Bovine Metabolome Database: Showing metabocard for Retinoyl b-glucuronide (BMDB0003141)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (15) Show 15 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:02:52 UTC

Update Date

2020-05-11 20:40:21 UTC

BMDB ID

BMDB0003141

Secondary Accession Numbers

BMDB03141

Metabolite Identification

Common Name

Retinoyl b-glucuronide

Description

Retinoyl b-retinoyl b-glucuronide, also known as Retinoyl b-retinoyl b-glucuronide, belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. Retinoyl b-retinoyl b-glucuronide is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Retinoyl b-retinoyl b-glucuronide can be biosynthesized from all-trans-retinoyl b-glucuronide; which is mediated by the enzyme UDP-glucuronosyltransferase 1-1. In cattle, retinoyl b-retinoyl b-glucuronide is involved in the metabolic pathway called the retinol metabolism pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
all-trans-Retinoyl-beta-glucuronide	ChEBI
Retinoyl glucuronide	ChEBI
all-trans-Retinoyl-b-glucuronide	Generator
all-trans-Retinoyl-β-glucuronide	Generator
13-cis-Retinoate	HMDB
13-cis-Retinoic acid	HMDB
13-cis-Retinoic acid acyl beta-D-glucuronide	HMDB
13-cis-Retinoic acid acyl beta-delta-glucuronide	HMDB
13-cis-Retinoyl glucuronide	HMDB
13-cis-Retinoyl-beta-D-glucuronide	HMDB
13-cis-Retinoyl-beta-delta-glucuronide	HMDB
13-cis-Retinoyl-beta-glucuronide	HMDB
9-cis-Retinoyl-beta-D-glucuronide	HMDB
9-cis-Retinoyl-beta-delta-glucuronide	HMDB
all-trans-Retinoyl-beta-D-glucuronide	HMDB
all-trans-Retinoyl-beta-delta-glucuronide	HMDB
Glucuronide	HMDB
Retinoate	HMDB
Retinoic acid	HMDB
Retinoic acid beta-D-glucuronide	HMDB
Retinoic acid beta-delta-glucuronide	HMDB
Retinoyl beta-glucuronide	HMDB
Retinoyl-beta-glucuronide	HMDB
trans-Retinoyl glucuronide	MeSH, HMDB

Chemical Formula

C₂₆H₃₆O₈

Average Molecular Weight

476.5592

Monoisotopic Molecular Weight

476.241018128

IUPAC Name

(2S,3S,4S,5R,6S)-6-{[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

Traditional Name

glucuronide

CAS Registry Number

401-10-5

SMILES

O[C@@H]1[C@@H](O)[C@@H](O[C@H](C(O)=O)[C@H]1O)OC(=O)\C=C(/C)\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C

InChI Identifier

InChI=1S/C26H36O8/c1-15(11-12-18-17(3)10-7-13-26(18,4)5)8-6-9-16(2)14-19(27)33-25-22(30)20(28)21(29)23(34-25)24(31)32/h6,8-9,11-12,14,20-23,25,28-30H,7,10,13H2,1-5H3,(H,31,32)/b9-6+,12-11+,15-8+,16-14+/t20-,21-,22+,23-,25+/m0/s1

InChI Key

MTGFYEHKPMOVNE-NEFMKCFNSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Diterpene glycosides

Alternative Parents

Substituents

Diterpene glycoside
Retinoid ester
Diterpenoid
Retinoid skeleton
1-o-glucuronide
O-glucuronide
Glucuronic acid or derivatives
Hexose monosaccharide
Beta-hydroxy acid
Fatty acid ester
Dicarboxylic acid or derivatives
Fatty acyl
Hydroxy acid
Monosaccharide
Oxane
Pyran
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary alcohol
Carboxylic acid ester
Carboxylic acid derivative
Organoheterocyclic compound
Polyol
Oxacycle
Acetal
Carboxylic acid
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

glucuronic acids (CHEBI:28870 )

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
Endoplasmic reticulum
Membrane

