Canmetcon
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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2006-08-13 13:18:56 UTC
Update Date2019-02-14 21:04:34 UTC
HMDB IDHMDB0004160
Secondary Accession Numbers
  • HMDB0004159
  • HMDB0004161
  • HMDB04159
  • HMDB04160
  • HMDB04161
Metabolite Identification
Common NameUrobilin
DescriptionUrobilin, also known as urochrome, is the tetrapyrrole chemical compound that is primarily responsible for the yellow color of urine. Urobilin is formed through the oxidation of its parent compound uroblinogen. Urobilin is actually generated through the degradation of heme, the red pigment in haemoglobin and red blood cells (RBCs). RBCs have a life span of about 120 days. When the RBCs have reached the end of their useful lifespan, the cells are engulfed by macrophages and their constituents recycled or disposed of. Heme is broken down when the heme ring is opened by the enzyme known as heme oxygenase, which is found in the endoplasmic reticulum of the macrophages. The oxidation process produces the linear tetrapyrrole known as biliverdin along with ferric iron (Fe3+), and carbon monoxide (CO). In the next reaction, a second methylene group (located between rings III and IV of the porphyrin ring) is reduced by the enzyme known as biliverdin reductase, producing bilirubin. Bilirubin is significantly less extensively conjugated than biliverdin. This reduction causes a change in the color of the biliverdin molecule from blue-green (vert or verd for green) to yellow-red, which is the color of bilirubin (ruby or rubi for red). In plasma virtually all the bilirubin is tightly bound to plasma proteins, largely albumin, because it is only sparingly soluble in aqueous solutions at physiological pH. In the sinusoids unconjugated bilirubin dissociates from albumin, enters the liver cells across the cell membrane through non-ionic diffusion to the smooth endoplasmatic reticulum. In hepatocytes, bilirubin-UDP-glucuronyltransferase (bilirubin-UGT) adds 2 additional glucuronic acid molecules to bilirubin to produce the more water-soluble version of the molecule known as bilirubin diglucuronide. The bilirubin diglucuronide is transferred rapidly across the canalicular membrane into the bile canaliculi where it is then excreted as bile into the large intestine. The bilirubin is further degraded (reduced) by microbes present in the large intestine to form a colorless product known as urobilinogen. Some of the urobilinogen produced by the gut bacteria is reabsorbed and re-enters the enterohepatic circulation. These urobilinogens are oxidized and converted to urobilin. The urobilin is processed through the kidneys and then excreted in the urine, which causes the yellowish color in urine. Many urine tests monitor the amount of urobilin in urine, as this provides some useful insight into urinary tract function. Normally, urine would appear as either light yellow or colorless. 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. Obstructive jaundice reduces biliary bilirubin excretion, which is then excreted directly from the blood stream into the urine, giving a dark-colored urine. This dark colored urine has a paradoxically low urobilin concentration.
Structure
Data?1550081153
Synonyms
ValueSource
3,18-Diethyl-1,4,5,15,16,19,22,24-octahydro-2,7,13,17-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acidChEBI
3,18-Diethyl-1,4,5,15,16,19,22,24-octahydro-2,7,13,17-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropionic acidChEBI
8,12-Bis(2-carboxyethyl)-3,18-diethyl-2,7,13,17-tetramethylbilene-b-1,19(4H,16H)-dioneChEBI
3,18-Diethyl-1,4,5,15,16,19,22,24-octahydro-2,7,13,17-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoateGenerator
3,18-Diethyl-1,4,5,15,16,19,22,24-octahydro-2,7,13,17-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropionateGenerator
(-)-UrobilinHMDB
3,18-Diethyl-1,4,5,15,16,19,22,24-octahydro-2,7,13,17-tetramethyl-1,19-dioxo-biline-8,12-dipropionic acidHMDB
Urobilin IXαHMDB
UrobilinHMDB
i-UrobilinChEBI
Urobilin IXalphaHMDB
Chemical FormulaC33H42N4O6
Average Molecular Weight590.721
Monoisotopic Molecular Weight590.310435088
IUPAC Name3-(2-{[3-(2-carboxyethyl)-5-[(4-ethyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl)methyl]-4-methyl-2H-pyrrol-2-ylidene]methyl}-5-[(3-ethyl-4-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl)propanoic acid
Traditional Nameurobilin
CAS Registry Number1856-98-0
SMILES
[H]C(C1=C(CCC(O)=O)C(C)=C(CC2NC(=O)C(C)=C2CC)N1)=C1N=C(CC2NC(=O)C(CC)=C2C)C(C)=C1CCC(O)=O
