Bovine Metabolome Database: Showing metabocard for Biliverdin (BMDB0001008)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (3) Show 3 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:39:49 UTC

Update Date

2020-05-11 20:48:18 UTC

BMDB ID

BMDB0001008

Secondary Accession Numbers

BMDB01008

Metabolite Identification

Common Name

Biliverdin

Description

Biliverdin belongs to the class of organic compounds known as bilirubins. These are organic compounds containing a dicarboxylic acyclic tetrapyrrole derivative. Biliverdin is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Biliverdin IX	HMDB, MeSH
1,3,6,7-Tetramethyl-4,5-dicarboxyethyl-2,8-divinylbilenone	HMDB
Biliverdin IX alpha	HMDB, MeSH
Biliverdine	HMDB, MeSH
Dehydrobilirubin	HMDB, MeSH
Protobiliverdin IX	HMDB
Uteroverdine	HMDB, MeSH
IX, biliverdin	MeSH
IX alpha, biliverdin	MeSH
Ooecyan	MeSH
alpha, Biliverdin IX	MeSH

Chemical Formula

C₃₃H₃₄N₄O₆

Average Molecular Weight

582.6463

Monoisotopic Molecular Weight

582.24783484

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 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

CAS Registry Number

114-25-0

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 Key

RCNSAJSGRJSBKK-YKSNQIBWSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as bilirubins. These are organic compounds containing a dicarboxylic acyclic tetrapyrrole derivative.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Bilirubins

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

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
Membrane
Nucleus

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	3.77	ALOGPS
logP	0.47	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	3.65	ChemAxon
pKa (Strongest Basic)	7.13	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	160.95 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	169.16 m³·mol⁻¹	ChemAxon
Polarizability	64.53 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dr-0100090000-0964294450d059cff3a0	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-059m-3100059000-890015c6bba015f420a9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0159-0000090000-31b6fa66f400b675cb50	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00y0-0110290000-c92b3d0b1da5e4894a00	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00fr-1922610000-473a2202d0d37bf34635	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0000090000-91f1d7eaf95141d16d23	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0540-1100190000-783211ee21a08943a513	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9110130000-988e6bd831f769cd79a4	View in MoNA

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Membrane
Nucleus

Biospecimen Locations

Blood
Liver
Neuron
Placenta
Prostate Tissue

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31867104	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Abnormal (male calves/vaccination biomarker)	PMID: 25828073	details

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Biliverdin

METLIN ID

Not Available

PubChem Compound

5353439

PDB ID

Not Available

ChEBI ID

Not Available

References

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

General References

Not Available

Enzymes

Enzyme Details

1. Heme oxygenase 1

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. Exhibits cytoprotective effects since excess of free heme sensitizes cells to undergo apoptosis.
Gene Name:: HMOX1
Uniprot ID:: Q5E9F2
Molecular weight:: 32940.0

Enzyme Details

2. Prostaglandin-H2 D-isomerase

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

Enzyme Details

3. Flavin reductase (NADPH)

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

Showing metabocard for Biliverdin (BMDB0001008)

Structure for BMDB0001008 (Biliverdin)

Enzymes