34
CONECT   16   17
CONECT   17   18
CONECT   18   19   19   35
CONECT   19   20
CONECT   20   21
CONECT   21   22   22
CONECT   23   24
CONECT   24   25   36   37
END

HMDB0034049
     RDKit          3D
Pachyrrhizin
 37 41  0  0  0  0  0  0  0  0999 V2000
    1.3233    0.1577    3.4251 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0459    0.2584    2.0447 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0209    0.2761    1.0682 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3644    0.1959    1.3638 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3364    0.2150    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9403    0.3169   -0.9445 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5814    0.3986   -1.2530 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6304    0.3778   -0.2465 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2215    0.4617   -0.5498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7448   -0.3307   -0.0143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0590   -0.1594   -0.3794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0820   -0.9391    0.1354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3979   -0.7594   -0.2376 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5942   -1.3608    0.0930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6153   -0.7529   -0.6064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0478    0.1797   -1.3298 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7500    0.2221   -1.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7182    0.9903   -1.6576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4020    0.8207   -1.2936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4343    1.5717   -1.7926 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1760    1.4291   -1.4619 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6995    2.1887   -1.9835 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0702    0.3166   -1.7503 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1590   -0.0192   -0.9128 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7143    0.1495    0.4132 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3534   -0.0025    3.9406 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7790    1.0803    3.8273 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9361   -0.7551    3.6494 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7031    0.1156    2.3750 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3022    0.4779   -2.3001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4637   -1.0932    0.6994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8375   -1.7089    0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7118   -2.1889    0.7984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6878   -1.0011   -0.5648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9445    1.7678   -2.3750 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4553   -1.0857   -1.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0303    0.6689   -1.1191 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  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
  6 23  1  0
 23 24  1  0
 24 25  1  0
  8  3  1  0
 21  9  1  0
 25  5  1  0
 19 11  1  0
 17 13  2  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  7 30  1  0
 10 31  1  0
 12 32  1  0
 14 33  1  0
 15 34  1  0
 18 35  1  0
 24 36  1  0
 24 37  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
6-(2-Methoxy-4,5-methylenedioxyphenyl)furocoumarin	HMDB
6-(6-Methoxy-1,3-benzodioxol-5-yl)-7H-furo[3,2-g][1]benzopyran-7-one, 9ci	HMDB
Neorautone	HMDB
Pachyrhizin	HMDB

Chemical Formula

C₁₉H₁₂O₆

Average Molecular Weight

336.295

Monoisotopic Molecular Weight

336.063388116

IUPAC Name

6-(6-methoxy-2H-1,3-benzodioxol-5-yl)-7H-furo[3,2-g]chromen-7-one

Traditional Name

pachyrrhizin

CAS Registry Number

10091-01-7

SMILES

COC1=CC2=C(OCO2)C=C1C1=CC2=C(OC1=O)C=C1OC=CC1=C2

InChI Identifier

InChI=1S/C19H12O6/c1-21-16-8-18-17(23-9-24-18)6-12(16)13-5-11-4-10-2-3-22-14(10)7-15(11)25-19(13)20/h2-8H,9H2,1H3

InChI Key

PENSQRMNZZWMGV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoflav-3-enones. These are flavonoids with a structure based on an isoflav-3-ene skeleton bearing an oxo-group at position C2.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

Isoflav-3-enes

Direct Parent

Isoflav-3-enones

Alternative Parents

Substituents

Furanoisoflavonoid skeleton
Isoflav-3-enone skeleton
Furanocoumarin
Linear furanocoumarin
Psoralen
Coumarin
Benzopyran
1-benzopyran
Benzodioxole
Benzofuran
Anisole
Pyranone
Alkyl aryl ether
Pyran
Benzenoid
Heteroaromatic compound
Furan
Lactone
Ether
Acetal
Organoheterocyclic compound
Oxacycle
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Other Flavonoids (LMPK12160013 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0034049)
Cell membrane (HMDB: HMDB0034049)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0034049)

Source

Exogenous

Exogenous (HMDB: HMDB0034049)

Food

Food (HMDB: HMDB0034049)

Vegetable

Root vegetable

Jicama (FooDB: FOOD00509)

Pulse

Pulses (FooDB: FOOD00867)

