Calcidiol (T3D2694)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationTargets (2)XML
Targets (2)
Record Information
Version2.0
Creation Date2009-07-21 20:26:08 UTC
Update Date2014-12-24 20:25:49 UTC
Accession NumberT3D2694
Identification
Common NameCalcidiol
ClassSmall Molecule
DescriptionThe major circulating metabolite of vitamin D3 (cholecalciferol). It is produced in the liver and is the best indicator of the body's vitamin D stores. It is effective in the treatment of rickets and osteomalacia, both in azotemic and non-azotemic patients. Calcifediol also has mineralizing properties.
Compound Type
  • Antihypocalcemic Agent
  • Antihypoparathyroid Agent
  • Antithyroid Agent
  • Bone Density Conservation Agent
  • Drug
  • Food Toxin
  • Metabolite
  • Natural Compound
  • Nutraceutical
  • Organic Compound
  • Vitamin
  • Vitamin D
Chemical Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
Synonym
(3beta,5Z,7e)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diol
(3S,5Z,7e)-9,10-Secocholesta-5,7,10-triene-3,25-diol
(3β,5Z,7E)-9,10-secocholesta-5,7,10(19)-triene-3,25-diol
(5Z,7e)-(3S)-9,10-Secocholesta-5,7,10(19)-triene-3,25-diol
25(OH)D3
25-Hydroxy-cholecalciferol
25-Hydroxycholecalciferol
25-Hydroxyvitamin D3
3-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7a-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexanol
5,6-cis-25-Hydroxyvitamin D3
9,10-Secocholesta-5,7,10(19)-triene-3b,25-diol
Calcifediol
Calcifediol anhydrous
Calcifediolum
Calderol
Caldiol
De Kai
Dedrogyl
Didrogyl
Hidroferol
Chemical FormulaC27H44O2
Average Molecular Mass400.637 g/mol
Monoisotopic Mass400.334 g/mol
CAS Registry Number19356-17-3
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
SMILES[H]\C(\C(\[H])=C1/CCC[C@@]2(C)[C@@]1([H])CC[C@]2([H])[C@]([H])(C)CCCC(C)(C)O)=C1/C[C@@]([H])(O)CCC1=C
InChI IdentifierInChI=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 KeyInChIKey=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.
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
Biological Properties
StatusDetected and Not Quantified
OriginEndogenous
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
  • Mitochondria
Biofluid LocationsNot Available
Tissue Locations
  • Epidermis
  • Gonads
  • Kidney
  • Prostate
PathwaysNot Available
Applications
Biological Roles
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityInsoluble
LogP6
Predicted Properties
PropertyValueSource
Water Solubility0.0022 g/LALOGPS
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 FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
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
Toxicity Profile
Route of ExposureOral, readily absorbed.
Mechanism of ToxicityCalcidiol is transformed in the kidney by 25-hydroxyvitamin D3-1-(alpha)-hydroxylase to calcitriol, the active form of vitamin D3. Calcitriol binds to intracellular receptors that then function as transcription factors to modulate gene expression. Like the receptors for other steroid hormones and thyroid hormones, the vitamin D receptor has hormone-binding and DNA-binding domains. The vitamin D receptor forms a complex with another intracellular receptor, the retinoid-X receptor, and that heterodimer is what binds to DNA. In most cases studied, the effect is to activate transcription, but situations are also known in which vitamin D suppresses transcription. Calcitriol increases the serum calcium concentrations by: increasing GI absorption of phosphorus and calcium, increasing osteoclastic resorption, and increasing distal renal tubular reabsorption of calcium. Calcitriol appears to promote intestinal absorption of calcium through binding to the vitamin D receptor in the mucosal cytoplasm of the intestine. Subsequently, calcium is absorbed through formation of a calcium-binding protein.
MetabolismCalcidiol undergoes hydroxylation in the mitochondria of kidney tissue, and this reaction is activated by the renal 25-hydroxyvitamin D3-1-(alpha)-hydroxylase to produce calcitriol (1,25- dihydroxycholecalciferol), the active form of vitamin D3. Half Life: 288 hours
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesUsed 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.
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsBone pain, constipation (especially in children or adolescents), diarrhea, drowsiness, dryness of mouth; headache (continuing), increased thirst, increase in frequency of urination, especially at night, or in amount of urine, irregular heartbeat, itching skin, loss of appetite, metallic taste, muscle pain, nausea or vomiting (especially in children or adolescents), unusual tiredness or weakness.
TreatmentNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDDB00146
HMDB IDHMDB03550
PubChem Compound ID5283731
ChEMBL IDCHEMBL1040
ChemSpider ID4446820
KEGG IDC01561
UniProt IDNot Available
OMIM ID259750 , 600081
ChEBI ID17933
BioCyc IDCALCIDIOL
CTD IDNot Available
Stitch IDCalcidiol
PDB IDVDY
ACToR IDNot Available
Wikipedia LinkCalcidiol
References
Synthesis Reference

Dae-Jung Kang, Jong-Hyuk Im, Hyun-Jung Jung, Jae-Hoon Kang, “BUFFER COMPOSITION FOR CATALYZING THE PREPARATION OF CALCITRIOL OR CALCIFEDIOL AND METHOD FOR PREPARING CALCITRIOL OR CALCIFEDIOL USING SAME.” U.S. Patent US20120064584, issued March 15, 2012.

MSDSLink
General References
  1. Shepard RM, Horst RL, Hamstra AJ, DeLuca HF: Determination of vitamin D and its metabolites in plasma from normal and anephric man. Biochem J. 1979 Jul 15;182(1):55-69. [227368 ]
  2. Passadakis P, Ersoy F, Tam P, Memmos D, Siamopoulos K, Ozener C, Akcicek F, Camsari T, Ates K, Ataman R, Vlachojannis J, Dombros N, Utas C, Akpolat T, Bozfakioglu S, Wu GG, Karayaylali I, Arinsoy T, Stathakis C, Yavuz M, Tsakiris D, Dimitriades A, Yilmaz ME, Gultekin M, Karayalcin B, Challa A, Polat N, Oreopoulos DG: Serum levels of prostate-specific antigen and vitamin D in peritoneal dialysis patients. Adv Perit Dial. 2004;20:203-8. [15384827 ]
  3. Park SB, Suh DH, Youn JI: A pilot study to assess the safety and efficacy of topical calcipotriol treatment in childhood psoriasis. Pediatr Dermatol. 1999 Jul-Aug;16(4):321-5. [10469423 ]
  4. Haden ST, Fuleihan GE, Angell JE, Cotran NM, LeBoff MS: Calcidiol and PTH levels in women attending an osteoporosis program. Calcif Tissue Int. 1999 Apr;64(4):275-9. [10089217 ]
  5. Flanagan JN, Young MV, Persons KS, Wang L, Mathieu JS, Whitlatch LW, Holick MF, Chen TC: Vitamin D metabolism in human prostate cells: implications for prostate cancer chemoprevention by vitamin D. Anticancer Res. 2006 Jul-Aug;26(4A):2567-72. [16886665 ]
  6. Gacad MA, Adams JS: Proteins in the heat shock-70 family specifically bind 25-hydroxyvitamin D3 and 17beta-estradiol. J Clin Endocrinol Metab. 1998 Apr;83(4):1264-7. [9543154 ]
  7. Feingold KR, Williams ML, Pillai S, Menon GK, Halloran BP, Bikle DD, Elias PM: The effect of vitamin D status on cutaneous sterologenesis in vivo and in vitro. Biochim Biophys Acta. 1987 Sep 14;930(2):193-200. [3040120 ]
  8. DeLuca HF: Overview of general physiologic features and functions of vitamin D. Am J Clin Nutr. 2004 Dec;80(6 Suppl):1689S-96S. [15585789 ]
  9. Drugs.com [Link]
Gene Regulation
Up-Regulated Genes
GeneGene SymbolGene IDInteractionChromosomeDetails
Down-Regulated GenesNot Available

Targets

Target Details
1. 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial
General Function:
Iron ion binding
Specific Function:
Catalyzes the conversion of 25-hydroxyvitamin D3 (25(OH)D) to 1-alpha,25-dihydroxyvitamin D3 (1,25(OH)2D) plays an important role in normal bone growth, calcium metabolism, and tissue differentiation.
Gene Name:
CYP27B1
Uniprot ID:
O15528
Molecular Weight:
56503.475 Da
References
  1. Diesel B, Radermacher J, Bureik M, Bernhardt R, Seifert M, Reichrath J, Fischer U, Meese E: Vitamin D(3) metabolism in human glioblastoma multiforme: functionality of CYP27B1 splice variants, metabolism of calcidiol, and effect of calcitriol. Clin Cancer Res. 2005 Aug 1;11(15):5370-80. [16061850 ]
  2. Hart GR, Furniss JL, Laurie D, Durham SK: Measurement of vitamin D status: background, clinical use, and methodologies. Clin Lab. 2006;52(7-8):335-43. [16955631 ]
  3. Bernad M, Jaramillo G, Aguado P, del Campo T, Coya J, Martin Mola E, Gijon Banos J, Saldana Barrera H, Martinez ME: [Polymorphism of the gene of vitamin D receptor and bone mineral density in postmenopausal women]. Med Clin (Barc). 1999 May 15;112(17):651-5. [10374186 ]
  4. Eto TA, Nakamura Y, Taniguchi T, Miyamoto K, Nagatomo J, Maeda Y, Higashi S, Okuda K, Setoguchi T: Assay of 25-hydroxyvitamin D3 1 alpha-hydroxylase in rat kidney mitochondria. Anal Biochem. 1998 Apr 10;258(1):53-8. [9527847 ]
  5. Vigo Gago E, Cadarso-Suarez C, Perez-Fernandez R, Romero Burgos R, Devesa Mugica J, Segura Iglesias C: Association between vitamin D receptor FokI. Polymorphism and serum parathyroid hormone level in patients with chronic renal failure. J Endocrinol Invest. 2005 Feb;28(2):117-21. [15887856 ]
Target Details
2. Vitamin D3 receptor
General Function:
Zinc ion binding
Specific Function:
Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Recruited to promoters via its interaction with BAZ1B/WSTF which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.
Gene Name:
VDR
Uniprot ID:
P11473
Molecular Weight:
48288.64 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [17016423 ]