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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 20:18:20 UTC

Update Date

2021-09-26 23:15:42 UTC

HMDB ID

HMDB0258642

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Swerchirin

Description

swerchirin belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. swerchirin 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 a small amount of articles have been published on swerchirin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Swerchirin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Swerchirin 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

HMDB0258642
     RDKit          3D
Swerchirin
 33 35  0  0  0  0  0  0  0  0999 V2000
    5.5913   -0.7237   -0.1222 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3437   -1.3316   -0.3786 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1983   -0.5688   -0.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2547    0.7127    0.3477 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1132    1.4994    0.6086 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2662    2.7521    1.0747 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8944    0.9265    0.3658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2867    1.5922    0.5811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2661    2.7455    1.0071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4751    0.9569    0.3161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6589    1.6391    0.5374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7617    2.8964    0.9986 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8627    0.9683    0.2590 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8418   -0.3055   -0.2105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6645   -0.9884   -0.4322 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5980   -2.2880   -0.9100 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7508   -3.0503   -1.2209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4808   -0.3443   -0.1641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3498   -0.9646   -0.3639 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8115   -0.3827   -0.1193 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9575   -1.1160   -0.3604 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6129    0.2088   -0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4420   -1.3763   -0.3078 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5627   -0.3597    0.9441 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2274    1.1367    0.5291 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6487    3.4379    1.3119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1453    3.5721    1.2638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7912    1.4856    0.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7519   -0.8767   -0.4447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3660   -3.2318   -0.3107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3615   -2.4736   -1.9609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4097   -4.0166   -1.6457 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8978   -2.1315   -0.7367 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  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 21  3  1  0
 20  7  1  0
 18 10  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  6 26  1  0
 12 27  1  0
 13 28  1  0
 14 29  1  0
 17 30  1  0
 17 31  1  0
 17 32  1  0
 21 33  1  0
M  END


  Mrv1533004251509462D          

 21 23  0  0  0  0            999 V2000
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  2  0  0  0  0
 10 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
  7 20  1  0  0  0  0
 20 21  2  0  0  0  0
  3 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258642

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC(O)=C2C(=O)C3=C(O)C=CC(OC)=C3OC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H12O6/c1-19-7-5-9(17)12-11(6-7)21-15-10(20-2)4-3-8(16)13(15)14(12)18/h3-6,16-17H,1-2H3

> <INCHI_KEY>
GNSHHHWDGOHNPC-UHFFFAOYSA-N

> <FORMULA>
C15H12O6

> <MOLECULAR_WEIGHT>
288.255

> <EXACT_MASS>
288.063388106

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
28.172529756403243

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,8-dihydroxy-3,5-dimethoxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
2.71

> <JCHEM_LOGP>
3.337167045666667

> <ALOGPS_LOGS>
-3.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.012735977207559

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.184813165497093

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7475221160487497

> <JCHEM_POLAR_SURFACE_AREA>
85.22000000000001

> <JCHEM_REFRACTIVITY>
73.70450000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.90e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
swerchirin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0258642
     RDKit          3D
Swerchirin
 33 35  0  0  0  0  0  0  0  0999 V2000
    5.5913   -0.7237   -0.1222 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3437   -1.3316   -0.3786 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1983   -0.5688   -0.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2547    0.7127    0.3477 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1132    1.4994    0.6086 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2662    2.7521    1.0747 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8944    0.9265    0.3658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2867    1.5922    0.5811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2661    2.7455    1.0071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4751    0.9569    0.3161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6589    1.6391    0.5374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7617    2.8964    0.9986 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8627    0.9683    0.2590 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8418   -0.3055   -0.2105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6645   -0.9884   -0.4322 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5980   -2.2880   -0.9100 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7508   -3.0503   -1.2209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4808   -0.3443   -0.1641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3498   -0.9646   -0.3639 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8115   -0.3827   -0.1193 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9575   -1.1160   -0.3604 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6129    0.2088   -0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4420   -1.3763   -0.3078 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5627   -0.3597    0.9441 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2274    1.1367    0.5291 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6487    3.4379    1.3119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1453    3.5721    1.2638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7912    1.4856    0.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7519   -0.8767   -0.4447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3660   -3.2318   -0.3107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3615   -2.4736   -1.9609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4097   -4.0166   -1.6457 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8978   -2.1315   -0.7367 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  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 21  3  1  0
 20  7  1  0
 18 10  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  6 26  1  0
 12 27  1  0
 13 28  1  0
 14 29  1  0
 17 30  1  0
 17 31  1  0
 17 32  1  0
 21 33  1  0
M  END

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   20                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   18                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   10   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19    7   21                                                  
CONECT   21   20    3                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

COMPND    HMDB0258642
HETATM    1  C1  UNL     1       5.591  -0.724  -0.122  1.00  0.00           C  
HETATM    2  O1  UNL     1       4.344  -1.332  -0.379  1.00  0.00           O  
HETATM    3  C2  UNL     1       3.198  -0.569  -0.127  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.255   0.713   0.348  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.113   1.499   0.609  1.00  0.00           C  
HETATM    6  O2  UNL     1       2.266   2.752   1.075  1.00  0.00           O  
HETATM    7  C5  UNL     1       0.894   0.926   0.366  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.287   1.592   0.581  1.00  0.00           C  
HETATM    9  O3  UNL     1      -0.266   2.745   1.007  1.00  0.00           O  
HETATM   10  C7  UNL     1      -1.475   0.957   0.316  1.00  0.00           C  
HETATM   11  C8  UNL     1      -2.659   1.639   0.537  1.00  0.00           C  
HETATM   12  O4  UNL     1      -2.762   2.896   0.999  1.00  0.00           O  
HETATM   13  C9  UNL     1      -3.863   0.968   0.259  1.00  0.00           C  
HETATM   14  C10 UNL     1      -3.842  -0.305  -0.210  1.00  0.00           C  
HETATM   15  C11 UNL     1      -2.665  -0.988  -0.432  1.00  0.00           C  
HETATM   16  O5  UNL     1      -2.598  -2.288  -0.910  1.00  0.00           O  
HETATM   17  C12 UNL     1      -3.751  -3.050  -1.221  1.00  0.00           C  
HETATM   18  C13 UNL     1      -1.481  -0.344  -0.164  1.00  0.00           C  
HETATM   19  O6  UNL     1      -0.350  -0.965  -0.364  1.00  0.00           O  
HETATM   20  C14 UNL     1       0.811  -0.383  -0.119  1.00  0.00           C  
HETATM   21  C15 UNL     1       1.957  -1.116  -0.360  1.00  0.00           C  
HETATM   22  H1  UNL     1       5.613   0.209  -0.756  1.00  0.00           H  
HETATM   23  H2  UNL     1       6.442  -1.376  -0.308  1.00  0.00           H  
HETATM   24  H3  UNL     1       5.563  -0.360   0.944  1.00  0.00           H  
HETATM   25  H4  UNL     1       4.227   1.137   0.529  1.00  0.00           H  
HETATM   26  H5  UNL     1       1.649   3.438   1.312  1.00  0.00           H  
HETATM   27  H6  UNL     1      -2.145   3.572   1.264  1.00  0.00           H  
HETATM   28  H7  UNL     1      -4.791   1.486   0.426  1.00  0.00           H  
HETATM   29  H8  UNL     1      -4.752  -0.877  -0.445  1.00  0.00           H  
HETATM   30  H9  UNL     1      -4.366  -3.232  -0.311  1.00  0.00           H  
HETATM   31  H10 UNL     1      -4.361  -2.474  -1.961  1.00  0.00           H  
HETATM   32  H11 UNL     1      -3.410  -4.017  -1.646  1.00  0.00           H  
HETATM   33  H12 UNL     1       1.898  -2.132  -0.737  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3
CONECT    3    4    4   21
CONECT    4    5   25
CONECT    5    6    7    7
CONECT    6   26
CONECT    7    8   20
CONECT    8    9    9   10
CONECT   10   11   11   18
CONECT   11   12   13
CONECT   12   27
CONECT   13   14   14   28
CONECT   14   15   29
CONECT   15   16   18   18
CONECT   16   17
CONECT   17   30   31   32
CONECT   18   19
CONECT   19   20
CONECT   20   21   21
CONECT   21   33
END

HMDB0258642
     RDKit          3D
Swerchirin
 33 35  0  0  0  0  0  0  0  0999 V2000
    5.5913   -0.7237   -0.1222 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3437   -1.3316   -0.3786 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1983   -0.5688   -0.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2547    0.7127    0.3477 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1132    1.4994    0.6086 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2662    2.7521    1.0747 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8944    0.9265    0.3658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2867    1.5922    0.5811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2661    2.7455    1.0071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4751    0.9569    0.3161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6589    1.6391    0.5374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7617    2.8964    0.9986 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8627    0.9683    0.2590 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8418   -0.3055   -0.2105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6645   -0.9884   -0.4322 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5980   -2.2880   -0.9100 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7508   -3.0503   -1.2209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4808   -0.3443   -0.1641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3498   -0.9646   -0.3639 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8115   -0.3827   -0.1193 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9575   -1.1160   -0.3604 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6129    0.2088   -0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4420   -1.3763   -0.3078 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5627   -0.3597    0.9441 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2274    1.1367    0.5291 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6487    3.4379    1.3119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1453    3.5721    1.2638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7912    1.4856    0.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7519   -0.8767   -0.4447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3660   -3.2318   -0.3107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3615   -2.4736   -1.9609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4097   -4.0166   -1.6457 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8978   -2.1315   -0.7367 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  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 21  3  1  0
 20  7  1  0
 18 10  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  6 26  1  0
 12 27  1  0
 13 28  1  0
 14 29  1  0
 17 30  1  0
 17 31  1  0
 17 32  1  0
 21 33  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1,8-Dihydroxy-3,5-dimethoxyxanthone	ChEBI
3,5-Dimethoxy-1,8-dihydroxyxanthone	ChEBI
5-O-Methylbellidifolin	ChEBI
Methylbellidifolin	ChEBI
1,8-Dihydroxy-3,5-dimethoxy-xanthenone	MeSH
1,8-Dihydroxy-3,5-dimethoxyxanthenone	MeSH

Chemical Formula

C₁₅H₁₂O₆

Average Molecular Weight

288.255

Monoisotopic Molecular Weight

288.063388106

IUPAC Name

1,8-dihydroxy-3,5-dimethoxy-9H-xanthen-9-one

Traditional Name

swerchirin

CAS Registry Number

Not Available

SMILES

COC1=CC(O)=C2C(=O)C3=C(O)C=CC(OC)=C3OC2=C1

InChI Identifier

InChI=1S/C15H12O6/c1-19-7-5-9(17)12-11(6-7)21-15-10(20-2)4-3-8(16)13(15)14(12)18/h3-6,16-17H,1-2H3

InChI Key

GNSHHHWDGOHNPC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Xanthone
Chromone
Anisole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Ether
Oxacycle
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

aromatic ether (CHEBI:9368 )
phenols (CHEBI:9368 )
xanthones (CHEBI:9368 )
xanthenes (C10091 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

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	2.71	ALOGPS
logP	3.34	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	8.18	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	85.22 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	73.7 m³·mol⁻¹	ChemAxon
Polarizability	28.17 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	168.171	30932474
DeepCCS	[M-H]-	165.813	30932474
DeepCCS	[M-2H]-	198.953	30932474
DeepCCS	[M+Na]+	174.265	30932474
AllCCS	[M+H]+	163.9	32859911
AllCCS	[M+H-H2O]+	160.2	32859911
AllCCS	[M+NH4]+	167.4	32859911
AllCCS	[M+Na]+	168.4	32859911
AllCCS	[M-H]-	166.3	32859911
AllCCS	[M+Na-2H]-	165.7	32859911
AllCCS	[M+HCOO]-	165.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Swerchirin	COC1=CC(O)=C2C(=O)C3=C(O)C=CC(OC)=C3OC2=C1	4536.2	Standard polar	33892256
Swerchirin	COC1=CC(O)=C2C(=O)C3=C(O)C=CC(OC)=C3OC2=C1	2803.6	Standard non polar	33892256
Swerchirin	COC1=CC(O)=C2C(=O)C3=C(O)C=CC(OC)=C3OC2=C1	2620.1	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 - Swerchirin GC-MS (Non-derivatized) - 70eV, Positive	splash10-08fs-0690000000-50f23365f400d9f2cdf8	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Swerchirin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Swerchirin GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Swerchirin GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Swerchirin GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Swerchirin GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Swerchirin GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Swerchirin GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

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

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

Not Available

KNApSAcK ID

C00002973

Chemspider ID

4444979

KEGG Compound ID

C10091

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

9368

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 Swerchirin (HMDB0258642)

MOL for HMDB0258642 (Swerchirin)

3D MOL for HMDB0258642 (Swerchirin)

3D SDF for HMDB0258642 (Swerchirin)

3D-SDF for HMDB0258642 (Swerchirin)

PDB for HMDB0258642 (Swerchirin)

3D PDB for HMDB0258642 (Swerchirin)

SMILES for HMDB0258642 (Swerchirin)

INCHI for HMDB0258642 (Swerchirin)

Structure for HMDB0258642 (Swerchirin)

3D Structure for HMDB0258642 (Swerchirin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra