Human Metabolome Database Version 3.5

Showing metabocard for Calcidiol (HMDB03550)

Record Information
Version 3.5
Creation Date 2006-08-12 17:33:54 -0600
Update Date 2013-02-08 17:12:38 -0700
HMDB ID HMDB03550
Secondary Accession Numbers
  • HMDB05997
Metabolite Identification
Common Name Calcidiol
Description The 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
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
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 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 IUPAC Name 25-hydroxycholecalciferol
CAS Registry Number 19356-17-3
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 Key JWUBBDSIWDLEOM-DTOXIADCSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Lipids
Class Prenol Lipids
Sub Class Sesterterpenes
Other Descriptors
  • Aliphatic Homopolycyclic Compounds
  • Vitamin D and Derivatives
Substituents
  • Cyclic Alcohol
  • Cyclohexane
  • Secondary Alcohol
  • Steroid
  • Tertiary Alcohol
Direct Parent Sesterterpenes
Ontology
Status Detected 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
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
Water Solubility 0.0022 g/L ALOGPS
LogP 6.71 ALOGPS
LogP 5.65 ChemAxon
LogS -5.26 ALOGPS
pKa (strongest acidic) 18.38 ChemAxon
pKa (strongest basic) -0.98 ChemAxon
Hydrogen Acceptor Count 2 ChemAxon
Hydrogen Donor Count 2 ChemAxon
Polar Surface Area 40.46 A2 ChemAxon
Rotatable Bond Count 6 ChemAxon
Refractivity 125.06 ChemAxon
Polarizability 50.42 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
MS/MS Spectrum GC-MS
MS/MS Spectrum GC-MS
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane (predicted from logP)
  • Mitochondria
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • Kidney
  • Epidermis
  • Prostate
  • Gonads
Pathways Not Available
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
0.0689 (0.0459-0.0919) uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
0.13 (0.13-0.14) uM Adult (>18 years old) Both Comment Normal
Blood Detected and Quantified
0.0245 +/- 0.023 uM Adult (>18 years old) Both Normal
  • Geigy Scient...
Urine Detected and Quantified
0.092 +/- 0.0037 umol/mmol creatinine Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 0.044 (0.013-0.074) uM Adult (>18 years old) Both Anephrism
Urine Detected and Quantified 0.0099 +/- 0.0019 umol/mmol creatinine Adult (>18 years old) Both Nephrotic syndrome
Associated Disorders and Diseases
Disease References
Anephric patients
  • 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 Link_out
      Nephrotic syndrome
      • 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 Link_out
          Associated OMIM IDs None
          DrugBank ID DB00146 Link_out
          DrugBank Metabolite ID Not Available
          Phenol Explorer Compound ID Not Available
          Phenol Explorer Metabolite ID Not Available
          FoodDB ID FDB021782
          KNApSAcK ID Not Available
          Chemspider ID 4446820 Link_out
          KEGG Compound ID C01561 Link_out
          BioCyc ID CALCIDIOL Link_out
          BiGG ID 2289142 Link_out
          Wikipedia Link Calcidiol Link_out
          NuGOwiki Link HMDB03550 Link_out
          Metagene Link HMDB03550 Link_out
          METLIN ID 6949 Link_out
          PubChem Compound 5283731 Link_out
          PDB ID VDY Link_out
          ChEBI ID 17933 Link_out
          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) Download (PDF)
          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. Pubmed: 227368 Link_out
          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. Pubmed: 15384827 Link_out
          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. Pubmed: 10469423 Link_out
          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. Pubmed: 10089217 Link_out
          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. Pubmed: 16886665 Link_out
          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 Link_out
          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 Link_out
          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 Link_out

          Enzymes
          Name: 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial
          Reactions:
          Calcidiol + NADPH + Oxygen unknown Calcitriol + NADP + Water details
          Calcidiol + Oxygen + NADPH + Hydrogen Ion unknown Calcitriol + NADP + Water details
          Gene Name: CYP27B1
          Uniprot ID: O15528 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Vitamin D3 receptor
          Reactions: Not Available
          Gene Name: VDR
          Uniprot ID: P11473 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
          Reactions:
          Calcidiol + NADPH + Oxygen unknown (24R)-24,25-Dihydroxycalciol + NADP + Water details
          Calcidiol + NADPH + Hydrogen Ion + Oxygen unknown Secalciferol + NADP + Water details
          Gene Name: CYP24A1
          Uniprot ID: Q07973 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Vitamin D 25-hydroxylase
          Reactions:
          Cholecalciferol + Oxygen + NADPH unknown Calcidiol + NADP(+) H(2)O details
          Calcidiol + NADP + Water unknown Cholecalciferol + NADPH + Hydrogen Ion + Oxygen details
          Gene Name: CYP2R1
          Uniprot ID: Q6VVX0 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA