MiMeDB: Showing metabocard for L-Urobilin (MMDBc0000602)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:50:52 UTC

Update Date

2022-08-31 06:10:16 UTC

Metabolite ID

MMDBc0000602

Metabolite Identification

Common Name

L-Urobilin

Description

L-Urobilin belongs to the class of organic compounds known as bilirubins. These are organic compounds containing a dicarboxylic acyclic tetrapyrrole derivative. L-Urobilin is a very strong basic compound (based on its pKa). Many urine tests (urinalysis) monitor the amount of urobilin in urine, as its levels can give insight on the effectiveness of urinary tract function. Darker urine can also be due to other chemicals, such as various ingested dietary components or drugs, porphyrins in patients with porphyria, and homogentisate in patients with alkaptonuria. Some of this remains in the large intestine, and its conversion to stercobilin gives feces its brown color. When urobilinogen is exposed to air, it is oxidized to urobilin, giving urine its yellow color. Bilirubin is then excreted as bile, which is further degraded by microbes present in the large intestine to urobilinogen. It is a linear tetrapyrrole compound that, along with the related compound urobilinogen, are degradation products of the cyclic tetrapyrrole heme. Urobilin is generated from the degradation of heme, which is first degraded through biliverdin to bilirubin. Urobilin or urochrome is the chemical primarily responsible for the yellow color of urine. Obstructive jaundice reduces biliary bilirubin excretion, which is then excreted directly from the blood stream into the urine, giving a dark-colored urine but with a paradoxically low urobilin concentration, no urobilinogen, and usually with correspondingly pale faeces. A lack of water intake, for example following sleep or dehydration, reduces the water content of urine, thereby concentrating urobilin and producing a darker color of urine.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231219532D          

 43 46  0  0  0  0            999 V2000
   26.9136  -25.0786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.1640  -18.6141    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.0629  -23.6574    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.3201  -19.4541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.5486  -19.9809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   33.7065  -23.3041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.4738  -21.1235    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   32.3966  -23.9716    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   28.4528  -22.7260    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   30.8302  -23.6386    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   32.8091  -26.0661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.3476  -21.3148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.2190  -24.4973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.0147  -20.0353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.3570  -25.0112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.7039  -23.8299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.0008  -22.4960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.3503  -20.7890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.5236  -26.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0120  -20.5611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.2450  -22.8692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   34.2612  -25.0112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.6013  -25.3843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.5553  -20.7890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.3876  -21.9440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.1416  -24.7562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5807  -22.1155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.8091  -25.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.1681  -21.4010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.4766  -24.7562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.3985  -24.4111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.4997  -19.3679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.9049  -22.4960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.7202  -20.7880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.2216  -23.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.7439  -24.4591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.0764  -23.3030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.9369  -24.6307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.5244  -23.9161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.7854  -22.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.1202  -22.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.0403  -21.4565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.8653  -21.4565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 31  1  0  0  0  0
  2 32  1  0  0  0  0
  3 31  2  0  0  0  0
  4 32  2  0  0  0  0
  5 34  2  0  0  0  0
  6 35  2  0  0  0  0
  7 25  1  0  0  0  0
  7 34  1  0  0  0  0
  8 26  1  0  0  0  0
  8 35  1  0  0  0  0
  9 40  1  0  0  0  0
  9 41  1  0  0  0  0
 10 36  2  0  0  0  0
 10 37  1  0  0  0  0
 11 19  1  0  0  0  0
 11 28  1  0  0  0  0
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 14 18  1  0  0  0  0
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 18 43  1  0  0  0  0
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 29 34  1  0  0  0  0
 30 35  1  0  0  0  0
 33 37  2  0  0  0  0
 33 41  1  0  0  0  0
 36 38  1  0  0  0  0
 37 39  1  0  0  0  0
 38 39  2  0  0  0  0
 40 42  2  0  0  0  0
 41 43  2  0  0  0  0
 42 43  1  0  0  0  0
M  END


  Mrv0541 02231219532D          

 43 46  0  0  0  0            999 V2000
   26.9136  -25.0786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.1640  -18.6141    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.0629  -23.6574    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.3201  -19.4541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.5486  -19.9809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   33.7065  -23.3041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.4738  -21.1235    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   32.3966  -23.9716    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   28.4528  -22.7260    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   30.8302  -23.6386    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   32.8091  -26.0661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.3476  -21.3148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.2190  -24.4973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.0147  -20.0353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.3570  -25.0112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.7039  -23.8299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.0008  -22.4960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.3503  -20.7890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.5236  -26.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0120  -20.5611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.2450  -22.8692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   34.2612  -25.0112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.6013  -25.3843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.5553  -20.7890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.3876  -21.9440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.1416  -24.7562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5807  -22.1155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.8091  -25.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.1681  -21.4010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.4766  -24.7562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.3985  -24.4111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.4997  -19.3679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.9049  -22.4960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.7202  -20.7880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.2216  -23.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.7439  -24.4591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.0764  -23.3030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.9369  -24.6307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.5244  -23.9161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.7854  -22.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.1202  -22.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.0403  -21.4565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.8653  -21.4565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 31  1  0  0  0  0
  2 32  1  0  0  0  0
  3 31  2  0  0  0  0
  4 32  2  0  0  0  0
  5 34  2  0  0  0  0
  6 35  2  0  0  0  0
  7 25  1  0  0  0  0
  7 34  1  0  0  0  0
  8 26  1  0  0  0  0
  8 35  1  0  0  0  0
  9 40  1  0  0  0  0
  9 41  1  0  0  0  0
 10 36  2  0  0  0  0
 10 37  1  0  0  0  0
 11 19  1  0  0  0  0
 11 28  1  0  0  0  0
 12 20  1  0  0  0  0
 12 29  1  0  0  0  0
 13 16  1  0  0  0  0
 13 31  1  0  0  0  0
 14 18  1  0  0  0  0
 14 32  1  0  0  0  0
 15 26  1  0  0  0  0
 15 36  1  0  0  0  0
 16 39  1  0  0  0  0
 17 25  1  0  0  0  0
 17 40  1  0  0  0  0
 18 43  1  0  0  0  0
 21 27  1  0  0  0  0
 22 30  1  0  0  0  0
 23 38  1  0  0  0  0
 24 42  1  0  0  0  0
 25 27  1  0  0  0  0
 26 28  1  0  0  0  0
 27 29  1  0  0  0  0
 28 30  1  0  0  0  0
 29 34  1  0  0  0  0
 30 35  1  0  0  0  0
 33 37  2  0  0  0  0
 33 41  1  0  0  0  0
 36 38  1  0  0  0  0
 37 39  1  0  0  0  0
 38 39  2  0  0  0  0
 40 42  2  0  0  0  0
 41 43  2  0  0  0  0
 42 43  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000602

> <DATABASE_NAME>
MIME

> <SMILES>
CCC1C(CC2=N\C(=C\C3=C(CCC(O)=O)C(C)=C(CC4NC(=O)C(CC)C4C)N3)C(CCC(O)=O)=C2C)NC(=O)C1C

> <INCHI_IDENTIFIER>
InChI=1S/C33H46N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h15-16,19-21,26-27,34H,7-14H2,1-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b29-15+

> <INCHI_KEY>
TYOWQSLRVAUSMI-WKULSOCRSA-N

> <FORMULA>
C33H46N4O6

> <MOLECULAR_WEIGHT>
594.7415

> <EXACT_MASS>
594.341735224

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
67.98114290837387

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(2E)-2-{[3-(2-carboxyethyl)-5-[(4-ethyl-3-methyl-5-oxopyrrolidin-2-yl)methyl]-4-methyl-1H-pyrrol-2-yl]methylidene}-5-[(3-ethyl-4-methyl-5-oxopyrrolidin-2-yl)methyl]-4-methyl-2H-pyrrol-3-yl]propanoic acid

> <ALOGPS_LOGP>
2.97

> <JCHEM_LOGP>
1.3830882880866981

> <ALOGPS_LOGS>
-4.73

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.4620159615769905

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.865640190778201

> <JCHEM_PKA_STRONGEST_BASIC>
6.07364616402409

> <JCHEM_POLAR_SURFACE_AREA>
160.95

> <JCHEM_REFRACTIVITY>
165.19520000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.10e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
stercobilin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      50.239 -46.813   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      54.439 -34.746   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      50.517 -44.160   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      56.598 -36.314   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      47.691 -37.298   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      62.919 -43.501   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      49.418 -39.431   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      60.474 -44.747   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0      53.112 -42.422   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      57.550 -44.125   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      61.244 -48.657   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      45.449 -39.788   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      52.675 -45.728   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      54.161 -37.399   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      58.533 -46.688   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      53.581 -44.482   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      50.401 -41.993   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      54.787 -38.806   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      62.577 -49.427   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      44.822 -38.381   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      47.124 -42.689   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      63.954 -46.688   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      55.256 -47.384   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      51.437 -38.806   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      49.257 -40.962   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      59.998 -46.212   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      47.751 -41.282   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      61.244 -47.117   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      46.980 -39.949   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      62.490 -46.212   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      51.144 -45.567   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      55.066 -36.153   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      55.822 -41.993   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      48.011 -38.804   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      62.014 -44.747   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      57.389 -45.657   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      56.143 -43.499   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      55.882 -45.977   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      55.112 -44.643   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      51.866 -41.517   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      54.358 -41.517   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      52.342 -40.052   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      53.882 -40.052   0.000  0.00  0.00           C+0
CONECT    1   31                                                            
CONECT    2   32                                                            
CONECT    3   31                                                            
CONECT    4   32                                                            
CONECT    5   34                                                            
CONECT    6   35                                                            
CONECT    7   25   34                                                       
CONECT    8   26   35                                                       
CONECT    9   40   41                                                       
CONECT   10   36   37                                                       
CONECT   11   19   28                                                       
CONECT   12   20   29                                                       
CONECT   13   16   31                                                       
CONECT   14   18   32                                                       
CONECT   15   26   36                                                       
CONECT   16   13   39                                                       
CONECT   17   25   40                                                       
CONECT   18   14   43                                                       
CONECT   19   11                                                            
CONECT   20   12                                                            
CONECT   21   27                                                            
CONECT   22   30                                                            
CONECT   23   38                                                            
CONECT   24   42                                                            
CONECT   25    7   17   27                                                  
CONECT   26    8   15   28                                                  
CONECT   27   21   25   29                                                  
CONECT   28   11   26   30                                                  
CONECT   29   12   27   34                                                  
CONECT   30   22   28   35                                                  
CONECT   31    1    3   13                                                  
CONECT   32    2    4   14                                                  
CONECT   33   37   41                                                       
CONECT   34    5    7   29                                                  
CONECT   35    6    8   30                                                  
CONECT   36   10   15   38                                                  
CONECT   37   10   33   39                                                  
CONECT   38   23   36   39                                                  
CONECT   39   16   37   38                                                  
CONECT   40    9   17   42                                                  
CONECT   41    9   33   43                                                  
CONECT   42   24   40   43                                                  
CONECT   43   18   41   42                                                  
MASTER        0    0    0    0    0    0    0    0   43    0   92    0
END

Synonyms

Value	Source
L-Stercobilin	HMDB
Stercobilin	HMDB, MeSH
Urobilin	HMDB
Stercobilin III alpha	MeSH, HMDB
3-(2-{[(2E)-3-(2-carboxyethyl)-5-[(3-ethyl-5-hydroxy-4-methyl-3,4-dihydro-2H-pyrrol-2-yl)methyl]-4-methyl-2H-pyrrol-2-ylidene]methyl}-5-[(4-ethyl-5-hydroxy-3-methyl-3,4-dihydro-2H-pyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl)propanoate	Generator

Molecular Formula

C₃₃H₄₆N₄O₆

Average Mass

594.7415

Monoisotopic Mass

594.341735224

IUPAC Name

3-[(2E)-2-{[3-(2-carboxyethyl)-5-[(4-ethyl-3-methyl-5-oxopyrrolidin-2-yl)methyl]-4-methyl-1H-pyrrol-2-yl]methylidene}-5-[(3-ethyl-4-methyl-5-oxopyrrolidin-2-yl)methyl]-4-methyl-2H-pyrrol-3-yl]propanoic acid

Traditional Name

stercobilin

CAS Registry Number

Not Available

SMILES

CCC1C(CC2=N\C(=C\C3=C(CCC(O)=O)C(C)=C(CC4NC(=O)C(CC)C4C)N3)C(CCC(O)=O)=C2C)NC(=O)C1C

InChI Identifier

InChI=1S/C33H46N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h15-16,19-21,26-27,34H,7-14H2,1-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b29-15+

InChI Key

TYOWQSLRVAUSMI-WKULSOCRSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bilirubins. These are organic compounds containing a dicarboxylic acyclic tetrapyrrole derivative.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Bilirubins

Direct Parent

Bilirubins

Alternative Parents

Substituents

Bilirubin skeleton
Dipyrrin
Dicarboxylic acid or derivatives
Pyrrolidone
2-pyrrolidone
Substituted pyrrole
Pyrrole
Pyrrolidine
Heteroaromatic compound
Carboxamide group
Secondary carboxylic acid amide
Ketimine
Lactam
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboxylic acid derivative
Carboxylic acid
Hydrocarbon derivative
Imine
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Organic oxide
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.011 g/L	ALOGPS
logP	2.97	ALOGPS
logP	1.38	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	3.87	ChemAxon
pKa (Strongest Basic)	6.07	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	160.95 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	165.2 m³·mol⁻¹	ChemAxon
Polarizability	67.98 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fms-2300290000-71808d764c4c5c7b61c9	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-0000090000-be73976b76f1266607e6	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-005j-0110390000-2ee7959b1fc171f76bb2	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00ks-2340940000-b080806706ac754b8401	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-0000090000-a3cc0dc5afce1240fbf1	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-002g-1100190000-5484c7fb0ea9d9ea86bd	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9010240000-c15aab9c620527fc60aa	2016-08-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	2		Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0004159

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Urobilin

METLIN ID

Not Available

PubChem Compound

5280818

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Showing metabocard for L-Urobilin (MMDBc0000602)

MOL for #<Metabolite:0x00007fd10cc1f9c8>

3D MOL for #<Metabolite:0x00007fd10cc1f9c8>

3D SDF for #<Metabolite:0x00007fd10cc1f9c8>

3D-SDF for #<Metabolite:0x00007fd10cc1f9c8>

PDB for #<Metabolite:0x00007fd10cc1f9c8>

3D PDB for #<Metabolite:0x00007fd10cc1f9c8>

SMILES for #<Metabolite:0x00007fd10cc1f9c8>

INCHI for #<Metabolite:0x00007fd10cc1f9c8>

Structure for #<Metabolite:0x00007fd10cc1f9c8>

3D Structure for #<Metabolite:0x00007fd10cc1f9c8>