Jump To Section:

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

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 19:45:59 UTC

Update Date

2022-09-22 17:45:02 UTC

HMDB ID

HMDB0258334

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Skimmin

Description

Skimmin belongs to the class of organic compounds known as coumarin glycosides. These are aromatic compounds containing a carbohydrate moiety glycosidically bound to a coumarin moiety. Skimmin has been detected, but not quantified in, sweet potatos (Ipomoea batatas). This could make skimmin a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Skimmin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Skimmin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Skimmin is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0258334
     RDKit          3D
Skimmin
 39 41  0  0  0  0  0  0  0  0999 V2000
    6.3715    0.1723   -1.9896 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5653    0.2206   -1.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0472    0.3965    0.2752 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1658    0.4453    1.3195 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8242    0.3163    1.0563 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9053    0.3584    2.0651 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5586    0.2282    1.7940 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0713    0.0512    0.5111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2691   -0.0664    0.3500 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0078   -0.2516   -0.8355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7662    0.8727   -1.0063 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0110    0.8938   -0.5045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1812    2.1829    0.3117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2226    2.1361    1.3230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3900   -0.2394    0.3946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7398   -0.1705    0.7081 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1467   -1.5095   -0.3924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0358   -1.5943   -1.4699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7245   -1.5474   -0.8012 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6563   -2.2041   -2.0397 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0174    0.0120   -0.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3728    0.1411   -0.2343 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2752    0.1049   -1.1787 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1131    0.4954    0.4523 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4934    0.5819    2.3428 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2328    0.4963    3.0998 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8680    0.2663    2.6111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2776   -0.2887   -1.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7697    0.9191   -1.3339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2133    2.2230    0.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9659    3.0511   -0.3252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4295    2.6449    1.0442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7949   -0.2852    1.3115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3146   -0.2114   -0.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3973   -2.3537    0.2789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6087   -1.4353   -2.3287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1767   -2.2203   -0.0821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5035   -1.4879   -2.7135 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7208   -0.1206   -1.4972 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
  8 21  1  0
 21 22  2  0
 22 23  1  0
 23  2  1  0
 22  5  1  0
 19 10  1  0
  3 24  1  0
  4 25  1  0
  6 26  1  0
  7 27  1  0
 10 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 21 39  1  0
M  END


  Mrv0541 02241218272D          

 23 25  0  0  0  0            999 V2000
   -0.3568   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3568    0.4126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7854   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5004   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2154   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9291   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2154    0.4126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5004    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7854    0.4126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7854    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9291   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2155   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2155    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5005    0.4126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7869    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0718    0.4126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3568    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3568   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0718   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7869   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5005   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 20  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3  4  1  0  0  0  0
  3 11  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6 10  1  0  0  0  0
  7  8  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 14 23  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 22  2  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258334

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(OC2=CC3=C(C=CC(=O)O3)C=C2)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H16O8/c16-6-10-12(18)13(19)14(20)15(23-10)21-8-3-1-7-2-4-11(17)22-9(7)5-8/h1-5,10,12-16,18-20H,6H2

> <INCHI_KEY>
VPAOSFFTKWUGAD-UHFFFAOYSA-N

> <FORMULA>
C15H16O8

> <MOLECULAR_WEIGHT>
324.2827

> <EXACT_MASS>
324.084517488

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
30.6402976774821

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-chromen-2-one

> <ALOGPS_LOGP>
-0.71

> <JCHEM_LOGP>
-0.7882737996666666

> <ALOGPS_LOGS>
-1.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.196090791020296

