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Record Information
Version1.0
Creation Date2016-09-30 22:19:02 UTC
Update Date2020-06-04 20:46:04 UTC
BMDB IDBMDB0000054
Secondary Accession Numbers
  • BMDB00054
Metabolite Identification
Common NameBilirubin
DescriptionBilirubin belongs to the class of organic compounds known as bilirubins. These are organic compounds containing a dicarboxylic acyclic tetrapyrrole derivative. Bilirubin is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Bilirubin exists in all living species, ranging from bacteria to humans. In cattle, bilirubin is involved in the metabolic pathway called the porphyrin metabolism pathway. Bilirubin is a potentially toxic compound.
Structure
Thumb
Synonyms
ValueSource
1,10,19,22,23,24-Hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acidChEBI
2,17-Diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acidChEBI
2,7,13,17-Tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acidChEBI
8,12-Bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dioneChEBI
Bilirubin(Z,Z)ChEBI
Bilirubin-ixalphaChEBI
1,10,19,22,23,24-Hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionateGenerator
2,17-Diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoateGenerator
2,7,13,17-Tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoateGenerator
Bilirubin ixalphaHMDB
(4Z,15Z)-Bilirubin ixaHMDB
(Z,Z)-Bilirubin ixaHMDB
1,10,19,22,23,24-Hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-biline-8,12-dipropionateHMDB
1,10,19,22,23,24-Hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-biline-8,12-dipropionic acidHMDB
3-(2-((3-(2-Carboxyethyl)-4-methyl-5-((3-methyl-5-oxo-4-vinyl-1,5-dihydro-2H-pyrrol-2-ylidene)methyl)-1H-pyrrol-2-yl)methyl)-4-methyl-5-((4-methyl-5-oxo-3-vinyl-1,5-dihydro-2H-pyrrol-2-ylidene)methyl)-1H-pyrrol-3-yl)propanoateHMDB
3-(2-((3-(2-Carboxyethyl)-4-methyl-5-((3-methyl-5-oxo-4-vinyl-1,5-dihydro-2H-pyrrol-2-ylidene)methyl)-1H-pyrrol-2-yl)methyl)-4-methyl-5-((4-methyl-5-oxo-3-vinyl-1,5-dihydro-2H-pyrrol-2-ylidene)methyl)-1H-pyrrol-3-yl)propanoic acidHMDB
3-(2-((3-(2-Carboxyethyl)-4-methyl-5-[(Z)-(3-methyl-5-oxo-4-vinyl-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-1H-pyrrol-2-yl)methyl)-4-methyl-5-[(Z)-(4-methyl-5-oxo-3-vinyl-1,5-dihydro-2H-pyrrol-2-ylideneHMDB
3-[2-[[3-(2-Carboxyethyl)-5-[(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(4-ethenyl-3-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoateHMDB
3-[2-[[3-(2-Carboxyethyl)-5-[(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(4-ethenyl-3-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acidHMDB
3-[2-[[3-(2-Carboxyethyl)-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(Z)-(4-ethenyl-3-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoateHMDB
3-[2-[[3-(2-Carboxyethyl)-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(Z)-(4-ethenyl-3-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acidHMDB
Bilirubin IX-alphaHMDB
CholerythrinHMDB
HematoidinHMDB
Bilirubin IX alphaHMDB
Chemical FormulaC33H36N4O6
Average Molecular Weight584.6621
Monoisotopic Molecular Weight584.263484904
IUPAC Name3-(2-{[3-(2-carboxyethyl)-5-{[(2Z)-4-ethenyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-ylidene]methyl}-4-methyl-1H-pyrrol-2-yl]methyl}-5-{[(2Z)-3-ethenyl-4-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-ylidene]methyl}-4-methyl-1H-pyrrol-3-yl)propanoic acid
Traditional Namebilirubin
CAS Registry Number635-65-4
SMILES
CC1=C(C=C)\C(NC1=O)=C\C1=C(C)C(CCC(O)=O)=C(CC2=C(CCC(O)=O)C(C)=C(N2)\C=C2/NC(=O)C(C=C)=C2C)N1
InChI Identifier
InChI=1S/C33H36N4O6/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/h7-8,13-14,34-35H,1-2,9-12,15H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-
InChI KeyBPYKTIZUTYGOLE-IFADSCNNSA-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
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Endoplasmic reticulum
  • Membrane
  • Myelin sheath
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.009 mg/mL at 25 °CNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP3.22ALOGPS
logP3.12ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)4.03ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area164.38 ŲChemAxon
Rotatable Bond Count12ChemAxon
Refractivity168.9 m³·mol⁻¹ChemAxon
Polarizability66.16 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
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, Positivesplash10-00vr-0100090000-d19585e898437e8be1d5View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-01vn-3100069000-c39a7113e7f8eb3fa22aView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ("Bilirubin,1TMS,#1" TMS) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , negativesplash10-000i-0090000000-50ff729317f07f6120b5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0002-0090000000-83d0d13757dcbce35604View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0002-0090000000-491b2676042d62727784View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-01p9-1090000000-1d547122826037e04cfbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-000i-1090000000-30f7fa38dcf8706b38c6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-001i-1030090000-dea3b39afc072d2855c5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-000i-1090010000-369d79a300efec3a6c78View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0002-0091050000-78e3736d034dec9b8fa9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0002-0091000000-cc507e875cc295800fa0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0002-0090000000-679d7d93f8aeb5b1c0d1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0002-0090020000-ea54f49e76225d251990View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0002-0091000000-24657f467af3adfa1e8cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-000i-0020090000-5bcce058438671178ee4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0002-0092030000-24054054aef5b235a850View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-000i-0030090000-b525a9b7bb66406e6afcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00ks-0000090000-ddf9acb7f968b9079764View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00g0-0110290000-ae6f323e9f5e9e26199cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0uml-1102910000-df5146b3612e4fb4ce5eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0000090000-6deb1aed1a9c3839e2a9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-053i-1010190000-7435a4388bade8e83d10View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9010240000-cc90fff0581c6bcefd0dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kr-0010090000-d21be2c11a0dfd17c6e9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00kr-0030190000-749f82b203e182b3e46fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0kac-0291230000-962a583eff6dd8d5cf73View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0010090000-467141ca1354a02b0aefView in MoNA
1D NMR1H NMR Spectrum (1D, 600 MHz, 100%_DMSO, experimental)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, C, experimental)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, DMSO, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, DMSO, experimental)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, 100%_DMSO, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Endoplasmic reticulum
  • Membrane
  • Myelin sheath
Biospecimen Locations
  • Bile
  • Blood
  • Bone Marrow
  • Brain
  • Epidermis
  • Erythrocyte
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Neuron
  • Pancreas
  • Placenta
  • Platelet
  • Skeletal Muscle
  • Spleen
  • Thyroid Gland
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BileExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
BloodDetected and Quantified2.52 uMNot SpecifiedNot Specified
Normal
details
Bone MarrowExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
BrainExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
EpidermisExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
ErythrocyteExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
FibroblastsExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
IntestineExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
KidneyExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
LiverExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
NeuronExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
PancreasExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
PlacentaExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
PlateletExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Skeletal MuscleExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
SpleenExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Thyroid GlandExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified2.01 uMNot SpecifiedNot Specified
Treated with bovine somatotropin
details
HMDB IDHMDB0000054
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021886
KNApSAcK IDC00029828
Chemspider ID4444055
KEGG Compound IDC00486
BioCyc IDBILIRUBIN
BiGG ID35117
Wikipedia LinkBilirubin
METLIN ID81
PubChem Compound5280352
PDB IDNot Available
ChEBI ID16990
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

General function:
Involved in prostaglandin-D synthase activity
Specific function:
Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophobic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system (By similarity).
Gene Name:
PTGDS
Uniprot ID:
O02853
Molecular weight:
21229.0
General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Broad specificity oxidoreductase that catalyzes the NADPH-dependent reduction of a variety of flavins, such as riboflavin, FAD or FMN, biliverdins, methemoglobin and PQQ (pyrroloquinoline quinone). Contributes to heme catabolism and metabolizes linear tetrapyrroles. Can also reduce the complexed Fe(3+) iron to Fe(2+) in the presence of FMN and NADPH. In the liver, converts biliverdin to bilirubin.
Gene Name:
BLVRB
Uniprot ID:
P52556
Molecular weight:
22132.0
General function:
Posttranslational modification, protein turnover, chaperones
Specific function:
Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Also binds steroids, bilirubin, carcinogens and numerous organic anions. Has dichloromethane dehalogenase activity.
Gene Name:
GSTT1
Uniprot ID:
Q2NL00
Molecular weight:
27149.0
General function:
Involved in copper ion binding
Specific function:
Binds copper, nickel, and fatty acids as well as, and bilirubin less well than, serum albumin.
Gene Name:
AFP
Uniprot ID:
Q3SZ57
Molecular weight:
68588.0
General function:
Involved in lipid binding
Specific function:
Plays a role in lipoprotein-mediated cholesterol uptake in hepatocytes. Binds cholesterol. Binds free fatty acids and their coenzyme A derivatives, bilirubin, and some other small molecules in the cytoplasm. May be involved in intracellular lipid transport.
Gene Name:
FABP1
Uniprot ID:
P80425
Molecular weight:
14227.0