Endogenous

Plant

Plant (HMDB: HMDB0034049)
Fabaceae (HMDB: HMDB0034049)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0034049)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	207 - 209 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	3.08 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.057 g/L	ALOGPS
logP	3.15	ALOGPS
logP	3.08	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	67.13 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	87.07 m³·mol⁻¹	ChemAxon
Polarizability	33.91 Å³	ChemAxon
Number of Rings	5	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]+	176.016	31661259
DarkChem	[M-H]-	179.003	31661259
DeepCCS	[M+H]+	174.187	30932474
DeepCCS	[M-H]-	171.829	30932474
DeepCCS	[M-2H]-	205.904	30932474
DeepCCS	[M+Na]+	181.131	30932474
AllCCS	[M+H]+	177.4	32859911
AllCCS	[M+H-H2O]+	173.9	32859911
AllCCS	[M+NH4]+	180.7	32859911
AllCCS	[M+Na]+	181.6	32859911
AllCCS	[M-H]-	179.2	32859911
AllCCS	[M+Na-2H]-	178.0	32859911
AllCCS	[M+HCOO]-	176.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pachyrrhizin	COC1=CC2=C(OCO2)C=C1C1=CC2=C(OC1=O)C=C1OC=CC1=C2	4407.2	Standard polar	33892256
Pachyrrhizin	COC1=CC2=C(OCO2)C=C1C1=CC2=C(OC1=O)C=C1OC=CC1=C2	3017.9	Standard non polar	33892256
Pachyrrhizin	COC1=CC2=C(OCO2)C=C1C1=CC2=C(OC1=O)C=C1OC=CC1=C2	3210.7	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 - Pachyrrhizin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4l-1169000000-374550ff8e39af1c9c85	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pachyrrhizin 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pachyrrhizin 40V, Positive-QTOF	splash10-00rj-0390000000-1710b32ae753b46b8813	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pachyrrhizin 10V, Positive-QTOF	splash10-000i-0119000000-4f0ad9ad0587fe29383b	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pachyrrhizin 20V, Positive-QTOF	splash10-0adr-0269000000-879536834d24c29c7d06	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 10V, Positive-QTOF	splash10-000i-0009000000-b2c4c976a55d762d0385	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 20V, Positive-QTOF	splash10-000i-0019000000-9061fae0bde6db8ff762	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 40V, Positive-QTOF	splash10-06rl-1092000000-0b627b170378b487616a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 10V, Negative-QTOF	splash10-000i-0019000000-e530bf3b45770445ae2d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 20V, Negative-QTOF	splash10-000i-0039000000-6c73fd50a072b2977831	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 40V, Negative-QTOF	splash10-01rf-1091000000-377bf81d2f33da78938a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 10V, Negative-QTOF	splash10-000i-0009000000-cf75db3fcf76086bc0a2	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 20V, Negative-QTOF	splash10-000i-0009000000-cf75db3fcf76086bc0a2	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 40V, Negative-QTOF	splash10-0a4i-0093000000-1794bdf37da1acff5953	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 10V, Positive-QTOF	splash10-000i-0009000000-a487dc1a344a66353635	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 20V, Positive-QTOF	splash10-000i-0009000000-1ef859e68262f16ed033	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pachyrrhizin 40V, Positive-QTOF	splash10-0a4l-0096000000-ff36862384daa809ffbd	2021-09-25	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

FDB012293

KNApSAcK ID

C00009783

Chemspider ID

91510

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101277

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1840061

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.. .

Showing metabocard for Pachyrrhizin (HMDB0034049)

MOL for HMDB0034049 (Pachyrrhizin)

3D MOL for HMDB0034049 (Pachyrrhizin)

3D SDF for HMDB0034049 (Pachyrrhizin)

3D-SDF for HMDB0034049 (Pachyrrhizin)

PDB for HMDB0034049 (Pachyrrhizin)

3D PDB for HMDB0034049 (Pachyrrhizin)

SMILES for HMDB0034049 (Pachyrrhizin)

INCHI for HMDB0034049 (Pachyrrhizin)

Structure for HMDB0034049 (Pachyrrhizin)

3D Structure for HMDB0034049 (Pachyrrhizin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra