You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2006-08-13 13:17:43 UTC
Update Date2018-05-20 18:53:01 UTC
HMDB IDHMDB0004159
Secondary Accession Numbers
  • HMDB04159
Metabolite Identification
Common NameL-Urobilin
DescriptionL-Urobilin or Stercobilin is a byproduct of bilirubin degradation. It is a tetrapyrrole chemical compound, responsible for the typical brown color of human feces. In urine, it is responsible for the yellow color of human urine. It is created by bacterial action on bilirubin and subsequent oxidation. 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 dissocates from albumin, enters the liver cells across the cell membrane through non-ionic diffusion to the smooth endoplasmatic reticulum, where it is converted to a water-soluble ester glucuronide by bilirubin UDP-glucuronyl transferase. Following conjugation, bilirubin is transferred rapidly across the canalicular membrane into the bile canaliculi. In the intestinal tract bilirubin is reduced to urobilinogen, which is subsequently reabsorbed to some extent into the enterohepatic circulation, removed from plasma by the liver and excreted unchanged in the bile. The residual part of urobilinogen is further reduced to urobilin, stercobilin and dipyrrolmethenes and excreted in the feces.
Structure
Thumb
Synonyms
ValueSource
L-StercobilinHMDB
StercobilinHMDB
UrobilinHMDB
Stercobilin III alphaMeSH
Chemical FormulaC33H46N4O6
Average Molecular Weight594.7415
Monoisotopic Molecular Weight594.341735224
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 Number34217-90-8
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
Chemical Taxonomy
DescriptionThis compound 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
  • 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 FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Source:

Biological location:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point236 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.011 g/LALOGPS
logP2.97ALOGPS
logP1.38ChemAxon
logS-4.7ALOGPS
pKa (Strongest Acidic)3.87ChemAxon
pKa (Strongest Basic)6.07ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area160.95 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity165.2 m³·mol⁻¹ChemAxon
Polarizability67.98 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fms-2300290000-71808d764c4c5c7b61c9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004j-0000090000-be73976b76f1266607e6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-005j-0110390000-2ee7959b1fc171f76bb2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00ks-2340940000-b080806706ac754b8401View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-0000090000-a3cc0dc5afce1240fbf1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-002g-1100190000-5484c7fb0ea9d9ea86bdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9010240000-c15aab9c620527fc60aaView in MoNA
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
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)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)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
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 IDFDB023324
KNApSAcK IDNot Available
Chemspider ID4444369
KEGG Compound IDC05793
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID7022
PubChem Compound5280818
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceFischer, Hans. The Bilo Pigments. I. Z. physiol. Chem. (1912), 73 204-39. CAN 6:565 AN 1912:565
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 ]