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Showing metabocard for Secalciferol (HMDB0060508)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2013-05-17 01:25:55 UTC
Update Date2019-07-23 07:14:29 UTC
HMDB IDHMDB0060508
Secondary Accession Numbers
  • HMDB60508
Metabolite Identification
Common NameSecalciferol
DescriptionSecalciferol 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. Secalciferol is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563866069
MOLSDFPDBSMILESInChI
SynonymsNot Available
Chemical FormulaC27H44O3
Average Molecular Weight416.6365
Monoisotopic Molecular Weight416.329045274
IUPAC Name(3R)-6-[(4E,7aR)-4-{2-[(1E,5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol
Traditional Name(3R)-6-[(4E,7aR)-4-{2-[(1E,5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol
CAS Registry NumberNot Available
SMILES
CC(CC[C@@H](O)C(C)(C)O)C1CCC2\C(CCC[C@]12C)=C\C=C1/C[C@@H](O)CCC1=C
InChI Identifier
InChI=1S/C27H44O3/c1-18-8-12-22(28)17-21(18)11-10-20-7-6-16-27(5)23(13-14-24(20)27)19(2)9-15-25(29)26(3,4)30/h10-11,19,22-25,28-30H,1,6-9,12-17H2,2-5H3/b20-10+,21-11+/t19?,22-,23?,24?,25+,27+/m0/s1
InChI KeyFCKJYANJHNLEEP-PSQIUDODSA-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 DescriptorsNot Available
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Biological role:

Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.0084 g/LALOGPS
logP5.47ALOGPS
logP4.58ChemAxon
logS-4.7ALOGPS
pKa (Strongest Acidic)13.85ChemAxon
pKa (Strongest Basic)-1.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area60.69 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity126.42 m³·mol⁻¹ChemAxon
Polarizability51.65 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-7029200000-c84dd427774a8bd55bf4Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-014i-1312049000-f6115b14a152464f5e1bSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00l2-0119200000-7bcd78fea8093a8230aeSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a5a-2369100000-04f3fb5d7d655a9ce470Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0zgi-4389100000-269c6b355710e7dcd9b8Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0004900000-7bbe3ea5eae60b2a2059Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-05mk-0009300000-4137913e2e1e7271894cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0079-9006000000-b2d6915fde38c349870aSpectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131769915
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH ID2425DHVITD3
MarkerDB ID
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]
  2. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  3. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  4. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  5. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Enzymes

Enzyme Details
1. 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
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 + Hydrogen Ion + Oxygen → Secalciferol + NADP + Waterdetails