Human Metabolome Database Version 3.5

Showing metabocard for Vitamin D3 (HMDB00876)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:09:30 -0700
HMDB ID HMDB00876
Secondary Accession Numbers None
Metabolite Identification
Common Name Vitamin D3
Description Vitamin D3 is a steroid hormone that has long been known for its important role in regulating body levels of calcium and phosphorus, in mineralization of bone, and for the assimilation of Vitamin A. It is structurally similar to steroids such as testosterone, cholesterol, and cortisol (though vitamin D3 itself is a secosteroid).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. (+)-Vitamin D3
  2. (3beta,Z,7E)-9,10-Secocholesta-5,7,10(19)-trien-3-ol
  3. (5E,7E)-9,10-Secocholesta-5,7,10-trien-3-ol
  4. 3-beta,Z,7E-9,10-Secocholestr-5,7,10(19)-trien-3-ol
  5. 9,10-Secocholesta-5,7,10(19)-trien-3-beta-ol
  6. 9,10-Secocholesta-5,7,10(19)-trien-3-ol
  7. 9,10-Secocholesta-5,7,10-trien-3-ol
  8. Arachitol
  9. Calciol
  10. CC
  11. Cholecalciferol
  12. Cholecalciferol D3
  13. Colecalciferol
  14. D3-Vigantol
  15. Delsterol
  16. Deparal
  17. Devaron
  18. Ebivit
  19. FeraCol
  20. Granuvit D3
  21. Micro-dee
  22. Oleovitamin D3
  23. Provitina
  24. Quintox
  25. Ricketon
  26. Trivitan
  27. Vi-De3
  28. VidDe-3-hydrosol
  29. Videkhol
  30. Vigantol
  31. Vigorsan
  32. Vitinc Dan-Dee-3
Chemical Formula C27H44O
Average Molecular Weight 384.6377
Monoisotopic Molecular Weight 384.33921603
IUPAC Name (1S,3Z)-3-{2-[(1R,4E,7aR)-7a-methyl-1-[(2R)-6-methylheptan-2-yl]-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexan-1-ol
Traditional IUPAC Name cholecalciferol
CAS Registry Number 67-97-0
SMILES CC(C)CCC[C@@H](C)[C@H]1CCC2\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C
InChI Identifier InChI=1S/C27H44O/c1-19(2)8-6-9-21(4)25-15-16-26-22(10-7-17-27(25,26)5)12-13-23-18-24(28)14-11-20(23)3/h12-13,19,21,24-26,28H,3,6-11,14-18H2,1-2,4-5H3/b22-12+,23-13-/t21-,24+,25-,26?,27-/m1/s1
InChI Key QYSXJUFSXHHAJI-QWSSABAFSA-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
Direct Parent Sesterterpenes
Ontology
Status Detected and Quantified
Origin
  • Drug
  • Endogenous
  • Food
Biofunction
  • Cell signaling
  • Essential vitamins
  • Fuel and energy storage
  • Fuel or energy source
  • Membrane integrity/stability
Application
  • Nutrients
  • Stabilizers
  • Surfactants and Emulsifiers
Cellular locations
  • Cytoplasm
  • Extracellular
  • Membrane
  • Mitochondria
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 84.5 °C 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 3.800E-04 g/L ALOGPS
LogP 7.98 ALOGPS
LogP 7.13 ChemAxon
LogS -6.01 ALOGPS
pKa (strongest acidic) 18.38 ChemAxon
pKa (strongest basic) -1.3 ChemAxon
Hydrogen Acceptor Count 1 ChemAxon
Hydrogen Donor Count 1 ChemAxon
Polar Surface Area 20.23 A2 ChemAxon
Rotatable Bond Count 6 ChemAxon
Refractivity 123.22 ChemAxon
Polarizability 49.39 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
1H NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
  • Mitochondria
Biofluid Locations
  • Blood
Tissue Location
  • Fibroblasts
  • Intestine
  • Placenta
  • Kidney
  • Liver
  • Prostate
  • Skin
  • Gonads
  • Spleen
  • Stratum Corneum
  • Keratinocyte
  • Liver Parathyroid Gland
Pathways
Name SMPDB Link KEGG Link
Steroid Biosynthesis SMP00023 map00100 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
0.0060 +/- 0.0042 uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
0.0681 +/- 0.01880 uM Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 0.0037 +/- 0.0016 uM Adult (>18 years old) Both Anephrism
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
      Associated OMIM IDs None
      DrugBank ID DB00169 Link_out
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB012732
      KNApSAcK ID Not Available
      Chemspider ID 9058792 Link_out
      KEGG Compound ID C05443 Link_out
      BioCyc ID VITAMIN_D_%7B3%7D Link_out
      BiGG ID 2288999 Link_out
      Wikipedia Link Vitamin D3 Link_out
      NuGOwiki Link HMDB00876 Link_out
      Metagene Link HMDB00876 Link_out
      METLIN ID 222 Link_out
      PubChem Compound 10883523 Link_out
      PDB ID Not Available
      ChEBI ID 283119 Link_out
      References
      Synthesis Reference Nemoto, Hideo; Kurobe, Hiroshi; Fukumoto, Keiichiro; Kametani, Tetsuji. A modified synthesis of the (+)-8a-phenylsulfonyl-des-AB-cholestane via an intramolecular nucleophilic attack to epoxide - a total synthesis of vitamin D3. Heterocycles (1985), 23(3),
      Material Safety Data Sheet (MSDS) Download (PDF)
      General References
      1. Rautureau M, Rambaud JC: Aqueous solubilisation of vitamin D3 in normal man. Gut. 1981 May;22(5):393-7. Pubmed: 6265326 Link_out
      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 Link_out
      3. Osborne JE, Hutchinson PE: Vitamin D and systemic cancer: is this relevant to malignant melanoma? Br J Dermatol. 2002 Aug;147(2):197-213. Pubmed: 12174089 Link_out
      4. Haddad JG, Jennings AS, Aw TC: Vitamin D uptake and metabolism by perfused rat liver: influences of carrier proteins. Endocrinology. 1988 Jul;123(1):498-504. Pubmed: 2838261 Link_out
      5. Kida K, Goodman DS: Studies on the transport of vitamin D and of 25-hydroxyvitamin D in human plasma. J Lipid Res. 1976 Sep;17(5):485-90. Pubmed: 184223 Link_out
      6. 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
      7. Lips P: Vitamin D deficiency and secondary hyperparathyroidism in the elderly: consequences for bone loss and fractures and therapeutic implications. Endocr Rev. 2001 Aug;22(4):477-501. Pubmed: 11493580 Link_out
      8. Svendsen ML, Daneels G, Geysen J, Binderup L, Kragballe K: Proliferation and differentiation of cultured human keratinocytes is modulated by 1,25(OH)2D3 and synthetic vitamin D3 analogues in a cell density-, calcium- and serum-dependent manner. Pharmacol Toxicol. 1997 Jan;80(1):49-56. Pubmed: 9148283 Link_out
      9. Yetgin S, Yalcin SS: The effect of vitamin D3 on CD34 progenitor cells in vitamin D deficiency rickets. Turk J Pediatr. 2004 Apr-Jun;46(2):164-6. Pubmed: 15214747 Link_out
      10. Astecker N, Reddy GS, Herzig G, Vorisek G, Schuster I: 1alpha,25-Dihydroxy-3-epi-vitamin D3 a physiological metabolite of 1alpha,25-dihydroxyvitamin D3: its production and metabolism in primary human keratinocytes. Mol Cell Endocrinol. 2000 Dec 22;170(1-2):91-101. Pubmed: 11162893 Link_out
      11. Murao N, Ohishi N, Nabuchi Y, Ishigai M, Kawanishi T, Aso Y: The determination of 2beta-(3-hydroxypropoxy)-1alpha,25-dihydroxy vitamin D3 (ED-71) in human serum by high-performance liquid chromatography-electrospray tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Sep 5;823(2):61-8. Epub 2004 Nov 19. Pubmed: 16102526 Link_out
      12. Lippens S, Kockx M, Denecker G, Knaapen M, Verheyen A, Christiaen R, Tschachler E, Vandenabeele P, Declercq W: Vitamin D3 induces caspase-14 expression in psoriatic lesions and enhances caspase-14 processing in organotypic skin cultures. Am J Pathol. 2004 Sep;165(3):833-41. Pubmed: 15331408 Link_out
      13. Bjorkhem I, Holmberg I, Kristiansen T, Pedersen JI: Assay of 1,25-dihydroxy vitamin D3 by isotope dilution--mass fragmentography. Clin Chem. 1979 Apr;25(4):584-8. Pubmed: 466767 Link_out
      14. Matsuoka LY, McConnachie P, Wortsman J, Holick MF: Immunological responses to ultraviolet light B radiation in Black individuals. Life Sci. 1999;64(17):1563-9. Pubmed: 10353621 Link_out
      15. Zimber A, Chedeville A, Abita JP, Barbu V, Gespach C: Functional interactions between bile acids, all-trans retinoic acid, and 1,25-dihydroxy-vitamin D3 on monocytic differentiation and myeloblastin gene down-regulation in HL60 and THP-1 human leukemia cells. Cancer Res. 2000 Feb 1;60(3):672-8. Pubmed: 10676652 Link_out
      16. Baggio B, Budakovic A, Nassuato MA, Vezzoli G, Manzato E, Luisetto G, Zaninotto M: Plasma phospholipid arachidonic acid content and calcium metabolism in idiopathic calcium nephrolithiasis. Kidney Int. 2000 Sep;58(3):1278-84. Pubmed: 10972691 Link_out
      17. MacLaughlin J, Holick MF: Aging decreases the capacity of human skin to produce vitamin D3. J Clin Invest. 1985 Oct;76(4):1536-8. Pubmed: 2997282 Link_out
      18. Lee YF, Young WJ, Lin WJ, Shyr CR, Chang C: Differential regulation of direct repeat 3 vitamin D3 and direct repeat 4 thyroid hormone signaling pathways by the human TR4 orphan receptor. J Biol Chem. 1999 Jun 4;274(23):16198-205. Pubmed: 10347174 Link_out
      19. Okano T, Kuroda E, Nakao H, Kodama S, Matsuo T, Nakamichi Y, Nakajima K, Hirao N, Kobayashi T: Lack of evidence for existence of vitamin D and 25-hydroxyvitamin D sulfates in human breast and cow's milk. J Nutr Sci Vitaminol (Tokyo). 1986 Oct;32(5):449-62. Pubmed: 3494111 Link_out
      20. Mata-Granados JM, Caballo-Lopez A, Luque de Castro MD, Quesada JM: Automated method for the determination of vitamin D3 hydroxymetabolites in serum. Anal Bioanal Chem. 2003 Sep;377(2):287-92. Epub 2003 Jul 9. Pubmed: 12955389 Link_out
      21. Armas LA, Hollis BW, Heaney RP: Vitamin D2 is much less effective than vitamin D3 in humans. J Clin Endocrinol Metab. 2004 Nov;89(11):5387-91. Pubmed: 15531486 Link_out

      Enzymes
      Name: Nuclear receptor coactivator 3
      Reactions: Not Available
      Gene Name: NCOA3
      Uniprot ID: Q9Y6Q9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cholesterol side-chain cleavage enzyme, mitochondrial
      Reactions: Not Available
      Gene Name: CYP11A1
      Uniprot ID: P05108 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytochrome P450 3A4
      Reactions: Not Available
      Gene Name: CYP3A4
      Uniprot ID: P08684 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytochrome P450 2C9
      Reactions: Not Available
      Gene Name: CYP2C9
      Uniprot ID: P11712 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Sterol 26-hydroxylase, mitochondrial
      Reactions: Not Available
      Gene Name: CYP27A1
      Uniprot ID: Q02318 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytochrome P450 2C19
      Reactions: Not Available
      Gene Name: CYP2C19
      Uniprot ID: P33261 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial
      Reactions: Not Available
      Gene Name: CYP27B1
      Uniprot ID: O15528 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytochrome P450 2D6
      Reactions: Not Available
      Gene Name: CYP2D6
      Uniprot ID: P10635 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytochrome P450 2B6
      Reactions: Not Available
      Gene Name: CYP2B6
      Uniprot ID: P20813 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytochrome P450 1A1
      Reactions: Not Available
      Gene Name: CYP1A1
      Uniprot ID: P04798 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytochrome P450 2C8
      Reactions: Not Available
      Gene Name: CYP2C8
      Uniprot ID: P10632 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytochrome P450 2J2
      Reactions: Not Available
      Gene Name: CYP2J2
      Uniprot ID: P51589 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: Not Available
      Gene Name: CYP24A1
      Uniprot ID: Q07973 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Vitamin D 25-hydroxylase
      Reactions: Not Available
      Gene Name: CYP2R1
      Uniprot ID: Q6VVX0 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Transcription initiation factor TFIID subunit 4
      Reactions: Not Available
      Gene Name: TAF4
      Uniprot ID: O00268 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Nuclear receptor coactivator 6
      Reactions: Not Available
      Gene Name: NCOA6
      Uniprot ID: Q14686 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA