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Showing metabocard for Urolithin B (HMDB0013696)

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enzymes (1) Show 1 protein
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-04-03 14:10:34 UTC
Update Date2021-10-13 05:41:11 UTC
HMDB IDHMDB0013696
Secondary Accession Numbers
  • HMDB13696
Metabolite Identification
Common NameUrolithin B
DescriptionUrolithin B belongs to the class of organic compounds known as coumarins and derivatives. These are polycyclic aromatic compounds containing a 1-benzopyran moiety with a ketone group at the C2 carbon atom (1-benzopyran-2-one). Based on a literature review a significant number of articles have been published on Urolithin B.
Structure
Data?1582753143
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013696 (Urolithin B)


  Mrv1652303102016532D          

 16 18  0  0  0  0            999 V2000
   -1.0326   -0.1759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2076   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2049    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0299    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4423   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0299   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2049   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2674   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5049    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9174   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5049   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2674    1.2531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799    1.9675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4423    1.2531    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
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
  4 16  1  0  0  0  0
M  END
Download

3D MOL for HMDB0013696 (Urolithin B)

HMDB0013696
     RDKit          3D
Urolithin B
 24 26  0  0  0  0  0  0  0  0999 V2000
   -1.4679    3.2783   -0.2095 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8038    2.2040   -0.1485 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4823    2.1581   -0.1117 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1461    1.0307   -0.0485 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5320    1.0049   -0.0098 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2675   -0.1578    0.0567 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6597   -0.1120    0.0927 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5917   -1.3384    0.0855 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2053   -1.3753    0.0493 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5098   -0.2170   -0.0159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8716   -0.2248   -0.0531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5991   -1.3911   -0.0263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9848   -1.3611   -0.0651 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6082   -0.1351   -0.1311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9002    1.0440   -0.1590 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5078    1.0185   -0.1202 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0496    1.9517   -0.0336 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0684   -0.0609    1.0246 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1246   -2.2543    0.1366 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7511   -2.3284    0.0751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0940   -2.3319    0.0251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4931   -2.3035   -0.0413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6840   -0.1141   -0.1612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3737    2.0154   -0.2108 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16  2  1  0
 10  4  1  0
 16 11  1  0
  5 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
 12 21  1  0
 13 22  1  0
 14 23  1  0
 15 24  1  0
M  END
Download

3D SDF for HMDB0013696 (Urolithin B)


  Mrv1652303102016532D          

 16 18  0  0  0  0            999 V2000
   -1.0326   -0.1759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2076   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2049    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0299    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4423   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0299   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2049   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2674   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5049    0.5386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9174   -0.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5049   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799   -0.8904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2674    1.2531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799    1.9675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4423    1.2531    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
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
  4 16  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013696

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC2=C(C=C1)C1=C(C=CC=C1)C(=O)O2

> <INCHI_IDENTIFIER>
InChI=1S/C13H8O3/c14-8-5-6-10-9-3-1-2-4-11(9)13(15)16-12(10)7-8/h1-7,14H

> <INCHI_KEY>
WXUQMTRHPNOXBV-UHFFFAOYSA-N

> <FORMULA>
C13H8O3

> <MOLECULAR_WEIGHT>
212.2008

> <EXACT_MASS>
212.047344122

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
21.20969230785844

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-hydroxy-6H-benzo[c]chromen-6-one

> <ALOGPS_LOGP>
2.65

> <JCHEM_LOGP>
2.6217621196666667

> <ALOGPS_LOGS>
-3.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.67363835878753

> <JCHEM_PKA_STRONGEST_BASIC>
-7.050380245017417

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
58.92000000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.45e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxybenzo[c]chromen-6-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0013696 (Urolithin B)

HMDB0013696
     RDKit          3D
Urolithin B
 24 26  0  0  0  0  0  0  0  0999 V2000
   -1.4679    3.2783   -0.2095 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8038    2.2040   -0.1485 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4823    2.1581   -0.1117 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1461    1.0307   -0.0485 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5320    1.0049   -0.0098 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2675   -0.1578    0.0567 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6597   -0.1120    0.0927 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5917   -1.3384    0.0855 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2053   -1.3753    0.0493 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5098   -0.2170   -0.0159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8716   -0.2248   -0.0531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5991   -1.3911   -0.0263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9848   -1.3611   -0.0651 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6082   -0.1351   -0.1311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9002    1.0440   -0.1590 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5078    1.0185   -0.1202 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0496    1.9517   -0.0336 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0684   -0.0609    1.0246 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1246   -2.2543    0.1366 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7511   -2.3284    0.0751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0940   -2.3319    0.0251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4931   -2.3035   -0.0413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6840   -0.1141   -0.1612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3737    2.0154   -0.2108 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16  2  1  0
 10  4  1  0
 16 11  1  0
  5 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
 12 21  1  0
 13 22  1  0
 14 23  1  0
 15 24  1  0
M  END
Download

PDB for HMDB0013696 (Urolithin B)

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  O   UNK     0      -1.928  -0.328   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.388  -0.328   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.382   1.005   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.922   1.005   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.692  -0.328   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.922  -1.662   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.382  -1.662   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.232  -0.328   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.002   1.005   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.542   1.005   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.312  -0.328   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.542  -1.662   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.002  -1.662   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.232   2.339   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.002   3.673   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.692   2.339   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   16                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
CONECT    8    5    9   13                                                  
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14    9   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14    4                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END
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3D PDB for HMDB0013696 (Urolithin B)

COMPND    HMDB0013696
HETATM    1  O1  UNL     1      -1.468   3.278  -0.209  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.804   2.204  -0.148  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.482   2.158  -0.112  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.146   1.031  -0.049  1.00  0.00           C  
HETATM    5  C3  UNL     1       2.532   1.005  -0.010  1.00  0.00           C  
HETATM    6  C4  UNL     1       3.268  -0.158   0.057  1.00  0.00           C  
HETATM    7  O3  UNL     1       4.660  -0.112   0.093  1.00  0.00           O  
HETATM    8  C5  UNL     1       2.592  -1.338   0.086  1.00  0.00           C  
HETATM    9  C6  UNL     1       1.205  -1.375   0.049  1.00  0.00           C  
HETATM   10  C7  UNL     1       0.510  -0.217  -0.016  1.00  0.00           C  
HETATM   11  C8  UNL     1      -0.872  -0.225  -0.053  1.00  0.00           C  
HETATM   12  C9  UNL     1      -1.599  -1.391  -0.026  1.00  0.00           C  
HETATM   13  C10 UNL     1      -2.985  -1.361  -0.065  1.00  0.00           C  
HETATM   14  C11 UNL     1      -3.608  -0.135  -0.131  1.00  0.00           C  
HETATM   15  C12 UNL     1      -2.900   1.044  -0.159  1.00  0.00           C  
HETATM   16  C13 UNL     1      -1.508   1.018  -0.120  1.00  0.00           C  
HETATM   17  H1  UNL     1       3.050   1.952  -0.034  1.00  0.00           H  
HETATM   18  H2  UNL     1       5.068  -0.061   1.025  1.00  0.00           H  
HETATM   19  H3  UNL     1       3.125  -2.254   0.137  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.751  -2.328   0.075  1.00  0.00           H  
HETATM   21  H5  UNL     1      -1.094  -2.332   0.025  1.00  0.00           H  
HETATM   22  H6  UNL     1      -3.493  -2.304  -0.041  1.00  0.00           H  
HETATM   23  H7  UNL     1      -4.684  -0.114  -0.161  1.00  0.00           H  
HETATM   24  H8  UNL     1      -3.374   2.015  -0.211  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   16
CONECT    3    4
CONECT    4    5    5   10
CONECT    5    6   17
CONECT    6    7    8    8
CONECT    7   18
CONECT    8    9   19
CONECT    9   10   10   20
CONECT   10   11
CONECT   11   12   12   16
CONECT   12   13   21
CONECT   13   14   14   22
CONECT   14   15   23
CONECT   15   16   16   24
END
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SMILES for HMDB0013696 (Urolithin B)

OC1=CC2=C(C=C1)C1=C(C=CC=C1)C(=O)O2
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INCHI for HMDB0013696 (Urolithin B)

InChI=1S/C13H8O3/c14-8-5-6-10-9-3-1-2-4-11(9)13(15)16-12(10)7-8/h1-7,14H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-hydroxy-6H-benzo[c]chromen-6-oneHMDB
3-hydroxy-urolithinHMDB
Chemical FormulaC13H8O3
Average Molecular Weight212.2008
Monoisotopic Molecular Weight212.047344122
IUPAC Name3-hydroxy-6H-benzo[c]chromen-6-one
Traditional Name3-hydroxybenzo[c]chromen-6-one
CAS Registry Number1139-83-9
SMILES
OC1=CC2=C(C=C1)C1=C(C=CC=C1)C(=O)O2
InChI Identifier
InChI=1S/C13H8O3/c14-8-5-6-10-9-3-1-2-4-11(9)13(15)16-12(10)7-8/h1-7,14H
InChI KeyWXUQMTRHPNOXBV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as coumarins and derivatives. These are polycyclic aromatic compounds containing a 1-benzopyran moiety with a ketone group at the C2 carbon atom (1-benzopyran-2-one).
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassCoumarins and derivatives
Sub ClassNot Available
Direct ParentCoumarins and derivatives
Alternative Parents
Substituents
  • Coumarin
  • Isocoumarin
  • Benzopyran
  • 1-benzopyran
  • 2-benzopyran
  • 1-hydroxy-2-unsubstituted benzenoid
  • Pyranone
  • Pyran
  • Benzenoid
  • Heteroaromatic compound
  • Lactone
  • Oxacycle
  • Organoheterocyclic compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point432.55 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility576.7 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.947 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.14 g/LALOGPS
logP2.65ALOGPS
logP2.62ChemAxon
logS-3.2ALOGPS
pKa (Strongest Acidic)7.67ChemAxon
pKa (Strongest Basic)-7.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area46.53 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity58.92 m³·mol⁻¹ChemAxon
Polarizability21.21 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+146.14531661259
DarkChem[M-H]-146.04231661259
DeepCCS[M+H]+146.84130932474
DeepCCS[M-H]-144.48330932474
DeepCCS[M-2H]-177.79230932474
DeepCCS[M+Na]+152.93430932474
AllCCS[M+H]+145.132859911
AllCCS[M+H-H2O]+140.832859911
AllCCS[M+NH4]+149.132859911
AllCCS[M+Na]+150.332859911
AllCCS[M-H]-146.732859911
AllCCS[M+Na-2H]-146.132859911
AllCCS[M+HCOO]-145.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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, 2022.6.74 minutes32390414
Predicted by Siyang on May 30, 202212.5128 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.44 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1860.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid403.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid155.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid227.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid237.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid526.9 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid515.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)75.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid916.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid419.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1434.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid335.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid337.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate414.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA256.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water68.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Urolithin BOC1=CC2=C(C=C1)C1=C(C=CC=C1)C(=O)O23262.6Standard polar33892256
Urolithin BOC1=CC2=C(C=C1)C1=C(C=CC=C1)C(=O)O22270.5Standard non polar33892256
Urolithin BOC1=CC2=C(C=C1)C1=C(C=CC=C1)C(=O)O22351.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Urolithin B,1TMS,isomer #1C[Si](C)(C)OC1=CC=C2C(=C1)OC(=O)C1=CC=CC=C122450.6Semi standard non polar33892256
Urolithin B,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CC=C2C(=C1)OC(=O)C1=CC=CC=C122650.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Urolithin B GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-1970000000-fd0fa569b607450a10402017-07-27Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Urolithin B GC-MS (1 TMS) - 70eV, Positivesplash10-00xr-4290000000-f746cc9bb48d4029b3072017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Urolithin B GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 10V, Positive-QTOFsplash10-03di-0090000000-546510672963f873f32b2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 20V, Positive-QTOFsplash10-03di-0190000000-171e9d9553181a07d7442015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 40V, Positive-QTOFsplash10-0gbi-2910000000-741662b9391006b4a8af2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 10V, Negative-QTOFsplash10-03di-0190000000-7bf375ca0199318e1ed72015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 20V, Negative-QTOFsplash10-03di-0390000000-00a3ce15bb3eb85599112015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 40V, Negative-QTOFsplash10-014i-0910000000-f4f5c2c7d56cb15faa552015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 10V, Negative-QTOFsplash10-03di-0090000000-fa5c46c2572ef8a7bf102021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 20V, Negative-QTOFsplash10-03di-0090000000-fa5c46c2572ef8a7bf102021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 40V, Negative-QTOFsplash10-00lr-0900000000-3ce29982bbde6664bd6c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 10V, Positive-QTOFsplash10-03di-0090000000-7d2e191c18d3f0b0ca512021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 20V, Positive-QTOFsplash10-03di-0090000000-7d2e191c18d3f0b0ca512021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Urolithin B 40V, Positive-QTOFsplash10-03di-0190000000-62cb0bc11bbf77eca97b2021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableConsuming polyphenols described by Phenol-Explorer entry 1038 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableConsuming polyphenols described by Phenol-Explorer entry 1038 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030000
KNApSAcK IDC00053885
Chemspider ID4528673
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkUrolithin B
METLIN IDNot Available
PubChem Compound5380406
PDB IDNot Available
ChEBI ID1050862
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1661681
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Reactions
Urolithin B → 3,4,5-trihydroxy-6-({6-oxo-6H-benzo[c]chromen-3-yl}oxy)oxane-2-carboxylic aciddetails