Showing metabocard for Calcidiol (BMDB0003550)

IdentificationTaxonomyPhysical propertiesSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 23:05:13 UTC
Update Date2020-06-04 20:45:49 UTC
MCDB ID BMDB0003550
Secondary Accession Numbers
  • BMDB03550
Metabolite Identification
Common NameCalcidiol
DescriptionCalcidiol, 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
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
(3beta,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diolChEBI
(3S,5Z,7E)-9,10-Secocholesta-5,7,10-triene-3,25-diolChEBI
(5Z,7E)-(3S)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diolChEBI
25(OH)D3ChEBI
25-HydroxycholecalciferolChEBI
25-Hydroxyvitamin D3ChEBI
3-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7a-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexanolChEBI
CalcifediolChEBI
Calcifediol anhydrousChEBI
CalcifediolumChEBI
RayaldeeChEBI
(3S,5Z,7E)-9,10-Seco-5,7,10(19)-cholestatriene-3,25-diolKegg
(3b,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diolGenerator
(3Β,5Z,7E)-9,10-secocholesta-5,7,10(19)-triene-3,25-diolGenerator
25-Hydroxy-cholecalciferolHMDB
5,6-cis-25-Hydroxyvitamin D3HMDB
9,10-Secocholesta-5,7,10(19)-triene-3b,25-diolHMDB
CalderolHMDB
DidrogylHMDB
HidroferolHMDB
25 Hydroxyvitamin D3HMDB
Calcifediol, (3 beta,5E,7E)-isomerHMDB
Monohydrate, 25-hydroxycholecalciferolHMDB
25-Hydroxycholecalciferol monohydrateHMDB
Anhydrous, calcifediolHMDB
Organon brand OF calcifediolHMDB
25 Hydroxyvitamin D 3HMDB
25-Hydroxyvitamin D 3HMDB
Aventis brand OF calcifediolHMDB
Calcifediol aventis brandHMDB
Calcifediol organon brandHMDB
DedrogylHMDB
25 HydroxycholecalciferolHMDB
25 Hydroxycholecalciferol monohydrateHMDB
Calcifediol faes brandHMDB
Calcifediol, (3 alpha,5Z,7E)-isomerHMDB
Faes brand OF calcifediolHMDB
CalcidiolMeSH
Chemical FormulaC27H44O2
Average Molecular Weight400.6371
Monoisotopic Molecular Weight400.334130652
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 Name25-hydroxyvitamin D3
CAS Registry Number19356-17-3
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 KeyJWUBBDSIWDLEOM-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSteroids and steroid derivatives
Sub ClassVitamin D and derivatives
Direct ParentVitamin 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 FrameworkAliphatic homopolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP6.71ALOGPS
logP5.65ChemAxon
logS-5.3ALOGPS
pKa (Strongest Acidic)18.38ChemAxon
pKa (Strongest Basic)-0.98ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity125.06 m³·mol⁻¹ChemAxon
Polarizability50.32 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-001i-2900000000-33a8e563016d6e2e358e2014-06-16View Spectrum
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-00lr-2900000000-f6bedf681276960630612014-06-16View Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-2900000000-33a8e563016d6e2e358e2017-09-12View Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00lr-2900000000-f6bedf681276960630612017-09-12View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0ab9-3029000000-4c75b5cfbc422ba2a3442017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-003r-1403290000-a8eb9294a6df1ce864d22017-10-06View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00lr-0119100000-d3e0a5d2ecb614d781d42016-06-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0api-0369000000-146e7a23795c22f5b8362016-06-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0kai-5296000000-412b0c2da61c93271acd2016-06-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-0009000000-ef5150b1dccaed2f95432016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000t-0009000000-4b22b5c88dc06c01fe892016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00si-2229000000-f4037186ef5a21a168592016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-0009000000-21157f4aa99daf6972712021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0002-0009000000-cac0e3874faca9c17f032021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-01ot-0339000000-37442d1a71c50883b3772021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0549100000-68f99126c8d8b4ca7eb72021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0g4i-5594100000-433f2a913eb577e9397a2021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0ab9-1940000000-e03ff70cb44513aa8ae82021-09-22View Spectrum
Concentrations
StatusValueReferenceDetails
Detected and Quantified2 IU/100 g
  • Park, Y. W; Juáre...
 details
Detected and Quantified0.000499 uM
  • Pirjo H. Mattila,...
 details
Detected and Quantified0.0005 +/- 0.0002 uM details
Detected and Quantified0.0006 +/- 0.0001 uM details
Detected and Quantified0.0007 +/- 0.0001 uM details
Detected and Quantified0.0004 +/- 0.0001 uM details
HMDB IDHMDB0003550
DrugBank IDDB00146
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021782
KNApSAcK IDC00040805
Chemspider ID4446820
KEGG Compound IDC01561
BioCyc IDNot Available
BiGG ID2289142
Wikipedia LinkCalcifediol
METLIN ID6949
PubChem Compound5283731
PDB IDNot Available
ChEBI ID17933
References
Synthesis ReferenceMascarenas, 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)Download (PDF)
General References
  1. 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.
  2. 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.
  3. 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.