Bovine Metabolome Database: Showing metabocard for Calcidiol (BMDB0003550)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:05:13 UTC

Update Date

2020-06-04 20:45:49 UTC

BMDB ID

BMDB0003550

Secondary Accession Numbers

BMDB03550

Metabolite Identification

Common Name

Calcidiol

Description

Calcidiol, also known as 25(OH)D3 or rayaldee, 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. Thus, calcidiol is considered to be a secosteroid lipid molecule. Calcidiol is a drug which is used to treat vitamin d deficiency or insufficiency, refractory rickets (vitamin d resistant rickets), familial hypophosphatemia and hypoparathyroidism, and in the management of hypocalcemia and renal osteodystrophy in patients with chronic renal failure undergoing dialysis. also used in conjunction with calcium in the management and prevention of primary or corticosteroid-induced osteoporosis. Calcidiol is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Calcidiol exists in all living organisms, ranging from bacteria to humans. Calcidiol is a potentially toxic compound.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
(3beta,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diol	ChEBI
(3S,5Z,7E)-9,10-Secocholesta-5,7,10-triene-3,25-diol	ChEBI
(5Z,7E)-(3S)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diol	ChEBI
25(OH)D3	ChEBI
25-Hydroxycholecalciferol	ChEBI
25-Hydroxyvitamin D3	ChEBI
3-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7a-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexanol	ChEBI
Calcifediol	ChEBI
Calcifediol anhydrous	ChEBI
Calcifediolum	ChEBI
Rayaldee	ChEBI
(3S,5Z,7E)-9,10-Seco-5,7,10(19)-cholestatriene-3,25-diol	Kegg
(3b,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diol	Generator
(3Β,5Z,7E)-9,10-secocholesta-5,7,10(19)-triene-3,25-diol	Generator
25-Hydroxy-cholecalciferol	HMDB
5,6-cis-25-Hydroxyvitamin D3	HMDB
9,10-Secocholesta-5,7,10(19)-triene-3b,25-diol	HMDB
Calderol	HMDB
Didrogyl	HMDB
Hidroferol	HMDB
25 Hydroxyvitamin D3	HMDB
Calcifediol, (3 beta,5E,7E)-isomer	HMDB
Monohydrate, 25-hydroxycholecalciferol	HMDB
25-Hydroxycholecalciferol monohydrate	HMDB
Anhydrous, calcifediol	HMDB
Organon brand OF calcifediol	HMDB
25 Hydroxyvitamin D 3	HMDB
25-Hydroxyvitamin D 3	HMDB
Aventis brand OF calcifediol	HMDB
Calcifediol aventis brand	HMDB
Calcifediol organon brand	HMDB
Dedrogyl	HMDB
25 Hydroxycholecalciferol	HMDB
25 Hydroxycholecalciferol monohydrate	HMDB
Calcifediol faes brand	HMDB
Calcifediol, (3 alpha,5Z,7E)-isomer	HMDB
Faes brand OF calcifediol	HMDB
Calcidiol	MeSH

Chemical Formula

C₂₇H₄₄O₂

Average Molecular Weight

400.6371

Monoisotopic Molecular Weight

400.334130652

IUPAC Name

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

Traditional Name

25-hydroxyvitamin D3

CAS Registry Number

19356-17-3

SMILES

C[C@H](CCCC(C)(C)O)[C@@]1([H])CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C

InChI Identifier

InChI=1S/C27H44O2/c1-19-10-13-23(28)18-22(19)12-11-21-9-7-17-27(5)24(14-15-25(21)27)20(2)8-6-16-26(3,4)29/h11-12,20,23-25,28-29H,1,6-10,13-18H2,2-5H3/b21-11+,22-12-/t20-,23+,24-,25+,27-/m1/s1

InChI Key

JWUBBDSIWDLEOM-DTOXIADCSA-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
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

diol (CHEBI:17933 )
D3 vitamins (CHEBI:17933 )
hydroxycalciol (CHEBI:17933 )
Vitamin D3 and derivatives (C01561 )
Vitamin D3 and derivatives (LMST03020246 )

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	6.71	ALOGPS
logP	5.65	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	18.38	ChemAxon
pKa (Strongest Basic)	-0.98	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	125.06 m³·mol⁻¹	ChemAxon
Polarizability	50.32 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
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-001i-2900000000-33a8e563016d6e2e358e	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-00lr-2900000000-f6bedf68127696063061	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-001i-2900000000-33a8e563016d6e2e358e	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00lr-2900000000-f6bedf68127696063061	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0ab9-3029000000-4c75b5cfbc422ba2a344	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-003r-1403290000-a8eb9294a6df1ce864d2	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
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	splash10-00lr-0119100000-d3e0a5d2ecb614d781d4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0api-0369000000-146e7a23795c22f5b836	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0kai-5296000000-412b0c2da61c93271acd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0009000000-ef5150b1dccaed2f9543	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000t-0009000000-4b22b5c88dc06c01fe89	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00si-2229000000-f4037186ef5a21a16859	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0009000000-21157f4aa99daf697271	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-0009000000-cac0e3874faca9c17f03	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-01ot-0339000000-37442d1a71c50883b377	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-0549100000-68f99126c8d8b4ca7eb7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0g4i-5594100000-433f2a913eb577e9397a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0ab9-1940000000-e03ff70cb44513aa8ae8	View in MoNA

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Membrane
Mitochondria

Biospecimen Locations

Epidermis
Kidney
Milk
Ovary
Prostate Tissue
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
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Milk	Detected and Quantified	2 IU/100 g	Not Specified	Not Specified	Normal	Park, Y. W; Juáre...	details
Milk	Detected and Quantified	0.0005 +/- 0.0002 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.0006 +/- 0.0001 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.0007 +/- 0.0001 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.0004 +/- 0.0001 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.000499 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
Prostate Tissue	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

HMDB0003550

DrugBank ID

DB00146

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17933

References

Synthesis Reference

Mascarenas, J. L.; Mourino, A.; Castedo, L. Studies on the synthesis of side-chain hydroxylated metabolites of vitamin D. 3. Synthesis of 25-ketovitamin D3 and 25-hydroxyvitamin D3. Journal of Organic Chemistry (1986), 51(8), 1269-72.

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.
Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W. (2007). Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W. Physico-chemical characteristics of goat and sheep milk. Small Ruminant Res.(2007) 68:88-113 doi: 10.1016/j.smallrumres.2006.09.013. Small Ruminant Research.
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.

Showing metabocard for Calcidiol (BMDB0003550)

Structure for BMDB0003550 (Calcidiol)