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Record Information
Version4.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-07 01:21:43 UTC
HMDB IDHMDB0001008
Secondary Accession Numbers
  • HMDB01008
  • 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
IX, biliverdinMeSH
IX alpha, biliverdinMeSH
OoecyanMeSH
alpha, Biliverdin IXMeSH
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 KeyRCNSAJSGRJSBKK-YKSNQIBWSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as bilirubins. These are organic compounds containing a dicarboxylic acyclic tetrapyrrole derivative.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganoheterocyclic compounds
Sub ClassTetrapyrroles and derivatives
Direct ParentBilirubins
Alternative Parents
Substituents
  • Bilirubin skeleton
  • Dipyrrin
  • Dicarboxylic acid or derivatives
  • Substituted pyrrole
  • Pyrrole
  • Pyrroline
  • Heteroaromatic compound
  • Carboxamide group
  • Lactam
  • N-acylimine
  • Secondary carboxylic acid amide
  • Azacycle
  • Organic 1,3-dipolar compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Propargyl-type 1,3-dipolar organic compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organonitrogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological Location:

  Subcellular:

  Biofluid and excreta:

  Tissue and substructures:

  Organ and components:

Source:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

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 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity169.16 m³·mol⁻¹ChemAxon
Polarizability64.53 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, Positivesplash10-00dr-0100090000-0964294450d059cff3a0View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-059m-3100059000-890015c6bba015f420a9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0159-0000090000-31b6fa66f400b675cb50View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00y0-0110290000-c92b3d0b1da5e4894a00View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00fr-1922610000-473a2202d0d37bf34635View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0000090000-91f1d7eaf95141d16d23View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0540-1100190000-783211ee21a08943a513View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9110130000-988e6bd831f769cd79a4View in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane (predicted from logP)
  • Nucleus
Biofluid Locations
  • Feces
Tissue Location
  • Most Tissues
  • Neuron
  • Placenta
  • Prostate
Pathways
NameSMPDB/PathwhizKEGG
Acute Intermittent PorphyriaPw000174Pw000174 greyscalePw000174 simpleNot Available
Congenital Erythropoietic Porphyria (CEP) or Gunther DiseasePw000176Pw000176 greyscalePw000176 simpleNot Available
Hereditary Coproporphyria (HCP)Pw000211Pw000211 greyscalePw000211 simpleNot Available
Porphyria Variegata (PV)Pw000175Pw000175 greyscalePw000175 simpleNot Available
Porphyrin MetabolismPw000158Pw000158 greyscalePw000158 simpleMap00860
Normal Concentrations
Not Available
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)BothColorectal Cancer details
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
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. doi: 10.1038/nature07762. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed:1175621 ]
  8. Chrastil J: Spectrophotometric determination of cysteine and cystine in urine. Analyst. 1990 Oct;115(10):1383-4. [PubMed: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