Bovine Metabolome Database: Showing metabocard for Vitamin D2 3-glucuronide (BMDB0010344)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-10-03 18:04:45 UTC

Update Date

2020-05-11 20:25:14 UTC

BMDB ID

BMDB0010344

Secondary Accession Numbers

BMDB10344

Metabolite Identification

Common Name

Vitamin D2 3-glucuronide

Description

Vitamin D2 3-glucuronide, also known as vitamin D2 glucosiduronate, belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane. Vitamin D2 3-glucuronide is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(3beta,5Z,7E,22E)-9,10-Secoergosta-5,7,10(19),22-tetraen-3-yl-beta-D-glucopyranosiduronic acid	HMDB
(3beta,5Z,7E,22E)-9,10-Secoergosta-5,7,10(19),22-tetraen-3-yl-beta-delta-glucopyranosiduronic acid	HMDB
Vitamin D2 3beta-glucosiduronate	HMDB
Vitamin D2 glucosiduronate	HMDB
Vitamin D2 3 beta-glucosiduronate	HMDB
(2S,3S,4S,5R,6R)-6-{[(3E)-3-{2-[(1R,4E,7ar)-1-[(2R,3E,5R)-5,6-dimethylhept-3-en-2-yl]-7a-methyl-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylate	HMDB
Vitamin D2 3-glucuronide	MeSH

Chemical Formula

C₃₄H₅₂O₇

Average Molecular Weight

572.7725

Monoisotopic Molecular Weight

572.371304018

IUPAC Name

(2S,3S,4S,5R,6R)-6-{[(3E)-3-{2-[(1R,4E,7aR)-1-[(2R,3E,5R)-5,6-dimethylhept-3-en-2-yl]-7a-methyl-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

Traditional Name

vitamin D2 3-glucuronide

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H](C)\C=C\[C@@H](C)[C@@]1([H])CCC2\C(CCC[C@]12C)=C\C=C1/CC(CCC1=C)O[C@@H]1O[C@H](C(O)=O)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C34H52O7/c1-19(2)20(3)9-10-22(5)26-15-16-27-23(8-7-17-34(26,27)6)12-13-24-18-25(14-11-21(24)4)40-33-30(37)28(35)29(36)31(41-33)32(38)39/h9-10,12-13,19-20,22,25-31,33,35-37H,4,7-8,11,14-18H2,1-3,5-6H3,(H,38,39)/b10-9+,23-12+,24-13+/t20-,22+,25?,26+,27?,28-,29-,30+,31-,33+,34+/m0/s1

InChI Key

NLCXHIGBBJLZMX-HLQYQDSBSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Vitamin D and derivatives

Direct Parent

Vitamin D and derivatives

Alternative Parents

Substituents

Triterpenoid
1-o-glucuronide
O-glucuronide
Glucuronic acid or derivatives
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Beta-hydroxy acid
Hydroxy acid
Monosaccharide
Pyran
Oxane
Secondary alcohol
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Acetal
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Polyol
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
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	5.4	ALOGPS
logP	5.6	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	3.56	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	161.17 m³·mol⁻¹	ChemAxon
Polarizability	64.99 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	splash10-056r-7301390000-3002db8427e8bda5a2f7	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-004i-6512239000-0a847383f208f599a4b7	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("Vitamin D2 3-glucuronide,1TMS,#1" TMS) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-05bb-1129060000-6c2645d8032487ebb292	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0092-2459000000-13fca8bbb8d57afe9418	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-02gk-4559000000-0ab28fa8b9019d8f5437	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00fs-1206090000-471451f9de78ce7d3ecf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-1209020000-c6a2cd83cd618e632ab8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0002-4209000000-e99246c5ae13f65568a2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0000090000-c8ca353f34d1adf9c459	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-2503290000-0f401f264c2622d6a512	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05di-6019220000-f491e6436c3abd4a9217	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fdk-0021950000-18c3b30f58579727bbb7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0zfr-2091020000-c5fbb1b02429a296f32e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a59-9280220000-6b432ff7d629d2a1d54e	View in MoNA

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Membrane

Biospecimen Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	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

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0010344

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB027496

KNApSAcK ID

Not Available

Chemspider ID

4947771

KEGG Compound ID

Not Available

BioCyc ID

Beta-D-Glucuronides

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6443809

PDB ID

Not Available

ChEBI ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Vitamin D2 3-glucuronide (BMDB0010344)

Structure for BMDB0010344 (Vitamin D2 3-glucuronide)