InChI Identifier
InChI=1S/C33H42N4O6/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/h15,26-27,35H,7-14H2,1-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)
InChI KeyKDCCOOGTVSRCHX-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as bilirubins. These are organic compounds containing a dicarboxylic acyclic tetrapyrrole derivative.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassBilirubins
Direct ParentBilirubins
Alternative Parents
Substituents
  • Bilirubin skeleton
  • Dipyrrin
  • Dicarboxylic acid or derivatives
  • Substituted pyrrole
  • Pyrrole
  • Pyrroline
  • Heteroaromatic compound
  • Carboxamide group
  • Ketimine
  • Lactam
  • Secondary carboxylic acid amide
  • Azacycle
  • Organic 1,3-dipolar compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Propargyl-type 1,3-dipolar organic compound
  • Hydrocarbon derivative
  • Imine
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic oxide
  • Organonitrogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Biological location:

Source:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP1.363Not Available
Predicted Properties
PropertyValueSource
Water Solubility0.048 g/LALOGPS
logP3.04ALOGPS
logP1.23ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)3.88ChemAxon
pKa (Strongest Basic)5.98ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area160.95 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity166.26 m³·mol⁻¹ChemAxon
Polarizability66.96 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
SpectraNot Available
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Not SpecifiedNormal details
FecesDetected but not Quantified Adult (>18 years old)BothNormal details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)BothNormal details
UrineDetected and Quantified3.36-15.13 umol/mmol creatinineAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)BothColorectal Cancer details
FecesDetected but not Quantified Adult (>18 years old)Not SpecifiedLiver cirrhosis details
FecesDetected but not Quantified Adult (>18 years old)Not Specifiedhepatocellular carcinoma details
FecesDetected but not Quantified Adult (>18 years old)Bothliver cirrhosis details
FecesDetected but not Quantified Adult (>18 years old)Both
Crohn disease
details
FecesDetected but not Quantified Adult (>18 years old)Both
Colorectal cancer
details
FecesDetected but not Quantified Adult (>18 years old)Both
Ulcerative colitis
details
Associated Disorders and Diseases
Disease References
Cirrhosis
  1. Cao H, Huang H, Xu W, Chen D, Yu J, Li J, Li L: Fecal metabolome profiling of liver cirrhosis and hepatocellular carcinoma patients by ultra performance liquid chromatography-mass spectrometry. Anal Chim Acta. 2011 Apr 8;691(1-2):68-75. doi: 10.1016/j.aca.2011.02.038. Epub 2011 Feb 23. [PubMed:21458633 ]
  2. Huang HJ, Zhang AY, Cao HC, Lu HF, Wang BH, Xie Q, Xu W, Li LJ: Metabolomic analyses of faeces reveals malabsorption in cirrhotic patients. Dig Liver Dis. 2013 Aug;45(8):677-82. doi: 10.1016/j.dld.2013.01.001. Epub 2013 Feb 4. [PubMed:23384618 ]
Hepatocellular carcinoma
  1. Cao H, Huang H, Xu W, Chen D, Yu J, Li J, Li L: Fecal metabolome profiling of liver cirrhosis and hepatocellular carcinoma patients by ultra performance liquid chromatography-mass spectrometry. Anal Chim Acta. 2011 Apr 8;691(1-2):68-75. doi: 10.1016/j.aca.2011.02.038. Epub 2011 Feb 23. [PubMed:21458633 ]
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Crohn's disease
  1. Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Ulcerative colitis
  1. Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023325
KNApSAcK IDNot Available
Chemspider ID389650
KEGG Compound IDC05794
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkUrobilin
METLIN IDNot Available
PubChem Compound440785
PDB IDNot Available
ChEBI ID36378
References
Synthesis ReferenceWatson, C. J.; Weimer, Mary; Hawkinson, Violet E. Differences in the formation of mesobiliviolin and glaucobilin from d- and i-urobilins. Journal of Biological Chemistry (1960), 235 787-94.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Treem WR, Malet PF, Gourley GR, Hyams JS: Bile and stone analysis in two infants with brown pigment gallstones and infected bile. Gastroenterology. 1989 Feb;96(2 Pt 1):519-23. [PubMed:2642880 ]
  2. Jones-Lepp TL: Chemical markers of human waste contamination: analysis of urobilin and pharmaceuticals in source waters. J Environ Monit. 2006 Apr;8(4):472-8. Epub 2006 Mar 10. [PubMed:16604237 ]