Human Metabolome Database Version 3.5

Showing metabocard for Ercalcitriol (HMDB06225)

Record Information
Version 3.5
Creation Date 2007-05-22 12:20:36 -0600
Update Date 2013-05-29 13:43:06 -0600
Secondary Accession Numbers None
Metabolite Identification
Common Name Ercalcitriol
Description Ercalcitriol is the active circulating metabolite of vitamin D2. Vitamin D2 is modified by 25-hydroxylase in the liver and 25-hydroxyvitamin D *-hydroxylase in the kidney to form the active metabolite, ercalcitriol, which is then metabolized by 25-hydroxyvitamin D-24-hydroxylase (24-OHase, CYP24A1, EC The binding of ercalcitriol or their analogs to Vitamin D receptor (VDR), a nuclear receptor, activates VDR to interact with retinoid X receptor (RXR) and forms the VDR/RXR/cofactor complex, which binds to Vitamin D response elements in the promoter region of target genes to regulate gene transcription. The kidney is the major site of 25-hydroxyvitamin D*-hydroxylase (CYP27B1, EC, which is responsible for the activation of 25-hydroxyvitamin D. Of all the steroid hormones, ercalcitriol represents the most difficult challenge to the analytical biochemist with respect to quantization. Ercalcitriol circulates at pmol concentrations, is highly lipophilic and its precursor, 25-hydroxyvitamin D2, circulates at nmol levels. (PMID: 16242929 Link_out, 17867378 Link_out, 17197173 Link_out).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
  1. 1,25-Dihydroxycalciferol
  2. 1,25-Dihydroxyergocalciferol
  3. 1,25-Dihydroxyvitamin D2
  4. 1a,25-Dihydroxycalciferol
  5. 1a,25-Dihydroxyergocalciferol
  6. 1a,25-Dihydroxyvitamin D2
  7. Ro 17-6218
Chemical Formula C28H44O3
Average Molecular Weight 428.6472
Monoisotopic Molecular Weight 428.329045274
IUPAC Name (1R,3S,5Z)-5-{2-[(1R,3aS,4E,7aR)-1-[(2R,3E,5S)-6-hydroxy-5,6-dimethylhept-3-en-2-yl]-7a-methyl-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol
Traditional IUPAC Name (1R,3S,5Z)-5-{2-[(1R,3aS,4E,7aR)-1-[(2R,3E,5S)-6-hydroxy-5,6-dimethylhept-3-en-2-yl]-7a-methyl-hexahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol
CAS Registry Number 60133-18-8
SMILES C[C@H](\C=C\[C@H](C)C(O)(C)C)[C@@]1([H])CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)C[C@H](O)C1=C
InChI Identifier InChI=1S/C28H44O3/c1-18(9-10-19(2)27(4,5)31)24-13-14-25-21(8-7-15-28(24,25)6)11-12-22-16-23(29)17-26(30)20(22)3/h9-12,18-19,23-26,29-31H,3,7-8,13-17H2,1-2,4-6H3/b10-9+,21-11+,22-12-/t18-,19+,23-,24-,25+,26+,28-/m1/s1
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Lipids
Class Steroids and Steroid Derivatives
Sub Class Vitamin D and Derivatives
Other Descriptors
  • Aliphatic Homopolycyclic Compounds
  • Sesterterpenes
  • Cyclic Alcohol
  • Cyclohexane
  • Secondary Alcohol
  • Tertiary Alcohol
Direct Parent Vitamin D and Derivatives
Status Expected and Not Quantified
  • Endogenous
  • Food
  • Cell signaling
  • Fuel and energy storage
  • Fuel or energy source
  • Hormones, Membrane component
  • Membrane integrity/stability
  • Nutrients
  • Stabilizers
  • Surfactants and Emulsifiers
Cellular locations
  • Extracellular
  • Membrane
  • 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 0.007 g/L ALOGPS
LogP 5.45 ALOGPS
LogP 4.35 ChemAxon
LogS -4.79 ALOGPS
pKa (strongest acidic) 14.39 ChemAxon
pKa (strongest basic) -1 ChemAxon
Hydrogen Acceptor Count 3 ChemAxon
Hydrogen Donor Count 3 ChemAxon
Polar Surface Area 60.69 A2 ChemAxon
Rotatable Bond Count 5 ChemAxon
Refractivity 132.12 ChemAxon
Polarizability 52.28 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Not Available
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
  • Mitochondria
Biofluid Locations Not Available
Tissue Location Not Available
Pathways Not Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID Not Available
DrugBank Metabolite ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB023845
KNApSAcK ID Not Available
Chemspider ID 7826183 Link_out
KEGG Compound ID Not Available
BiGG ID 2289254 Link_out
Wikipedia Link Not Available
NuGOwiki Link HMDB06225 Link_out
Metagene Link HMDB06225 Link_out
METLIN ID Not Available
PubChem Compound 9547243 Link_out
PDB ID Not Available
ChEBI ID Not Available
Synthesis Reference Sicinski, Rafal R.; Tanaka, Yoko; Schnoes, Heinrich K.; DeLuca, Hector F. Synthesis of 1a, 25-dihydroxyvitamin D2, its 24 epimer and related isomers, and their binding affinity for the 1,25-dihydroxyvitamin D3 receptor. Bioorganic Chemistry (1985), 13(2), 158-69.
Material Safety Data Sheet (MSDS) Download (PDF)
General References
  1. Nakane M, Fey TA, Dixon DB, Ma J, Brune ME, Li YC, Wu-Wong JR: Differential effects of Vitamin D analogs on bone formation and resorption. J Steroid Biochem Mol Biol. 2006 Jan;98(1):72-7. Epub 2005 Oct 20. Pubmed: 16242929 Link_out
  2. Hollis BW: Assessment of circulating 25(OH)D and 1,25(OH)2D: emergence as clinically important diagnostic tools. Nutr Rev. 2007 Aug;65(8 Pt 2):S87-90. Pubmed: 17867378 Link_out
  3. Hollis BW, Horst RL: The assessment of circulating 25(OH)D and 1,25(OH)2D: where we are and where we are going. J Steroid Biochem Mol Biol. 2007 Mar;103(3-5):473-6. Epub 2007 Jan 2. Pubmed: 17197173 Link_out

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: 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