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Record Information
Version3.6
Creation Date2006-08-12 23:33:54 UTC
Update Date2013-02-09 00:12:38 UTC
HMDB IDHMDB03550
Secondary Accession Numbers
  • HMDB05997
Metabolite Identification
Common NameCalcidiol
DescriptionThe major circulating metabolite of vitamin D3 (calciferon). 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.
Structure
Thumb
Synonyms
  1. 25-Hydroxy-cholecalciferol
  2. 25-Hydroxycholecalciferol
  3. 25-Hydroxyvitamin D3
  4. 5,6-cis-25-Hydroxyvitamin D3
  5. 9,10-Secocholesta-5,7,10(19)-triene-3b,25-diol
  6. Calcidiol
  7. Calcifediol
  8. Calcifediol anhydrous
  9. Calderol
  10. Didrogyl
  11. Hidroferol
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-hydroxycholecalciferol
CAS Registry Number19356-17-3
SMILES
C[C@H](CCCC(O)(C)C)[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
KingdomOrganic Compounds
Super ClassLipids
ClassPrenol Lipids
Sub ClassSesterterpenes
Other Descriptors
  • Aliphatic Homopolycyclic Compounds
  • Vitamin D and Derivatives
Substituents
  • Cyclic Alcohol
  • Cyclohexane
  • Secondary Alcohol
  • Steroid
  • Tertiary Alcohol
Direct ParentSesterterpenes
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
  • Food
Biofunction
  • Cell signaling
  • Fuel and energy storage
  • Fuel or energy source
  • Membrane integrity/stability
Application
  • Nutrients
  • Stabilizers
  • Surfactants and Emulsifiers
Cellular locations
  • Cytoplasm
  • Extracellular
  • Membrane (predicted from logP)
  • Mitochondria
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
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 Area40.46ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity125.06ChemAxon
Polarizability50.42ChemAxon
Spectra
SpectraGC-MS
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane (predicted from logP)
  • Mitochondria
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • Epidermis
  • Gonads
  • Kidney
  • Prostate
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0689 (0.0459-0.0919) uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.13 (0.13-0.14) uMAdult (>18 years old)Both
Normal
details
BloodDetected and Quantified0.0245 +/- 0.023 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
UrineDetected and Quantified0.092 +/- 0.0037 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.044 (0.013-0.074) uMAdult (>18 years old)BothAnephrism details
UrineDetected and Quantified0.0099 +/- 0.0019 umol/mmol creatinineAdult (>18 years old)BothNephrotic syndrome details
Associated Disorders and Diseases
Disease References
Anephric patients
  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. Pubmed: 227368
Nephrotic syndrome
  1. Goldstein DA, Haldimann B, Sherman D, Norman AW, Massry SG: Vitamin D metabolites and calcium metabolism in patients with nephrotic syndrome and normal renal function. J Clin Endocrinol Metab. 1981 Jan;52(1):116-21. Pubmed: 6969729
Associated OMIM IDsNone
DrugBank IDDB00146
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB021782
KNApSAcK IDNot Available
Chemspider ID4446820
KEGG Compound IDC01561
BioCyc IDCALCIDIOL
BiGG ID2289142
Wikipedia LinkCalcidiol
NuGOwiki LinkHMDB03550
Metagene LinkHMDB03550
METLIN ID6949
PubChem Compound5283731
PDB IDVDY
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. 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. Pubmed: 16886665
  2. 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. Pubmed: 227368
  3. 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. Pubmed: 15384827
  4. 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. Pubmed: 10469423
  5. 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. Pubmed: 10089217
  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. Pubmed: 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. Pubmed: 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. Pubmed: 15585789

Enzymes

General function:
Involved in monooxygenase activity
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
Reactions
Calcidiol + NADPH + Oxygen → Calcitriol + NADP + Waterdetails
Calcidiol + Oxygen + NADPH + Hydrogen Ion → Calcitriol + NADP + Waterdetails
References
  1. Schuster I: Cytochromes P450 are essential players in the vitamin D signaling system. Biochim Biophys Acta. 2011 Jan;1814(1):186-99. Epub 2010 Jul 7. Pubmed: 20619365
  2. 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. Pubmed: 10374186
  3. 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. Pubmed: 16061850
  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. Pubmed: 9527847
  5. 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. Pubmed: 16955631
  6. 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. Pubmed: 15887856
General function:
Involved in sequence-specific DNA binding transcription factor activity
Specific function:
Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit 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:
48288.6
References
  1. Reinhart GA: Vitamin D analogs: novel therapeutic agents for cardiovascular disease? Curr Opin Investig Drugs. 2004 Sep;5(9):947-51. Pubmed: 15503649
  2. Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. Pubmed: 11752352
General function:
Involved in monooxygenase activity
Specific function:
Has a role in maintaining calcium homeostasis. Catalyzes the NADPH-dependent 24-hydroxylation of calcidiol (25-hydroxyvitamin D(3)) and calcitriol (1-alpha,25-dihydroxyvitamin D(3)). The enzyme can perform up to 6 rounds of hydroxylation of calcitriol leading to calcitroic acid. It also shows 23-hydroxylating activity leading to 1-alpha,25-dihydroxyvitamin D(3)-26,23-lactone as end product.
Gene Name:
CYP24A1
Uniprot ID:
Q07973
Molecular weight:
58874.695
Reactions
Calcidiol + NADPH + Oxygen → (24R)-24,25-Dihydroxycalciol + NADP + Waterdetails
Calcidiol + NADPH + Hydrogen Ion + Oxygen → Secalciferol + NADP + Waterdetails
References
  1. Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. Epub 2009 Nov 24. Pubmed: 19934256
General function:
Involved in monooxygenase activity
Specific function:
Has a D-25-hydroxylase activity on both forms of vitamin D, vitamin D(2) and D(3).
Gene Name:
CYP2R1
Uniprot ID:
Q6VVX0
Molecular weight:
57358.82
Reactions
Cholecalciferol + Oxygen + NADPH → Calcidiol + NADP(+) H(2)Odetails
Calcidiol + NADP + Water → Cholecalciferol + NADPH + Hydrogen Ion + Oxygendetails