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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:49:40 UTC

Update Date

2022-03-07 02:53:58 UTC

HMDB ID

HMDB0034050

Secondary Accession Numbers

HMDB34050

Metabolite Identification

Common Name

Psoralidin

Description

Psoralidin belongs to the class of organic compounds known as coumestans. These are polycyclic aromatic compounds containing a coumestan moiety, which consists of a benzoxole fused to a chromen-2-one to form 1-Benzoxolo[3,2-c]chromen-6-one. They are oxidation products of pterocarpan. Thus, psoralidin is considered to be a flavonoid. Psoralidin has been detected, but not quantified in, a few different foods, such as fruits, lima beans (Phaseolus lunatus), and pulses. This could make psoralidin a potential biomarker for the consumption of these foods. Psoralidin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on Psoralidin.

Structure

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

HMDB0034050
     RDKit          3D
Psoralidin
 41 44  0  0  0  0  0  0  0  0999 V2000
   -5.7020    0.4122    0.4910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8232   -0.7039    0.0718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4304   -1.7956   -0.7444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5519   -0.7572    0.3910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8123    0.2533    1.1930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6968    0.7583    0.3372 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3971    0.3090    0.5826 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6753    0.7325   -0.1673 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4330    1.6326   -1.1919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8346    2.1025   -1.4694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9011    1.6530   -0.6895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1984    2.0877   -0.9180 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4599    2.0369   -1.9084 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6837    1.6022   -1.6634 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6751    1.9944   -2.3572 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9701    0.7077   -0.6555 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1478    0.1233   -0.2207 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4634    0.1972   -0.6062 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4393   -0.5222    0.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0526   -1.3337    1.0961 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0202   -2.0757    1.7674 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7319   -1.4071    1.4823 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7420   -0.6889    0.8448 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4413   -0.5782    1.0057 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9307    0.2463    0.1324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7153    1.1921   -0.3026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4391    0.8337    1.4884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7594    0.0236    0.5084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6727   -2.2636   -1.4212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2386   -1.3485   -1.3570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8200   -2.5530   -0.0433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9583   -1.6132    0.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3615   -0.2663    2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4351    1.0811    1.5567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2131   -0.3938    1.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0442    2.8075   -2.2668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3424    2.7449   -1.6737 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7200    0.8363   -1.4301 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4853   -0.4689   -0.2643 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7814   -2.6711    2.5355 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4943   -2.0567    2.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
  9 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 11  6  1  0
 25 16  2  0
 25  8  1  0
 23 17  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  3 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  7 35  1  0
 10 36  1  0
 12 37  1  0
 18 38  1  0
 19 39  1  0
 21 40  1  0
 22 41  1  0
M  END

  Mrv0541 05061307322D          

 25 28  0  0  0  0            999 V2000
    6.8417    0.8232    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6471    0.0392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5654    1.4658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7418    1.4187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4867    3.2441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2466    3.6222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4655    2.0613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1682    1.9741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2075    3.5350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0181    0.7761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2891    2.1084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5259    2.4201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9407    3.1762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0128    2.7510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6601    2.8453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9014    2.3522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3838    3.4879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7365    3.3936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1892    2.7039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1075    4.1305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2591    2.0420    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4838    2.8924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6548    4.8202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6731    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9312    4.1776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  2  0  0  0  0
 10  1  1  0  0  0  0
 10  2  1  0  0  0  0
 10  3  2  0  0  0  0
 11  4  1  0  0  0  0
 11  7  2  0  0  0  0
 12  5  1  0  0  0  0
 12  8  2  0  0  0  0
 13  6  1  0  0  0  0
 14  7  1  0  0  0  0
 15  9  2  0  0  0  0
 15 11  1  0  0  0  0
 16  8  1  0  0  0  0
 16 13  2  0  0  0  0
 17  9  1  0  0  0  0
 17 14  2  0  0  0  0
 18 13  1  0  0  0  0
 19 14  1  0  0  0  0
 19 18  2  0  0  0  0
 20 18  1  0  0  0  0
 21 12  1  0  0  0  0
 22 15  1  0  0  0  0
 23 20  2  0  0  0  0
 24 16  1  0  0  0  0
 24 19  1  0  0  0  0
 25 17  1  0  0  0  0
 25 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034050

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCC1=CC2=C(OC(=O)C3=C2OC2=C3C=CC(O)=C2)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H16O5/c1-10(2)3-4-11-7-14-17(9-15(11)22)25-20(23)18-13-6-5-12(21)8-16(13)24-19(14)18/h3,5-9,21-22H,4H2,1-2H3

> <INCHI_KEY>
YABIJLLNNFURIJ-UHFFFAOYSA-N

> <FORMULA>
C20H16O5

> <MOLECULAR_WEIGHT>
336.338

> <EXACT_MASS>
336.099773622

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
36.18785761290899

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,14-dihydroxy-4-(3-methylbut-2-en-1-yl)-8,17-dioxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-1(10),2(7),3,5,11(16),12,14-heptaen-9-one

> <ALOGPS_LOGP>
4.63

> <JCHEM_LOGP>
4.125888321666666

> <ALOGPS_LOGS>
-3.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.109940009002456

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.919911801174257

> <JCHEM_PKA_STRONGEST_BASIC>
-4.325477635685441

> <JCHEM_POLAR_SURFACE_AREA>
79.9

> <JCHEM_REFRACTIVITY>
93.86229999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.40e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
psoralidin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0034050
     RDKit          3D
Psoralidin
 41 44  0  0  0  0  0  0  0  0999 V2000
   -5.7020    0.4122    0.4910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8232   -0.7039    0.0718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4304   -1.7956   -0.7444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5519   -0.7572    0.3910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8123    0.2533    1.1930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6968    0.7583    0.3372 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3971    0.3090    0.5826 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6753    0.7325   -0.1673 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4330    1.6326   -1.1919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8346    2.1025   -1.4694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9011    1.6530   -0.6895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1984    2.0877   -0.9180 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4599    2.0369   -1.9084 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6837    1.6022   -1.6634 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6751    1.9944   -2.3572 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9701    0.7077   -0.6555 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1478    0.1233   -0.2207 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4634    0.1972   -0.6062 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4393   -0.5222    0.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0526   -1.3337    1.0961 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0202   -2.0757    1.7674 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7319   -1.4071    1.4823 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7420   -0.6889    0.8448 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4413   -0.5782    1.0057 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9307    0.2463    0.1324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7153    1.1921   -0.3026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4391    0.8337    1.4884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7594    0.0236    0.5084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6727   -2.2636   -1.4212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2386   -1.3485   -1.3570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8200   -2.5530   -0.0433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9583   -1.6132    0.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3615   -0.2663    2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4351    1.0811    1.5567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2131   -0.3938    1.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0442    2.8075   -2.2668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3424    2.7449   -1.6737 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7200    0.8363   -1.4301 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4853   -0.4689   -0.2643 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7814   -2.6711    2.5355 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4943   -2.0567    2.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
  9 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 11  6  1  0
 25 16  2  0
 25  8  1  0
 23 17  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  3 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  7 35  1  0
 10 36  1  0
 12 37  1  0
 18 38  1  0
 19 39  1  0
 21 40  1  0
 22 41  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      12.771   1.537   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.541   0.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.389   2.736   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.851   2.648   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.909   6.056   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.460   6.761   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.469   3.848   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.314   3.685   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.854   6.599   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.234   1.449   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.006   3.936   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.982   4.518   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.756   5.929   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.624   5.135   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.699   5.311   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.683   4.391   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.316   6.511   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.241   6.335   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.087   5.047   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.934   7.710   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -2.350   3.812   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      10.236   5.399   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       3.089   8.998   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       3.123   3.846   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.472   7.798   0.000  0.00  0.00           O+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3    4   10                                                       
CONECT    4    3   11                                                       
CONECT    5    6   12                                                       
CONECT    6    5   13                                                       
CONECT    7   11   14                                                       
CONECT    8   12   16                                                       
CONECT    9   15   17                                                       
CONECT   10    1    2    3                                                  
CONECT   11    4    7   15                                                  
CONECT   12    5    8   21                                                  
CONECT   13    6   16   18                                                  
CONECT   14    7   17   19                                                  
CONECT   15    9   11   22                                                  
CONECT   16    8   13   24                                                  
CONECT   17    9   14   25                                                  
CONECT   18   13   19   20                                                  
CONECT   19   14   18   24                                                  
CONECT   20   18   23   25                                                  
CONECT   21   12                                                            
CONECT   22   15                                                            
CONECT   23   20                                                            
CONECT   24   16   19                                                       
CONECT   25   17   20                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

COMPND    HMDB0034050
HETATM    1  C1  UNL     1      -5.702   0.412   0.491  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.823  -0.704   0.072  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.430  -1.796  -0.744  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.552  -0.757   0.391  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.812   0.253   1.193  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.697   0.758   0.337  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.397   0.309   0.583  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.675   0.733  -0.167  1.00  0.00           C  
HETATM    9  C9  UNL     1       0.433   1.633  -1.192  1.00  0.00           C  
HETATM   10  C10 UNL     1      -0.835   2.102  -1.469  1.00  0.00           C  
HETATM   11  C11 UNL     1      -1.901   1.653  -0.690  1.00  0.00           C  
HETATM   12  O1  UNL     1      -3.198   2.088  -0.918  1.00  0.00           O  
HETATM   13  O2  UNL     1       1.460   2.037  -1.908  1.00  0.00           O  
HETATM   14  C12 UNL     1       2.684   1.602  -1.663  1.00  0.00           C  
HETATM   15  O3  UNL     1       3.675   1.994  -2.357  1.00  0.00           O  
HETATM   16  C13 UNL     1       2.970   0.708  -0.656  1.00  0.00           C  
HETATM   17  C14 UNL     1       4.148   0.123  -0.221  1.00  0.00           C  
HETATM   18  C15 UNL     1       5.463   0.197  -0.606  1.00  0.00           C  
HETATM   19  C16 UNL     1       6.439  -0.522   0.036  1.00  0.00           C  
HETATM   20  C17 UNL     1       6.053  -1.334   1.096  1.00  0.00           C  
HETATM   21  O4  UNL     1       7.020  -2.076   1.767  1.00  0.00           O  
HETATM   22  C18 UNL     1       4.732  -1.407   1.482  1.00  0.00           C  
HETATM   23  C19 UNL     1       3.742  -0.689   0.845  1.00  0.00           C  
HETATM   24  O5  UNL     1       2.441  -0.578   1.006  1.00  0.00           O  
HETATM   25  C20 UNL     1       1.931   0.246   0.132  1.00  0.00           C  
HETATM   26  H1  UNL     1      -5.715   1.192  -0.303  1.00  0.00           H  
HETATM   27  H2  UNL     1      -5.439   0.834   1.488  1.00  0.00           H  
HETATM   28  H3  UNL     1      -6.759   0.024   0.508  1.00  0.00           H  
HETATM   29  H4  UNL     1      -4.673  -2.264  -1.421  1.00  0.00           H  
HETATM   30  H5  UNL     1      -6.239  -1.349  -1.357  1.00  0.00           H  
HETATM   31  H6  UNL     1      -5.820  -2.553  -0.043  1.00  0.00           H  
HETATM   32  H7  UNL     1      -2.958  -1.613   0.048  1.00  0.00           H  
HETATM   33  H8  UNL     1      -2.362  -0.266   2.083  1.00  0.00           H  
HETATM   34  H9  UNL     1      -3.435   1.081   1.557  1.00  0.00           H  
HETATM   35  H10 UNL     1      -0.213  -0.394   1.385  1.00  0.00           H  
HETATM   36  H11 UNL     1      -1.044   2.807  -2.267  1.00  0.00           H  
HETATM   37  H12 UNL     1      -3.342   2.745  -1.674  1.00  0.00           H  
HETATM   38  H13 UNL     1       5.720   0.836  -1.430  1.00  0.00           H  
HETATM   39  H14 UNL     1       7.485  -0.469  -0.264  1.00  0.00           H  
HETATM   40  H15 UNL     1       6.781  -2.671   2.536  1.00  0.00           H  
HETATM   41  H16 UNL     1       4.494  -2.057   2.315  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3    4    4
CONECT    3   29   30   31
CONECT    4    5   32
CONECT    5    6   33   34
CONECT    6    7    7   11
CONECT    7    8   35
CONECT    8    9    9   25
CONECT    9   10   13
CONECT   10   11   11   36
CONECT   11   12
CONECT   12   37
CONECT   13   14
CONECT   14   15   15   16
CONECT   16   17   25   25
CONECT   17   18   18   23
CONECT   18   19   38
CONECT   19   20   20   39
CONECT   20   21   22
CONECT   21   40
CONECT   22   23   23   41
CONECT   23   24
CONECT   24   25
END

HMDB0034050
     RDKit          3D
Psoralidin
 41 44  0  0  0  0  0  0  0  0999 V2000
   -5.7020    0.4122    0.4910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8232   -0.7039    0.0718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4304   -1.7956   -0.7444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5519   -0.7572    0.3910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8123    0.2533    1.1930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6968    0.7583    0.3372 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3971    0.3090    0.5826 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6753    0.7325   -0.1673 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4330    1.6326   -1.1919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8346    2.1025   -1.4694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9011    1.6530   -0.6895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1984    2.0877   -0.9180 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4599    2.0369   -1.9084 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6837    1.6022   -1.6634 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6751    1.9944   -2.3572 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9701    0.7077   -0.6555 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1478    0.1233   -0.2207 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4634    0.1972   -0.6062 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4393   -0.5222    0.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0526   -1.3337    1.0961 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0202   -2.0757    1.7674 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7319   -1.4071    1.4823 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7420   -0.6889    0.8448 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4413   -0.5782    1.0057 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9307    0.2463    0.1324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7153    1.1921   -0.3026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4391    0.8337    1.4884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7594    0.0236    0.5084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6727   -2.2636   -1.4212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2386   -1.3485   -1.3570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8200   -2.5530   -0.0433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9583   -1.6132    0.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3615   -0.2663    2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4351    1.0811    1.5567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2131   -0.3938    1.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0442    2.8075   -2.2668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3424    2.7449   -1.6737 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7200    0.8363   -1.4301 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4853   -0.4689   -0.2643 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7814   -2.6711    2.5355 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4943   -2.0567    2.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
  9 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 11  6  1  0
 25 16  2  0
 25  8  1  0
 23 17  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  3 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  7 35  1  0
 10 36  1  0
 12 37  1  0
 18 38  1  0
 19 39  1  0
 21 40  1  0
 22 41  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3,9-Dihydroxy-2-prenylcoumestan	ChEBI

Chemical Formula

C₂₀H₁₆O₅

Average Molecular Weight

336.338

Monoisotopic Molecular Weight

336.099773622

IUPAC Name

5,14-dihydroxy-4-(3-methylbut-2-en-1-yl)-8,17-dioxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-1(10),2(7),3,5,11(16),12,14-heptaen-9-one

Traditional Name

psoralidin

CAS Registry Number

18642-23-4

SMILES

CC(C)=CCC1=CC2=C(OC(=O)C3=C2OC2=C3C=CC(O)=C2)C=C1O

InChI Identifier

InChI=1S/C20H16O5/c1-10(2)3-4-11-7-14-17(9-15(11)22)25-20(23)18-13-6-5-12(21)8-16(13)24-19(14)18/h3,5-9,21-22H,4H2,1-2H3

InChI Key

YABIJLLNNFURIJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumestans. These are polycyclic aromatic compounds containing a coumestan moiety, which consists of a benzoxole fused to a chromen-2-one to form 1-Benzoxolo[3,2-c]chromen-6-one. They are oxidation products of pterocarpan.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

Coumestans

Direct Parent

Coumestans

Alternative Parents

Substituents

Coumestan
Angular furanocoumarin
Furanocoumarin
Coumarin
Benzopyran
1-benzopyran
Benzofuran
Furopyran
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Pyran
Benzenoid
Furan
Heteroaromatic compound
Lactone
Organoheterocyclic compound
Oxacycle
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

polyphenol (CHEBI:8616 )
delta-lactone (CHEBI:8616 )
coumestans (CHEBI:8616 )
Coumestan flavonoids (C10523 )
Coumestanes (C10523 )
Coumestan flavonoids (LMPK12090007 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0034050)
Cell membrane (HMDB: HMDB0034050)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0034050)

Source

Exogenous

Exogenous (HMDB: HMDB0034050)

Food

Food (HMDB: HMDB0034050)

Pulse

Bean

Lima bean (FooDB: FOOD00133)

Pulses (FooDB: FOOD00867)

Fruit

Fruits (FooDB: FOOD00871)

