Bovine Metabolome Database: Showing metabocard for Vitamin D3 (BMDB0000876)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:37:55 UTC

Update Date

2020-06-04 20:48:42 UTC

BMDB ID

BMDB0000876

Secondary Accession Numbers

BMDB00876

Metabolite Identification

Common Name

Vitamin D3

Description

Vitamin D3 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 D3 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(+)-Vitamin D3	HMDB
(3beta,Z,7E)-9,10-Secocholesta-5,7,10(19)-trien-3-ol	HMDB
(5E,7E)-9,10-Secocholesta-5,7,10-trien-3-ol	HMDB
3-beta,Z,7E-9,10-Secocholestr-5,7,10(19)-trien-3-ol	HMDB
9,10-Secocholesta-5,7,10(19)-trien-3-beta-ol	HMDB
9,10-Secocholesta-5,7,10(19)-trien-3-ol	HMDB
9,10-Secocholesta-5,7,10-trien-3-ol	HMDB
Arachitol	HMDB
Calciol	HMDB
CC	HMDB
Cholecalciferol	HMDB
Cholecalciferol D3	HMDB
Colecalciferol	HMDB
D3-Vigantol	HMDB
Delsterol	HMDB
Deparal	HMDB
Devaron	HMDB
Ebivit	HMDB
FeraCol	HMDB
Granuvit D3	HMDB
micro-Dee	HMDB
Oleovitamin D3	HMDB
Provitina	HMDB
Quintox	HMDB
Ricketon	HMDB
Trivitan	HMDB
Vi-de3	HMDB
VidDe-3-hydrosol	HMDB
Videkhol	HMDB
Vigantol	HMDB
Vigorsan	HMDB
Vitinc dan-dee-3	HMDB
(3 beta,5Z,7E)-9,10-Secocholesta-5,7,10(19)-trien-3-ol	MeSH
Cholecalciferols	MeSH
Vitamin D 3	MeSH

Chemical Formula

C₂₇H₄₄O

Average Molecular Weight

384.6377

Monoisotopic Molecular Weight

384.33921603

IUPAC Name

(1S,3Z)-3-{2-[(1R,4E,7aR)-7a-methyl-1-[(2R)-6-methylheptan-2-yl]-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexan-1-ol

Traditional Name

rampage

CAS Registry Number

67-97-0

SMILES

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

InChI Identifier

InChI=1S/C27H44O/c1-19(2)8-6-9-21(4)25-15-16-26-22(10-7-17-27(25,26)5)12-13-23-18-24(28)14-11-20(23)3/h12-13,19,21,24-26,28H,3,6-11,14-18H2,1-2,4-5H3/b22-12+,23-13-/t21-,24+,25-,26?,27-/m1/s1

InChI Key

QYSXJUFSXHHAJI-QWSSABAFSA-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
Cyclic alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Ontology

Status

Detected and Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
Membrane
Mitochondria

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	7.98	ALOGPS
logP	7.13	ChemAxon
logS	-6	ALOGPS
pKa (Strongest Acidic)	18.38	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	20.23 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	123.22 m³·mol⁻¹	ChemAxon
Polarizability	49.44 Å³	ChemAxon
Number of Rings	3	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	splash10-0aou-3029000000-1950c74de34369a70400	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-002f-9207800000-c6f808a014153de38d58	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014r-0129000000-442693b5a55274aeb0b3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0c09-3496000000-bf01a7ddf350733d39f2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-8298000000-b9136b2dd6e2c22c1123	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0009000000-70ba08bf3cd328c6087e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-0009000000-c16445787a057993951a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-066r-1239000000-328f37347d493ff8f54a	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl₃, experimental)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl₃, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Membrane
Mitochondria

Biospecimen Locations

Epidermis
Fibroblasts
Intestine
Kidney
Liver
Milk
Ovary
Placenta
Prostate Tissue
Spleen
Testis

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	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
Milk	Detected and Quantified	0.00013 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.00013 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.000182 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.00198 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.000182 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.0026 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.000234 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.000208 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.0147 +/- 0.0002 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.019 +/- 0.001 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.0435 +/- 0.0002 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.015 +/- 0.001 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.00052 uM	Not Specified	Not Specified	Normal	Pirjo H. Mattila,...	details
Ovary	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
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Testis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0014315

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

Cholecalciferol

METLIN ID

Not Available

PubChem Compound

10883523

PDB ID

Not Available

ChEBI ID

Not Available

References

Synthesis Reference

Nemoto, Hideo; Kurobe, Hiroshi; Fukumoto, Keiichiro; Kametani, Tetsuji. A modified synthesis of the (+)-8a-phenylsulfonyl-des-AB-cholestane via an intramolecular nucleophilic attack to epoxide - a total synthesis of vitamin D3. Heterocycles (1985), 23(3),

Material Safety Data Sheet (MSDS)

Not Available

General References

A. Foroutan et al. (2019). A. Foroutan et al. The Chemical Composition of Commercial Cow's Milk (in preparation). Journal of Agricultural and Food Chemistry.
Pirjo H. Mattila, Vieno I. Piironen, Esko J. Uusi-Rauva, and Pekka E. Koivistoinen (1995). Pirjo H. Mattila, Vieno I. Piironen, Esko J. Uusi-Rauva, and Pekka E. Koivistoinen. 1995. Contents of Cholecalciferol, Ergocalciferol, and Their 25-Hydroxylated Metabolites in Milk Products and Raw Meat and Liver As Determined by HPLC. J. Agric. Food Chem. 43 (9), pp 2394–2399. J. Agric. Food Chem.
Fooddata+, The Technical University of Denmark (DTU) [Link]

Enzymes

Enzyme Details

1. Vitamin D3 receptor

General function:: Involved in sequence-specific DNA binding
Specific function:: Nuclear receptor for calcitriol, the active form of vitamin D3 which mediates the action of this vitamin on cells (By similarity). Enters the nucleus upon vitamin D3 binding where it forms heterodimers with the retinoid X receptor/RXR (By similarity). The VDR-RXR heterodimers bind to specific response elements on DNA and activate the transcription of vitamin D3-responsive target genes (By similarity). Plays a central role in calcium homeostasis (By similarity).
Gene Name:: VDR
Uniprot ID:: Q28037
Molecular weight:: 48318.0

Enzyme Details

2. Vitamin D3 receptor

General function:: Involved in steroid hormone receptor activity
Specific function:: Not Available
Gene Name:: VDR
Uniprot ID:: Q19MM0
Molecular weight:: 6042.0

Showing metabocard for Vitamin D3 (BMDB0000876)

Structure for BMDB0000876 (Vitamin D3)

Enzymes