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.20014001345451

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092343722586

> <JCHEM_POLAR_SURFACE_AREA>
125.68000000000002

> <JCHEM_REFRACTIVITY>
75.6739

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}chromen-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0258334
     RDKit          3D
Skimmin
 39 41  0  0  0  0  0  0  0  0999 V2000
    6.3715    0.1723   -1.9896 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5653    0.2206   -1.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0472    0.3965    0.2752 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1658    0.4453    1.3195 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8242    0.3163    1.0563 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9053    0.3584    2.0651 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5586    0.2282    1.7940 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0713    0.0512    0.5111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2691   -0.0664    0.3500 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0078   -0.2516   -0.8355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7662    0.8727   -1.0063 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0110    0.8938   -0.5045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1812    2.1829    0.3117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2226    2.1361    1.3230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3900   -0.2394    0.3946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7398   -0.1705    0.7081 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1467   -1.5095   -0.3924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0358   -1.5943   -1.4699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7245   -1.5474   -0.8012 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6563   -2.2041   -2.0397 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0174    0.0120   -0.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3728    0.1411   -0.2343 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2752    0.1049   -1.1787 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1131    0.4954    0.4523 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4934    0.5819    2.3428 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2328    0.4963    3.0998 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8680    0.2663    2.6111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2776   -0.2887   -1.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7697    0.9191   -1.3339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2133    2.2230    0.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9659    3.0511   -0.3252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4295    2.6449    1.0442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7949   -0.2852    1.3115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3146   -0.2114   -0.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3973   -2.3537    0.2789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6087   -1.4353   -2.3287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1767   -2.2203   -0.0821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5035   -1.4879   -2.7135 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7208   -0.1206   -1.4972 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
  8 21  1  0
 21 22  2  0
 22 23  1  0
 23  2  1  0
 22  5  1  0
 19 10  1  0
  3 24  1  0
  4 25  1  0
  6 26  1  0
  7 27  1  0
 10 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 21 39  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      -0.666  -2.310   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.001  -1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.001   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.666   0.770   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -3.333  -2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.667  -1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.002  -2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -7.334  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -6.002   0.770   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -4.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.333   0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -3.333   2.310   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       7.334  -2.310   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.002  -1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.002   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.668   0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.336   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.001   0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.666   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.666  -1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.001  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.336  -1.540   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       4.668  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2   20                                                       
CONECT    2    1    3    5                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9   10                                                            
CONECT   10    6    9   11                                                  
CONECT   11    3   10   12                                                  
CONECT   12   11                                                            
CONECT   13   14                                                            
CONECT   14   13   15   23                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20    1   19   21                                                  
CONECT   21   20   22                                                       
CONECT   22   17   21   23                                                  
CONECT   23   14   22                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

COMPND    HMDB0258334
HETATM    1  O1  UNL     1       6.371   0.172  -1.990  1.00  0.00           O  
HETATM    2  C1  UNL     1       5.565   0.221  -1.001  1.00  0.00           C  
HETATM    3  C2  UNL     1       6.047   0.396   0.275  1.00  0.00           C  
HETATM    4  C3  UNL     1       5.166   0.445   1.319  1.00  0.00           C  
HETATM    5  C4  UNL     1       3.824   0.316   1.056  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.905   0.358   2.065  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.559   0.228   1.794  1.00  0.00           C  
HETATM    8  C7  UNL     1       1.071   0.051   0.511  1.00  0.00           C  
HETATM    9  O2  UNL     1      -0.269  -0.066   0.350  1.00  0.00           O  
HETATM   10  C8  UNL     1      -1.008  -0.252  -0.836  1.00  0.00           C  
HETATM   11  O3  UNL     1      -1.766   0.873  -1.006  1.00  0.00           O  
HETATM   12  C9  UNL     1      -3.011   0.894  -0.504  1.00  0.00           C  
HETATM   13  C10 UNL     1      -3.181   2.183   0.312  1.00  0.00           C  
HETATM   14  O4  UNL     1      -2.223   2.136   1.323  1.00  0.00           O  
HETATM   15  C11 UNL     1      -3.390  -0.239   0.395  1.00  0.00           C  
HETATM   16  O5  UNL     1      -4.740  -0.170   0.708  1.00  0.00           O  
HETATM   17  C12 UNL     1      -3.147  -1.510  -0.392  1.00  0.00           C  
HETATM   18  O6  UNL     1      -4.036  -1.594  -1.470  1.00  0.00           O  
HETATM   19  C13 UNL     1      -1.724  -1.547  -0.801  1.00  0.00           C  
HETATM   20  O7  UNL     1      -1.656  -2.204  -2.040  1.00  0.00           O  
HETATM   21  C14 UNL     1       2.017   0.012  -0.490  1.00  0.00           C  
HETATM   22  C15 UNL     1       3.373   0.141  -0.234  1.00  0.00           C  
HETATM   23  O8  UNL     1       4.275   0.105  -1.179  1.00  0.00           O  
HETATM   24  H1  UNL     1       7.113   0.495   0.452  1.00  0.00           H  
HETATM   25  H2  UNL     1       5.493   0.582   2.343  1.00  0.00           H  
HETATM   26  H3  UNL     1       3.233   0.496   3.100  1.00  0.00           H  
HETATM   27  H4  UNL     1       0.868   0.266   2.611  1.00  0.00           H  
HETATM   28  H5  UNL     1      -0.278  -0.289  -1.670  1.00  0.00           H  
HETATM   29  H6  UNL     1      -3.770   0.919  -1.334  1.00  0.00           H  
HETATM   30  H7  UNL     1      -4.213   2.223   0.730  1.00  0.00           H  
HETATM   31  H8  UNL     1      -2.966   3.051  -0.325  1.00  0.00           H  
HETATM   32  H9  UNL     1      -1.430   2.645   1.044  1.00  0.00           H  
HETATM   33  H10 UNL     1      -2.795  -0.285   1.311  1.00  0.00           H  
HETATM   34  H11 UNL     1      -5.315  -0.211  -0.086  1.00  0.00           H  
HETATM   35  H12 UNL     1      -3.397  -2.354   0.279  1.00  0.00           H  
HETATM   36  H13 UNL     1      -3.609  -1.435  -2.329  1.00  0.00           H  
HETATM   37  H14 UNL     1      -1.177  -2.220  -0.082  1.00  0.00           H  
HETATM   38  H15 UNL     1      -1.503  -1.488  -2.713  1.00  0.00           H  
HETATM   39  H16 UNL     1       1.721  -0.121  -1.497  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   23
CONECT    3    4    4   24
CONECT    4    5   25
CONECT    5    6    6   22
CONECT    6    7   26
CONECT    7    8    8   27
CONECT    8    9   21
CONECT    9   10
CONECT   10   11   19   28
CONECT   11   12
CONECT   12   13   15   29
CONECT   13   14   30   31
CONECT   14   32
CONECT   15   16   17   33
CONECT   16   34
CONECT   17   18   19   35
CONECT   18   36
CONECT   19   20   37
CONECT   20   38
CONECT   21   22   22   39
CONECT   22   23
END

HMDB0258334
     RDKit          3D
Skimmin
 39 41  0  0  0  0  0  0  0  0999 V2000
    6.3715    0.1723   -1.9896 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5653    0.2206   -1.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0472    0.3965    0.2752 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1658    0.4453    1.3195 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8242    0.3163    1.0563 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9053    0.3584    2.0651 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5586    0.2282    1.7940 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0713    0.0512    0.5111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2691   -0.0664    0.3500 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0078   -0.2516   -0.8355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7662    0.8727   -1.0063 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0110    0.8938   -0.5045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1812    2.1829    0.3117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2226    2.1361    1.3230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3900   -0.2394    0.3946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7398   -0.1705    0.7081 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1467   -1.5095   -0.3924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0358   -1.5943   -1.4699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7245   -1.5474   -0.8012 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6563   -2.2041   -2.0397 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0174    0.0120   -0.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3728    0.1411   -0.2343 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2752    0.1049   -1.1787 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1131    0.4954    0.4523 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4934    0.5819    2.3428 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2328    0.4963    3.0998 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8680    0.2663    2.6111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2776   -0.2887   -1.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7697    0.9191   -1.3339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2133    2.2230    0.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9659    3.0511   -0.3252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4295    2.6449    1.0442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7949   -0.2852    1.3115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3146   -0.2114   -0.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3973   -2.3537    0.2789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6087   -1.4353   -2.3287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1767   -2.2203   -0.0821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5035   -1.4879   -2.7135 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7208   -0.1206   -1.4972 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
  8 21  1  0
 21 22  2  0
 22 23  1  0
 23  2  1  0
 22  5  1  0
 19 10  1  0
  3 24  1  0
  4 25  1  0
  6 26  1  0
  7 27  1  0
 10 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 21 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₅H₁₆O₈

Average Molecular Weight

324.2827

Monoisotopic Molecular Weight

324.084517488

IUPAC Name

7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-chromen-2-one

Traditional Name

7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}chromen-2-one

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2=CC3=C(C=CC(=O)O3)C=C2)C(O)C(O)C1O

InChI Identifier

InChI=1S/C15H16O8/c16-6-10-12(18)13(19)14(20)15(23-10)21-8-3-1-7-2-4-11(17)22-9(7)5-8/h1-5,10,12-16,18-20H,6H2

InChI Key

VPAOSFFTKWUGAD-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumarin glycosides. These are aromatic compounds containing a carbohydrate moiety glycosidically bound to a coumarin moiety.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Coumarin glycosides

Direct Parent

Coumarin glycosides

Alternative Parents

Substituents

Coumarin-7-o-glycoside
Coumarin o-glycoside
Phenolic glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Benzopyran
1-benzopyran
Pyranone
Monosaccharide
Oxane
Benzenoid
Pyran
Heteroaromatic compound
Lactone
Secondary alcohol
Polyol
Organoheterocyclic compound
Acetal
Oxacycle
Alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Primary alcohol
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Sweet potato (FooDB: FOOD00092)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	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
logP	-0.71	ALOGPS
logP	-0.79	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	125.68 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	75.67 m³·mol⁻¹	ChemAxon
Polarizability	30.64 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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]+	170.042	30932474
DeepCCS	[M-H]-	167.684	30932474
DeepCCS	[M-2H]-	201.48	30932474
DeepCCS	[M+Na]+	176.708	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Skimmin	OCC1OC(OC2=CC3=C(C=CC(=O)O3)C=C2)C(O)C(O)C1O	4015.3	Standard polar	33892256
Skimmin	OCC1OC(OC2=CC3=C(C=CC(=O)O3)C=C2)C(O)C(O)C1O	2983.6	Standard non polar	33892256
Skimmin	OCC1OC(OC2=CC3=C(C=CC(=O)O3)C=C2)C(O)C(O)C1O	3234.4	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 - Skimmin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-9773000000-5129db7487ecf22b5b12	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TMS_4_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Skimmin GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-05	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 - Skimmin 10V, Positive-QTOF	splash10-03fr-0906000000-5a42a8b2417a5047dd36	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Skimmin 20V, Positive-QTOF	splash10-03di-0900000000-bac44801149c8aebcdd9	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Skimmin 40V, Positive-QTOF	splash10-03dj-1900000000-f0f3b4625a63fe7cddf7	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Skimmin 10V, Negative-QTOF	splash10-0229-1739000000-c0ed3c85b7c5f4a0f9b4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Skimmin 20V, Negative-QTOF	splash10-03di-1911000000-65eb11ab0f4adba0c5cb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Skimmin 40V, Negative-QTOF	splash10-02t9-2900000000-b4a29b66f32a7f230b1a	2016-08-03	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details

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

FDB000962

KNApSAcK ID

C00029702

Chemspider ID

283584

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Skimmin

METLIN ID

Not Available

PubChem Compound

320361

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Skimmin (HMDB0258334)

MOL for HMDB0258334 (Skimmin)

3D MOL for HMDB0258334 (Skimmin)

3D SDF for HMDB0258334 (Skimmin)

3D-SDF for HMDB0258334 (Skimmin)

PDB for HMDB0258334 (Skimmin)

3D PDB for HMDB0258334 (Skimmin)

SMILES for HMDB0258334 (Skimmin)

INCHI for HMDB0258334 (Skimmin)

Structure for HMDB0258334 (Skimmin)

3D Structure for HMDB0258334 (Skimmin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra