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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 18:17:19 UTC

Update Date

2021-09-26 23:13:39 UTC

HMDB ID

HMDB0257354

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Rubiadin

Description

rubiadin belongs to the class of organic compounds known as hydroxyanthraquinones. Hydroxyanthraquinones are compounds containing a hydroxyanthraquinone moiety, which consists of an anthracene bearing a quinone, and hydroxyl group. Thus, rubiadin is considered to be an aromatic polyketide. rubiadin 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 significant number of articles have been published on rubiadin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Rubiadin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Rubiadin 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

HMDB0257354
     RDKit          3D
Rubiadin
 29 31  0  0  0  0  0  0  0  0999 V2000
   -4.2326   -0.8300   -0.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8856   -0.2607   -0.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7324    0.9435    0.5879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9022    1.5939    0.9728 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4796    1.4633    0.8400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3261    0.8137    0.4559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4684   -0.3916   -0.1988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7296   -0.9085   -0.4492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8258   -2.1200   -1.1085 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7521   -1.0806   -0.6061 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6279   -2.1757   -1.2012 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0864   -0.5620   -0.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2512   -1.1992   -0.7344 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4952   -0.6622   -0.4726 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6273    0.5445    0.1831 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4529    1.1821    0.5612 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2128    0.6444    0.2990 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0174    1.3632    0.7219 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0978    2.4685    1.3236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5155   -1.5916    0.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9937    0.0037   -0.3413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3046   -1.2744   -1.3586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7961    2.4796    1.4539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3834    2.4101    1.3547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7139   -2.5509   -1.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1812   -2.1454   -1.2494 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3568   -1.2319   -0.8056 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5980    0.9402    0.3747 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5324    2.1341    1.0792 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  7 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  8  2  1  0
 17 12  1  0
 18  6  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  5 24  1  0
  9 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  0
M  END


  Mrv1533004171513102D          

 19 21  0  0  0  0            999 V2000
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   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
    2.8579   -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
    5.7158   -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
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    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
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
  6 17  1  0  0  0  0
 17 18  2  0  0  0  0
  2 18  1  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0257354

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=C(O)C=C2C(=O)C3=CC=CC=C3C(=O)C2=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H10O4/c1-7-11(16)6-10-12(13(7)17)15(19)9-5-3-2-4-8(9)14(10)18/h2-6,16-17H,1H3

> <INCHI_KEY>
IRZTUXPRIUZXMP-UHFFFAOYSA-N

> <FORMULA>
C15H10O4

> <MOLECULAR_WEIGHT>
254.241

> <EXACT_MASS>
254.057908802

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
25.537984217669567

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,3-dihydroxy-2-methyl-9,10-dihydroanthracene-9,10-dione

> <ALOGPS_LOGP>
3.08

> <JCHEM_LOGP>
3.474996820666666

> <ALOGPS_LOGS>
-3.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.320114277849258

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.810127622375624

> <JCHEM_PKA_STRONGEST_BASIC>
-5.335470634745806

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
70.15400000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.48e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
rubiadin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0257354
     RDKit          3D
Rubiadin
 29 31  0  0  0  0  0  0  0  0999 V2000
   -4.2326   -0.8300   -0.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8856   -0.2607   -0.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7324    0.9435    0.5879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9022    1.5939    0.9728 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4796    1.4633    0.8400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3261    0.8137    0.4559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4684   -0.3916   -0.1988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7296   -0.9085   -0.4492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8258   -2.1200   -1.1085 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7521   -1.0806   -0.6061 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6279   -2.1757   -1.2012 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0864   -0.5620   -0.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2512   -1.1992   -0.7344 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4952   -0.6622   -0.4726 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6273    0.5445    0.1831 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4529    1.1821    0.5612 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2128    0.6444    0.2990 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0174    1.3632    0.7219 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0978    2.4685    1.3236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5155   -1.5916    0.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9937    0.0037   -0.3413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3046   -1.2744   -1.3586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7961    2.4796    1.4539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3834    2.4101    1.3547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7139   -2.5509   -1.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1812   -2.1454   -1.2494 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3568   -1.2319   -0.8056 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5980    0.9402    0.3747 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5324    2.1341    1.0792 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  7 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  8  2  1  0
 17 12  1  0
 18  6  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  5 24  1  0
  9 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  0
M  END

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   18                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   17                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    9   15                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    6   18                                                  
CONECT   18   17    2   19                                                  
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0257354
HETATM    1  C1  UNL     1      -4.233  -0.830  -0.343  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.886  -0.261  -0.066  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.732   0.944   0.588  1.00  0.00           C  
HETATM    4  O1  UNL     1      -3.902   1.594   0.973  1.00  0.00           O  
HETATM    5  C4  UNL     1      -1.480   1.463   0.840  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.326   0.814   0.456  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.468  -0.392  -0.199  1.00  0.00           C  
HETATM    8  C7  UNL     1      -1.730  -0.909  -0.449  1.00  0.00           C  
HETATM    9  O2  UNL     1      -1.826  -2.120  -1.108  1.00  0.00           O  
HETATM   10  C8  UNL     1       0.752  -1.081  -0.606  1.00  0.00           C  
HETATM   11  O3  UNL     1       0.628  -2.176  -1.201  1.00  0.00           O  
HETATM   12  C9  UNL     1       2.086  -0.562  -0.357  1.00  0.00           C  
HETATM   13  C10 UNL     1       3.251  -1.199  -0.734  1.00  0.00           C  
HETATM   14  C11 UNL     1       4.495  -0.662  -0.473  1.00  0.00           C  
HETATM   15  C12 UNL     1       4.627   0.544   0.183  1.00  0.00           C  
HETATM   16  C13 UNL     1       3.453   1.182   0.561  1.00  0.00           C  
HETATM   17  C14 UNL     1       2.213   0.644   0.299  1.00  0.00           C  
HETATM   18  C15 UNL     1       1.017   1.363   0.722  1.00  0.00           C  
HETATM   19  O4  UNL     1       1.098   2.468   1.324  1.00  0.00           O  
HETATM   20  H1  UNL     1      -4.515  -1.592   0.404  1.00  0.00           H  
HETATM   21  H2  UNL     1      -4.994   0.004  -0.341  1.00  0.00           H  
HETATM   22  H3  UNL     1      -4.305  -1.274  -1.359  1.00  0.00           H  
HETATM   23  H4  UNL     1      -3.796   2.480   1.454  1.00  0.00           H  
HETATM   24  H5  UNL     1      -1.383   2.410   1.355  1.00  0.00           H  
HETATM   25  H6  UNL     1      -2.714  -2.551  -1.321  1.00  0.00           H  
HETATM   26  H7  UNL     1       3.181  -2.145  -1.249  1.00  0.00           H  
HETATM   27  H8  UNL     1       5.357  -1.232  -0.806  1.00  0.00           H  
HETATM   28  H9  UNL     1       5.598   0.940   0.375  1.00  0.00           H  
HETATM   29  H10 UNL     1       3.532   2.134   1.079  1.00  0.00           H  
CONECT    1    2   20   21   22
CONECT    2    3    3    8
CONECT    3    4    5
CONECT    4   23
CONECT    5    6    6   24
CONECT    6    7   18
CONECT    7    8    8   10
CONECT    8    9
CONECT    9   25
CONECT   10   11   11   12
CONECT   12   13   13   17
CONECT   13   14   26
CONECT   14   15   15   27
CONECT   15   16   28
CONECT   16   17   17   29
CONECT   17   18
CONECT   18   19   19
END

HMDB0257354
     RDKit          3D
Rubiadin
 29 31  0  0  0  0  0  0  0  0999 V2000
   -4.2326   -0.8300   -0.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8856   -0.2607   -0.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7324    0.9435    0.5879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9022    1.5939    0.9728 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4796    1.4633    0.8400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3261    0.8137    0.4559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4684   -0.3916   -0.1988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7296   -0.9085   -0.4492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8258   -2.1200   -1.1085 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7521   -1.0806   -0.6061 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6279   -2.1757   -1.2012 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0864   -0.5620   -0.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2512   -1.1992   -0.7344 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4952   -0.6622   -0.4726 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6273    0.5445    0.1831 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4529    1.1821    0.5612 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2128    0.6444    0.2990 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0174    1.3632    0.7219 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0978    2.4685    1.3236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5155   -1.5916    0.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9937    0.0037   -0.3413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3046   -1.2744   -1.3586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7961    2.4796    1.4539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3834    2.4101    1.3547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7139   -2.5509   -1.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1812   -2.1454   -1.2494 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3568   -1.2319   -0.8056 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5980    0.9402    0.3747 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5324    2.1341    1.0792 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  7 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  8  2  1  0
 17 12  1  0
 18  6  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  5 24  1  0
  9 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1,3-Dihydroxy-2-methyl-9,10-anthracenedione	MeSH

Chemical Formula

C₁₅H₁₀O₄

Average Molecular Weight

254.241

Monoisotopic Molecular Weight

254.057908802

IUPAC Name

1,3-dihydroxy-2-methyl-9,10-dihydroanthracene-9,10-dione

Traditional Name

rubiadin

CAS Registry Number

Not Available

SMILES

CC1=C(O)C=C2C(=O)C3=CC=CC=C3C(=O)C2=C1O

InChI Identifier

InChI=1S/C15H10O4/c1-7-11(16)6-10-12(13(7)17)15(19)9-5-3-2-4-8(9)14(10)18/h2-6,16-17H,1H3

InChI Key

IRZTUXPRIUZXMP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxyanthraquinones. Hydroxyanthraquinones are compounds containing a hydroxyanthraquinone moiety, which consists of an anthracene bearing a quinone, and hydroxyl group.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Hydroxyanthraquinones

Alternative Parents

Substituents

Hydroxyanthraquinone
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Vinylogous acid
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

dihydroxyanthraquinone (CHEBI:69533 )
Anthraquinone type (C10402 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (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	3.08	ALOGPS
logP	3.47	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	7.81	ChemAxon
pKa (Strongest Basic)	-5.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	70.15 m³·mol⁻¹	ChemAxon
Polarizability	25.54 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]+	157.635	30932474
DeepCCS	[M-H]-	155.277	30932474
DeepCCS	[M-2H]-	188.696	30932474
DeepCCS	[M+Na]+	163.883	30932474
AllCCS	[M+H]+	156.0	32859911
AllCCS	[M+H-H2O]+	152.1	32859911
AllCCS	[M+NH4]+	159.7	32859911
AllCCS	[M+Na]+	160.7	32859911
AllCCS	[M-H]-	158.3	32859911
AllCCS	[M+Na-2H]-	157.6	32859911
AllCCS	[M+HCOO]-	156.9	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	6.54 minutes	32390414
Predicted by Siyang on May 30, 2022	12.9194 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.18 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2460.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	348.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	143.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	204.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	246.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	645.3 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	806.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	67.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1105.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	433.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1464.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	450.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	471.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	404.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	203.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	131.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Rubiadin	CC1=C(O)C=C2C(=O)C3=CC=CC=C3C(=O)C2=C1O	3476.2	Standard polar	33892256
Rubiadin	CC1=C(O)C=C2C(=O)C3=CC=CC=C3C(=O)C2=C1O	2191.3	Standard non polar	33892256
Rubiadin	CC1=C(O)C=C2C(=O)C3=CC=CC=C3C(=O)C2=C1O	2630.6	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 - Rubiadin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fba-0690000000-956621f2931b11f26ca1	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rubiadin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rubiadin GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rubiadin GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rubiadin GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rubiadin GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rubiadin GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Rubiadin GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Rubiadin 40V, Negative-QTOF	splash10-00fr-0190000000-65bd3a79e3fb09aeb7aa	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Rubiadin 20V, Negative-QTOF	splash10-0udi-0090000000-c8d3fe03fa20462a1ccd	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Rubiadin 10V, Positive-QTOF	splash10-0a4i-0090000000-9c84c0a6171be97ae458	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Rubiadin 20V, Positive-QTOF	splash10-0a4i-0590000000-d08a8123b6787ae4c5f7	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Rubiadin 10V, Negative-QTOF	splash10-0udi-0090000000-711473018b841bc95843	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Rubiadin 40V, Positive-QTOF	splash10-0uxu-1900000000-ea1172f4923f173d882a	2021-09-20	HMDB team, MONA	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

C00002862

Chemspider ID

110563

KEGG Compound ID

C10402

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Rubiadin

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

69533

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 Rubiadin (HMDB0257354)

MOL for HMDB0257354 (Rubiadin)

3D MOL for HMDB0257354 (Rubiadin)

3D SDF for HMDB0257354 (Rubiadin)

3D-SDF for HMDB0257354 (Rubiadin)

PDB for HMDB0257354 (Rubiadin)

3D PDB for HMDB0257354 (Rubiadin)

SMILES for HMDB0257354 (Rubiadin)

INCHI for HMDB0257354 (Rubiadin)

Structure for HMDB0257354 (Rubiadin)

3D Structure for HMDB0257354 (Rubiadin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra