biliverdin-IX-α (PAMDB120516)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB120516
Identification
Name: biliverdin-IX-α
Description:Dicarboxylate anion of biliverdin; major species at pH 7.3.
Structure
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🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • biliverdin
  • biliverdin dianion
Chemical Formula: C33H32N4O6
Average Molecular Weight: 580.639
Monoisotopic Molecular Weight: 582.24786
InChI Key: QBUVFDKTZJNUPP-BBROENKCSA-L
InChI: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/h7-8,13-15,35H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/p-2/b26-13-,27-14-,28-15-
CAS number: 114-25-0
IUPAC Name:3-(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 IUPAC Name: 3-(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
SMILES:C=CC1(=C(C)C(NC1=CC4(=C(C)C(CCC(=O)[O-])=C(C=C2(C(CCC(=O)[O-])=C(C)C(=N2)C=C3(C(C)=C(C=C)C(=O)N3)))N4))=O)
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of chemical entities known as bilirubins. These are organic compounds containing a dicarboxylic acyclic tetrapyrrole derivative.
Kingdom Chemical entities
Super ClassOrganic compounds
Class Organoheterocyclic compounds
Sub ClassTetrapyrroles and derivatives
Direct Parent Bilirubins
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 Framework Aromatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Solid
Charge:-2
Melting point: > 300 °C
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
Biological Properties
Cellular Locations: Not Available
Reactions:
ferroheme b + Oxygen + Donor-H2 + Hydrogen ion → biliverdin-IX-α + FE+2 + CO + Acceptor + Water
Pathways:
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
References
References:
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • 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 ]
  • Chrastil J: Spectrophotometric determination of cysteine and cystine in urine. Analyst. 1990 Oct;115(10):1383-4. [2270876 ]
Synthesis Reference: Mora, 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
External Links:
ResourceLink
METABOLIGHTSMTBLC57991
HMDBHMDB01008
CHEBI57991
PUBCHEM25245769
LIGAND-CPDC00500