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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2006-08-13 13:17:12 UTC
Update Date2020-02-26 21:25:01 UTC
HMDB IDHMDB0004158
Secondary Accession Numbers
  • HMDB04158
Metabolite Identification
Common NameUrobilinogen
DescriptionUrobilinogen is a tetrapyrrole chemical compound that is that is the parent compound of both stercobilin (the pigment that is responsible for the brown color of feces) and urobilin (the pigment that is responsible for the yellow color of urine). Urobilinogen is formed through the microbial degradation of its parent compound bilirubin. Urobilinogen 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. Urobilinogen that remains in the colon can either be reduced to stercobilinogen and finally oxidized to stercobilin, or it can be directly reduced to stercobilin. Some of the urobilinogen produced by the gut bacteria is reabsorbed and re-enters the enterohepatic circulation. This reabsorbed urobilinogen is 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. Urobilinogen (also known as D-urobilinogen) is closely related to two other compounds: mesobilirubinogen (also known as I-urobilinogen) and stercobilinogen (also known as. L-urobilinogen). Specifically, urobilinogen can be reduced to form mesobilirubinogen, and mesobilirubinogen can be further reduced to form stercobilinogen. Confusingly, all three of these compounds are frequently collectively referred to as "urobilinogens". Urobilinogen content can be determined by a reaction with Ehrlich's reagent, which contains para-dimethylaminobenzaldehyde. Ehrlich's reagent reacts with urobilinogen to give a pink-red color. Low urine urobilinogen may result from complete obstructive jaundice or treatment with broad-spectrum antibiotics, which destroy the intestinal bacterial flora. Low urine urobilinogen levels may also result from congenital enzymatic jaundice (hyperbilirubinemia syndromes) or from treatment with drugs that acidify urine, such as ammonium chloride or ascorbic acid. Elevated urine levels of urinobilinogen may indicate hemolytic anaemia, a large hematoma, restricted liver function, hepatic infection, poisoning or liver cirrhosis.
Structure
Data?1582752301
Synonyms
ValueSource
D-UrobilinogenHMDB
UrobilinogenHMDB
Chemical FormulaC33H42N4O6
Average Molecular Weight590.7098
Monoisotopic Molecular Weight590.310435096
IUPAC Name3-(2-{[3-(2-carboxyethyl)-5-[(4-ethenyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-2-yl]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 Name3-(2-{[3-(2-carboxyethyl)-5-[(4-ethenyl-3-methyl-5-oxo-1,2-dihydropyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-2-yl]methyl}-5-[(3-ethyl-4-methyl-5-oxo-1,2-dihydropyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl)propanoic acid
CAS Registry Number17208-65-0
SMILES
CCC1=C(C)C(=O)NC1CC1=C(C)C(CCC(O)=O)=C(CC2=C(CCC(O)=O)C(C)=C(CC3NC(=O)C(C=C)=C3C)N2)N1
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/h8,26-27,34-35H,2,7,9-15H2,1,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)
InChI KeyKSQFFJKKJAEKTB-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
  • Dicarboxylic acid or derivatives
  • Substituted pyrrole
  • Pyrrole
  • Pyrroline
  • Heteroaromatic compound
  • Secondary carboxylic acid amide
  • Lactam
  • Carboxamide group
  • Azacycle
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organopnictogen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.02 g/LALOGPS
logP2.77ALOGPS
logP3.46ChemAxon
logS-4.5ALOGPS
pKa (Strongest Acidic)4.06ChemAxon
pKa (Strongest Basic)-0.038ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area164.38 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity166.09 m³·mol⁻¹ChemAxon
Polarizability65.82 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-5600190000-39b380b30d3296452a8aSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00di-7600019000-726abed506367aa18efcSpectrum
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-0006-0009110000-22201ddfa15f4e8ab99fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-0000090000-e7d752494982063db039Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00dj-0200290000-a50512ce586c48b2dd77Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00kr-2000920000-82cae0801f5ae06ee29dSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0079-0000090000-c473bc91332a49995cbbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00ds-1100090000-63230997999368b5e280Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9010220000-1e3be1cd0f823364b481Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.000-2.878 umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0.00-2.88 umol/mmol creatinineAdult (>18 years old)BothNormal
    • David F. Putnam C...
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Crohn disease
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative colitis
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer
details
Associated Disorders and Diseases
Disease References
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 ]
Colorectal cancer
  1. 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 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023323
KNApSAcK IDNot Available
Chemspider ID389649
KEGG Compound IDC05791
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkUrobilinogen
METLIN ID7021
PubChem Compound440784
PDB IDNot Available
ChEBI ID4260
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
References
Synthesis ReferenceWatson, C. J.; Lowry, P. T. A further study of crystalline d-urobilin. Journal of Biological Chemistry (1956), 218 633-9.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Binder L, Smith D, Kupka T, Nelson B, Glass B, Wainscott M, Haynes J: Failure of prediction of liver function test abnormalities with the urine urobilinogen and urine bilirubin assays. Arch Pathol Lab Med. 1989 Jan;113(1):73-6. [PubMed:2642693 ]

Enzymes

General function:
Involved in hydrolase activity, hydrolyzing O-glycosyl compounds
Specific function:
Plays an important role in the degradation of dermatan and keratan sulfates.
Gene Name:
GUSB
Uniprot ID:
P08236
Molecular weight:
74731.46
Reactions
Bilirubin diglucuronide + Water + Reduced acceptor → Urobilinogen + D-Glucuronic acid + Acceptordetails