Endogenous

Plant

Plant (HMDB: HMDB0034050)
Fabaceae (HMDB: HMDB0034050)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0034050)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	290 - 292 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.98 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	0.064 g/L	ALOGPS
logP	4.63	ALOGPS
logP	4.13	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	6.92	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	79.9 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	93.86 m³·mol⁻¹	ChemAxon
Polarizability	36.19 Å³	ChemAxon
Number of Rings	4	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]+	182.051	31661259
DarkChem	[M-H]-	180.184	31661259
DeepCCS	[M+H]+	176.031	30932474
DeepCCS	[M-H]-	173.674	30932474
DeepCCS	[M-2H]-	207.701	30932474
DeepCCS	[M+Na]+	182.928	30932474
AllCCS	[M+H]+	180.1	32859911
AllCCS	[M+H-H2O]+	176.8	32859911
AllCCS	[M+NH4]+	183.2	32859911
AllCCS	[M+Na]+	184.1	32859911
AllCCS	[M-H]-	180.4	32859911
AllCCS	[M+Na-2H]-	179.6	32859911
AllCCS	[M+HCOO]-	178.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Psoralidin	CC(C)=CCC1=CC2=C(OC(=O)C3=C2OC2=C3C=CC(O)=C2)C=C1O	4524.2	Standard polar	33892256
Psoralidin	CC(C)=CCC1=CC2=C(OC(=O)C3=C2OC2=C3C=CC(O)=C2)C=C1O	3172.1	Standard non polar	33892256
Psoralidin	CC(C)=CCC1=CC2=C(OC(=O)C3=C2OC2=C3C=CC(O)=C2)C=C1O	3483.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Psoralidin,1TMS,isomer #1	CC(C)=CCC1=CC2=C(C=C1O)OC(=O)C1=C2OC2=CC(O[Si](C)(C)C)=CC=C21	3441.2	Semi standard non polar	33892256
Psoralidin,1TMS,isomer #2	CC(C)=CCC1=CC2=C(C=C1O[Si](C)(C)C)OC(=O)C1=C2OC2=CC(O)=CC=C21	3421.5	Semi standard non polar	33892256
Psoralidin,2TMS,isomer #1	CC(C)=CCC1=CC2=C(C=C1O[Si](C)(C)C)OC(=O)C1=C2OC2=CC(O[Si](C)(C)C)=CC=C21	3465.2	Semi standard non polar	33892256
Psoralidin,1TBDMS,isomer #1	CC(C)=CCC1=CC2=C(C=C1O)OC(=O)C1=C2OC2=CC(O[Si](C)(C)C(C)(C)C)=CC=C21	3640.9	Semi standard non polar	33892256
Psoralidin,1TBDMS,isomer #2	CC(C)=CCC1=CC2=C(C=C1O[Si](C)(C)C(C)(C)C)OC(=O)C1=C2OC2=CC(O)=CC=C21	3617.7	Semi standard non polar	33892256
Psoralidin,2TBDMS,isomer #1	CC(C)=CCC1=CC2=C(C=C1O[Si](C)(C)C(C)(C)C)OC(=O)C1=C2OC2=CC(O[Si](C)(C)C(C)(C)C)=CC=C21	3897.7	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 - Psoralidin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a6u-3649000000-fb4bed2219264a94b2c0	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Psoralidin GC-MS (2 TMS) - 70eV, Positive	splash10-06di-2021900000-af5a7fcfd2abc930bab8	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Psoralidin 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 - Psoralidin 10V, Positive-QTOF	splash10-000i-0029000000-611c9c21982e8c8417bc	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 20V, Positive-QTOF	splash10-00m0-5097000000-522ed689eb20e83a6060	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 40V, Positive-QTOF	splash10-0159-9160000000-7eabc2db1056ba50d5b1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 10V, Negative-QTOF	splash10-000i-0029000000-7390a95ac6006bbd4672	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 20V, Negative-QTOF	splash10-000i-0039000000-6317b2200c19c15fe546	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 40V, Negative-QTOF	splash10-0a5c-2892000000-2dc8e8c23fe68b07d783	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 10V, Negative-QTOF	splash10-000i-0009000000-dc81427ba733f47873d1	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 20V, Negative-QTOF	splash10-000i-0019000000-acb098f91f6b555322c7	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 40V, Negative-QTOF	splash10-0umr-0190000000-a3b3ed9e9206503a2435	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 10V, Positive-QTOF	splash10-000i-0019000000-af3d0665d7147a8a9b18	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 20V, Positive-QTOF	splash10-001r-0095000000-7b1aff3dc2da88d695d5	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Psoralidin 40V, Positive-QTOF	splash10-0far-0090000000-319a7d07214529aec4af	2021-09-24	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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Psoralidin

METLIN ID

Not Available

PubChem Compound

5281806

PDB ID

Not Available

ChEBI ID

8616

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1840071

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 Psoralidin (HMDB0034050)

MOL for HMDB0034050 (Psoralidin)

3D MOL for HMDB0034050 (Psoralidin)

3D SDF for HMDB0034050 (Psoralidin)

3D-SDF for HMDB0034050 (Psoralidin)

PDB for HMDB0034050 (Psoralidin)

3D PDB for HMDB0034050 (Psoralidin)

SMILES for HMDB0034050 (Psoralidin)

INCHI for HMDB0034050 (Psoralidin)

Structure for HMDB0034050 (Psoralidin)

3D Structure for HMDB0034050 (Psoralidin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra