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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:03:40 UTC
HMDB IDHMDB01008
Secondary Accession Numbers
  • HMDB02309
Metabolite Identification
Common NameBiliverdin
DescriptionBiliverdin is a green pigment formed as a byproduct of hemoglobin breakdown. It consists of four linearly connected pyrrole rings (a tetrapyrrole). Biliverdin is formed when the heme group in hemoglobin is cleaved at its alpha-methene bridge. The resulting biliverdin is then reduced to bilirubin, a yellow pigment, by the enzyme biliverdin reductase. The changing color of a bruise from deep purple to yellow over time is a graphical indicator of this reaction. Biosynthesized from hemoglobin as a precursor of bilirubin. Occurs in the bile of amphibia and of birds, but not in normal human bile or serum.
Structure
Thumb
Synonyms
ValueSource
Biliverdin IXHMDB
1,3,6,7-Tetramethyl-4,5-dicarboxyethyl-2,8-divinylbilenoneHMDB
Biliverdin IX alphaHMDB
BiliverdineHMDB
DehydrobilirubinHMDB
Protobiliverdin IXHMDB
UteroverdineHMDB
Chemical FormulaC33H34N4O6
Average Molecular Weight582.6463
Monoisotopic Molecular Weight582.24783484
IUPAC Name3-(2-{[(2Z,5E)-3-(2-carboxyethyl)-5-[(3-ethenyl-4-methyl-2-oxo-2H-pyrrol-5-yl)methylidene]-4-methyl-2,5-dihydro-1H-pyrrol-2-ylidene]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 Name3-(2-{[(2Z,5E)-3-(2-carboxyethyl)-5-[(4-ethenyl-3-methyl-5-oxopyrrol-2-yl)methylidene]-4-methyl-1H-pyrrol-2-ylidene]methyl}-5-{[(2Z)-3-ethenyl-4-methyl-5-oxo-1H-pyrrol-2-ylidene]methyl}-4-methyl-1H-pyrrol-3-yl)propanoic acid
CAS Registry Number114-25-0
SMILES
CC1=C(C=C)\C(NC1=O)=C\C1=C(C)C(CCC(O)=O)=C(N1)\C=C1/N\C(=C\C2=NC(=O)C(C=C)=C2C)C(C)=C1CCC(O)=O
InChI Identifier
InChI=1S/C33H34N4O6/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/h7-8,13-15,34-35H,1-2,9-12H2,3-6H3,(H,37,42)(H,38,39)(H,40,41)/b24-13+,27-14-,28-15-
InChI KeyInChIKey=RCNSAJSGRJSBKK-YKSNQIBWSA-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
  • Substituted pyrrole
  • Dicarboxylic acid or derivatives
  • Heteroaromatic compound
  • Pyrroline
  • Pyrrole
  • N-acylimine
  • Secondary carboxylic acid amide
  • Lactam
  • Carboxamide group
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Enamine
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboxylic acid amide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
Biofunction
  • Component of Porphyrin and chlorophyll metabolism
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Membrane (predicted from logP)
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.012 mg/mLALOGPS
logP3.77ALOGPS
logP0.47ChemAxon
logS-4.7ALOGPS
pKa (Strongest Acidic)3.65ChemAxon
pKa (Strongest Basic)7.13ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area160.95 Å2ChemAxon
Rotatable Bond Count11ChemAxon
Refractivity169.16 m3·mol-1ChemAxon
Polarizability64.53 Å3ChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane (predicted from logP)
  • Nucleus
Biofluid LocationsNot Available
Tissue Location
  • Most Tissues
  • Neuron
  • Placenta
  • Prostate
Pathways
NameSMPDB LinkKEGG Link
Acute Intermittent PorphyriaSMP00344Not Available
Congenital Erythropoietic Porphyria (CEP) or Gunther DiseaseSMP00345Not Available
Hereditary Coproporphyria (HCP)SMP00342Not Available
Porphyria Variegata (PV)SMP00346Not Available
Porphyrin MetabolismSMP00024map00860
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022366
KNApSAcK IDNot Available
Chemspider ID4510089
KEGG Compound IDC00500