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	3.57	ALOGPS
logP	3.3	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	3.39	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	133.52 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	130.09 m³·mol⁻¹	ChemAxon
Polarizability	51.85 Å³	ChemAxon
Number of Rings	2	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	splash10-0a4i-9432400000-25dd7257fa97ce57c686	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-004i-3051009000-fd7898490f7303f898cc	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ke9-0693400000-31eed182f08fe6786169	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-052u-0891000000-ca789901418c22bb0493	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-1920000000-e38e08d95bad4a423551	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-1190200000-9141a0351cb4c8689ff4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000t-3690100000-f02b84b6d3b8cceeb6cf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0535-8590000000-12eae5811075d2fce9f9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-057r-0565900000-0aac4f4c541ab0976b56	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-009f-0923100000-bb8c1ba6dc7f05b15be7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0ac0-2900000000-b37fb8c36dde85ab4488	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0059-0390700000-eddabec40f40511d435f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a6s-2391400000-4b33ff2150a642a78136	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0r01-3390000000-158c7d14c4f6713d87da	View in MoNA

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Endoplasmic reticulum
Membrane

Biospecimen Locations

Adipose Tissue
Epidermis
Fibroblasts
Intestine
Kidney
Liver
Pancreas
Placenta

Pathways

Name	SMPDB/Pathwhiz	KEGG
Retinol Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Adipose Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Pancreas	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

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0003141

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023112

KNApSAcK ID

Not Available

Chemspider ID

4445170

KEGG Compound ID

C11061

BioCyc ID

Not Available

BiGG ID

2304843

Wikipedia Link

Not Available

METLIN ID

2280

PubChem Compound

5281877

PDB ID

Not Available

ChEBI ID

28870

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. 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

2. Retinal dehydrogenase 1

General function:: Energy production and conversion
Specific function:: Can convert/oxidize retinaldehyde to retinoic acid. Binds free retinal and cellular retinol-binding protein-bound retinal. May have a broader specificity and oxidize other aldehydes in vivo.
Gene Name:: ALDH1A1
Uniprot ID:: P48644
Molecular weight:: 54806.0

Enzyme Details

3. Polycomb group RING finger protein 1

General function:: Transcription
Specific function:: Component of the Polycomb group (PcG) multiprotein BCOR complex, a complex required to maintain the transcriptionally repressive state of some genes, such as BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. Transcriptional repressor that may be targeted to the DNA by BCL6; this transcription repressor activity may be related to PKC signaling pathway. Represses CDKN1A expression by binding to its promoter, and this repression is dependent on the retinoic acid response element (RARE element). Promotes cell cycle progression and enhances cell proliferation as well. May have a positive role in tumor cell growth by down-regulating CDKN1A. Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility. Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity. Regulates the expression of DPPA4 and NANOG in the NT2 embryonic carcinoma cells.
Gene Name:: PCGF1
Uniprot ID:: Q2YDF9
Molecular weight:: 30324.0

Enzyme Details

4. Retinoic acid receptor responder (Tazarotene induced) 1

General function:: Involved in receptor activity
Specific function:: Not Available
Gene Name:: RARRES1
Uniprot ID:: Q0P5D6
Molecular weight:: 32771.0

Enzyme Details

5. Retinoic acid receptor beta

General function:: Involved in retinoic acid receptor activity
Specific function:: Not Available
Gene Name:: Not Available
Uniprot ID:: Q45UD6
Molecular weight:: 10459.0

Enzyme Details

6. Retinoic acid receptor responder protein 2

General function:: Not Available
Specific function:: Adipocyte-secreted protein (adipokine) that regulates adipogenesis, metabolism and inflammation through activation of the chemokine-like receptor 1 (CMKLR1). Its other ligands include G protein-coupled receptor 1 (GPR1) and chemokine receptor-like 2 (CCRL2). Positively regulates adipocyte differentiation, modulates the expression of adipocyte genes involved in lipid and glucose metabolism and might play a role in angiogenesis, a process essential for the expansion of white adipose tissue. Also acts as a proinflammatory adipokine, causing an increase in secretion of proinflammatory and prodiabetic adipokines, which further impair adipose tissue metabolic function and have negative systemic effects including impaired insulin sensitivity, altered glucose and lipid metabolism, and a decrease in vascular function in other tissues. Can have both pro- and anti-inflammatory properties depending on the modality of enzymatic cleavage by different classes of proteases. Acts as a chemotactic factor for leukocyte populations expressing CMKLR1, particularly immature plasmacytoid dendritic cells, but also immature myeloid DCs, macrophages and natural killer cells. Exerts an anti-inflammatory role by preventing TNF/TNFA-induced VCAM1 expression and monocytes adhesion in vascular endothelial cells. The effect is mediated via inhibiting activation of NF-kappa-B and CRK/p38 through stimulation of AKT1/NOS3 signaling and nitric oxide production. Exhibits an antimicrobial function in the skin (By similarity).
Gene Name:: RARRES2
Uniprot ID:: Q29RS5
Molecular weight:: 18357.0

Enzyme Details

7. Retinoic acid receptor, alpha

General function:: Involved in retinoic acid receptor activity
Specific function:: Not Available
Gene Name:: RARA
Uniprot ID:: Q58DG3
Molecular weight:: 30654.0

Enzyme Details

8. RARG protein

General function:: Involved in retinoic acid receptor activity
Specific function:: Not Available
Gene Name:: RARG
Uniprot ID:: Q08DD4
Molecular weight:: 50946.0

Enzyme Details

9. Peroxisome proliferator-activated receptor gamma

General function:: Involved in protein binding
Specific function:: Nuclear receptor that binds peroxisome proliferators such as hypolipidemic drugs and fatty acids. Once activated by a ligand, the nuclear receptor binds to DNA specific PPAR response elements (PPRE) and modulates the transcription of its target genes, such as acyl-CoA oxidase. It therefore controls the peroxisomal beta-oxidation pathway of fatty acids. Key regulator of adipocyte differentiation and glucose homeostasis. ARF6 acts as a key regulator of the tissue-specific adipocyte P2 (aP2) enhancer. Acts as a critical regulator of gut homeostasis by suppressing NF-kappa-B-mediated proinflammatory responses. Plays a role in the regulation of cardiovascular circadian rhythms by regulating the transcription of ARNTL/BMAL1 in the blood vessels.
Gene Name:: PPARG
Uniprot ID:: O18971
Molecular weight:: 57579.0

Enzyme Details

10. Fatty acid-binding protein, adipocyte

General function:: Involved in lipid binding
Specific function:: Lipid transport protein in adipocytes. Binds both long chain fatty acids and retinoic acid. Delivers long-chain fatty acids and retinoic acid to their cognate receptors in the nucleus.
Gene Name:: FABP4
Uniprot ID:: P48035
Molecular weight:: 14678.0

Enzyme Details

11. Cellular retinoic acid-binding protein 1

General function:: Involved in retinal binding
Specific function:: Cytosolic CRABPs may regulate the access of retinoic acid to the nuclear retinoic acid receptors.
Gene Name:: CRABP1
Uniprot ID:: P62964
Molecular weight:: 15592.0

Enzyme Details

12. LOC100138545 protein

General function:: Involved in SMAD binding
Specific function:: Not Available
Gene Name:: LOC100138545
Uniprot ID:: A6QQE3
Molecular weight:: 91118.0

Enzyme Details

13. Retinoic acid receptor RXR-gamma

General function:: Involved in steroid binding
Specific function:: Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid (By similarity).
Gene Name:: RXRG
Uniprot ID:: Q0VC20
Molecular weight:: 50882.0

Enzyme Details

14. Cellular retinoic acid-binding protein 2

General function:: Involved in retinal binding
Specific function:: Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors (By similarity).
Gene Name:: CRABP2
Uniprot ID:: Q5PXY7
Molecular weight:: 15735.0

Enzyme Details

15. Multidrug resistance-associated protein 1

General function:: Defense mechanisms
Specific function:: Mediates export of organic anions and drugs from the cytoplasm. Mediates ATP-dependent transport of glutathione and glutathione conjugates, leukotriene C4, estradiol-17-beta-o-glucuronide, methotrexate, antiviral drugs and other xenobiotics. Confers resistance to anticancer drugs by decreasing accumulation of drug in cells, and by mediating ATP- and GSH-dependent drug export (PubMed:12067707). Hydrolyzes ATP with low efficiency. Catalyzes the export of sphingosine 1-phosphate from mast cells independently of their degranulation (By similarity). Participates in inflammatory response by allowing export of leukotriene C4 from leukotriene C4-synthezing cells (By similarity).
Gene Name:: ABCC1
Uniprot ID:: Q8HXQ5
Molecular weight:: 171666.0

Showing metabocard for Retinoyl b-glucuronide (BMDB0003141)

Structure for BMDB0003141 (Retinoyl b-glucuronide)

Enzymes