Cannabis Compound Database: Showing Compound Card for Biliverdin (CDB004876)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (4) Show 8 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:45:55 UTC

Updated at

2020-11-18 16:38:55 UTC

CannabisDB ID

CDB004876

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

Biliverdin

Description

Biliverdin, also known as biliverdin IX α or dehydrobilirubin, 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). Biliverdin exists in all living organisms, ranging from bacteria to humans. In humans, biliverdin is involved in the metabolic disorder called congenital erythropoietic porphyria (cep) or gunther disease pathway. A linear tetrapyrrole produced in the reticuloendothelial system by the first step of heme degradation, catalysed by heme oxygenase. Biliverdin is expected to be in Cannabis as all living plants are known to produce and metabolize it.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
8,12-Bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbilin-1(19)(21H,24H)-dione	ChEBI
Biliverdin IX alpha	ChEBI
Biliverdin ixalpha	ChEBI
Biliverdine	ChEBI
BILIVERDINE IX ALPHA	ChEBI
Biliverdin IX a	Generator
Biliverdin IX α	Generator
BILIVERDINE IX a	Generator
BILIVERDINE IX α	Generator
Biliverdin IX	HMDB
1,3,6,7-Tetramethyl-4,5-dicarboxyethyl-2,8-divinylbilenone	HMDB
Dehydrobilirubin	HMDB
Protobiliverdin IX	HMDB
Uteroverdine	HMDB

Chemical Formula

C₃₃H₃₄N₄O₆

Average Molecular Weight

582.66

Monoisotopic Molecular Weight

582.2478

IUPAC Name

3-(2-{[(2Z)-3-(2-carboxyethyl)-5-{[(2Z)-4-ethenyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-ylidene]methyl}-4-methyl-2H-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

biliverdine

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/h7-8,13-15,35H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,28-15-

InChI Key

QBUVFDKTZJNUPP-BBROENKCSA-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
Ketimine
Lactam
Secondary carboxylic acid amide
Azacycle
Organic 1,3-dipolar compound
Carboxylic acid derivative
Carboxylic acid
Propargyl-type 1,3-dipolar organic compound
Hydrocarbon derivative
Imine
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Organic oxide
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

bilins (CHEBI:17033 )

Ontology

Disposition

Source:

Endogenous

Biological location:

Organ and components:

Prostate

Cell and elements:

Cell:

Nerve cell

Tissue and substructures:

Placenta

Biofluid and excreta:

Subcellular:

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	> 300 °C	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	3.44	ALOGPS
logP	0.57	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	3.87	ChemAxon
pKa (Strongest Basic)	5.86	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	160.95 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	169.36 m³·mol⁻¹	ChemAxon
Polarizability	64.76 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
Predicted GC-MS	Biliverdin, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, "Biliverdin,1TMS,#1" TMS, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_9, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TMS_2_10, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TBDMS_1_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TBDMS_1_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Biliverdin, TBDMS_2_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, positive	splash10-001i-0020090000-874093fd6fe6d5f0da55	2020-07-21	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 25V, positive	splash10-001i-0000090000-242e3cfb1074431707cd	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 36V, positive	splash10-001i-0040090000-83f503dd74fa46d0b8c3	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 46V, positive	splash10-0002-0090030000-2b21a14ef4c3d9f0fe28	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 58V, positive	splash10-0002-0090000000-48e89a30c017d91911ca	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 68V, positive	splash10-0002-0090000000-23cad1d9dabd8152a37e	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 79V, positive	splash10-000b-0190100000-198c1c8608121dc207a2	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 89V, positive	splash10-0a4s-0491100000-c2bc552b31380512ee3f	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 100V, positive	splash10-0a4j-0691100000-a0bcc22a3e04d7c03a3b	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 110V, positive	splash10-0a4j-0982100000-edd8e7ace1f0d2dab0bc	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 121V, positive	splash10-0a4j-0962000000-3bbd19a9fb91f72836fd	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 131V, positive	splash10-0aos-0962000000-36cc065c1628bd7bddc9	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 142V, positive	splash10-0apm-0952000000-67cd6753793276126c5f	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 152V, positive	splash10-066v-0952000000-d41423feb72202517842	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 164V, positive	splash10-067l-0952000000-b520e882d402bb5acddf	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 174V, positive	splash10-014i-0951000000-3b12ad8a32687e14b0b8	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 185V, positive	splash10-014i-0951000000-897becf9303fb0568aa3	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 195V, positive	splash10-014l-0951000000-895b6d3b15be956c2630	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 206V, positive	splash10-014l-0951000000-fe8747b84f037f5e5224	2020-07-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0159-0000090000-ea485acf588e19908463	2017-07-25	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00y0-0120390000-06e57745836cc9c214a2	2017-07-25	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0fbi-1512920000-e84010eaf624b552acd4	2017-07-25	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0000090000-9bc7e68d2e9ed37b5c9b	2017-07-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0540-1000190000-b9e5e8f35aa309a0ed2b	2017-07-26	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9010230000-260f7a168e7f7d25eb1f	2017-07-26	View Spectrum

NMR

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Porphyrin Metabolism
Acute Intermittent Porphyria		Not Available
Porphyria Variegata (PV)		Not Available
Congenital Erythropoietic Porphyria (CEP) or Gunther Disease		Not Available
Hereditary Coproporphyria (HCP)		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Heme oxygenase 2	HMOX2	16p13.3	P30519	details
Heme oxygenase 1	HMOX1	22q13.1	P09601	details
Biliverdin reductase A	BLVRA	7p13	P53004	details
Flavin reductase (NADPH)	BLVRB	19q13.1-q13.2	P30043	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	Details
Heme oxygenase 2	HMOX2	16p13.3	P30519	details
Heme oxygenase 1	HMOX1	22q13.1	P09601	details
Biliverdin reductase A	BLVRA	7p13	P53004	details

Receptors

Not Available

Transcriptional Factors

Protein Name	Gene Name	Locus	Uniprot ID	Details
Heme oxygenase 1	HMOX1	22q13.1	P09601	details

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0001008

DrugBank ID

DB02073

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022366

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17033

References

General References

Not Available

Enzymes

Enzyme Details

1. Heme oxygenase 2

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

Enzyme Details

2. 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.
Gene Name:: HMOX1
Uniprot ID:: P09601
Molecular weight:: 32818.345

Enzyme Details

3. Biliverdin reductase A

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

Enzyme Details

4. Flavin reductase (NADPH)

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

Showing Compound Card for Biliverdin (CDB004876)

Structure for CDB004876 (Biliverdin)

Enzymes