BioCyc IDBILIVERDINE
BiGG ID35167
Wikipedia LinkBiliverdin
NuGOwiki LinkHMDB01008
Metagene LinkHMDB01008
METLIN ID5938
PubChem Compound5353439
PDB IDNot Available
ChEBI ID17033
References
Synthesis ReferenceMora, Maria E.; Bari, Sara E.; Awruch, Josefina; Delfino, Jose M. On how the conformation of biliverdins influences their reduction to bilirubins: A biological and molecular modeling study. Bioorganic & Medicinal Chemistry (2003), 11(21), 4661-467
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. [19212411 ]
  2. Briz O, Macias RI, Serrano MA, Gonzalez-Gallego J, Bayon JE, Marin JJ: Excretion of foetal bilirubin by the rat placenta-maternal liver tandem. Placenta. 2003 May;24(5):462-72. [12744922 ]
  3. Trull FR, Ibars O, Lightner DA: Conformation inversion of bilirubin formed by reduction of the biliverdin-human serum albumin complex: evidence from circular dichroism. Arch Biochem Biophys. 1992 Nov 1;298(2):710-4. [1416999 ]
  4. Kunikata T, Itoh S, Ozaki T, Kondo M, Isobe K, Onishi S: Formation of propentdyopents and biliverdin, oxidized metabolites of bilirubin, in infants receiving oxygen therapy. Pediatr Int. 2000 Aug;42(4):331-6. [10986860 ]
  5. Odrcich MJ, Graham CH, Kimura KA, McLaughlin BE, Marks GS, Nakatsu K, Brien JF: Heme oxygenase and nitric oxide synthase in the placenta of the guinea-pig during gestation. Placenta. 1998 Sep;19(7):509-16. [9778124 ]
  6. Poon HF, Calabrese V, Scapagnini G, Butterfield DA: Free radicals: key to brain aging and heme oxygenase as a cellular response to oxidative stress. J Gerontol A Biol Sci Med Sci. 2004 May;59(5):478-93. [15123759 ]
  7. Beruter J, Colombo JP, Schlunegger UP: Isolation and identification of the urinary pigment uroerythrin. Eur J Biochem. 1975 Aug 1;56(1):239-44. [1175621 ]
  8. Chrastil J: Spectrophotometric determination of cysteine and cystine in urine. Analyst. 1990 Oct;115(10):1383-4. [2270876 ]

Enzymes

General function:
Involved in heme oxygenase (decyclizing) activity
Specific function:
Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed. Heme oxygenase 2 could be implicated in the production of carbon monoxide in brain where it could act as a neurotransmitter.
Gene Name:
HMOX2
Uniprot ID:
P30519
Molecular weight:
36032.615
Reactions
Heme + AH(2) + Oxygen → Biliverdin + Fe2+ + CO + A + Waterdetails
Hemoglobin + FADH + Oxygen → Globin + Biliverdin + Carbon monoxide + Fe3+ + FAD + Waterdetails
General function:
Involved in heme oxygenase (decyclizing) activity
Specific function:
Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.
Gene Name:
HMOX1
Uniprot ID:
P09601
Molecular weight:
32818.345
Reactions
Heme + AH(2) + Oxygen → Biliverdin + Fe2+ + CO + A + Waterdetails
Hemoglobin + FADH + Oxygen → Globin + Biliverdin + Carbon monoxide + Fe3+ + FAD + Waterdetails
General function:
Involved in biliverdin reductase activity
Specific function:
Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.
Gene Name:
BLVRA
Uniprot ID:
P53004
Molecular weight:
33428.225
Reactions
Bilirubin + NAD(P)(+) → Biliverdin + NAD(P)Hdetails
Bilirubin + NAD → Biliverdin + NADH + Hydrogen Iondetails
Bilirubin + NADP → Biliverdin + NADPH + Hydrogen Iondetails
General function:
Involved in catalytic activity
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:
P30043
Molecular weight:
22119.215
Reactions
Bilirubin + NAD(P)(+) → Biliverdin + NAD(P)Hdetails
Bilirubin + NAD → Biliverdin + NADH + Hydrogen Iondetails
Bilirubin + NADP → Biliverdin + NADPH + Hydrogen Iondetails