Showing metabocard for L-Urobilin (MMDBc0000602)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:50:52 UTC
Update Date2022-08-31 06:10:16 UTC
Metabolite IDMMDBc0000602
Metabolite Identification
Common NameL-Urobilin
DescriptionL-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
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007f920f22bc78>


  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
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   28.7039  -23.8299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   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
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M  END
Download

3D MOL for #<Metabolite:0x00007f920f22bc78>

Download
3D SDF for #<Metabolite:0x00007f920f22bc78>

  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
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   30.3201  -19.4541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   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
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   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
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   33.5236  -26.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   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
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   27.3985  -24.4111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   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
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  8 26  1  0  0  0  0
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 36 38  1  0  0  0  0
 37 39  1  0  0  0  0
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 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

$$$$

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3D-SDF for #<Metabolite:0x00007f920f22bc78>
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PDB for #<Metabolite:0x00007f920f22bc78>
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

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3D PDB for #<Metabolite:0x00007f920f22bc78>
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SMILES for #<Metabolite:0x00007f920f22bc78>
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
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INCHI for #<Metabolite:0x00007f920f22bc78>
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+
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Synonyms
ValueSource
L-StercobilinHMDB
StercobilinHMDB, MeSH
UrobilinHMDB
Stercobilin III alphaMeSH, 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)propanoateGenerator
Molecular FormulaC33H46N4O6
Average Mass594.7415
Monoisotopic Mass594.341735224
IUPAC Name3-[(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 Namestercobilin
CAS Registry NumberNot 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 KeyTYOWQSLRVAUSMI-WKULSOCRSA-N