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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 01:25:55 UTC
Update Date2022-03-07 03:17:46 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
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
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular 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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+196.90531661259
DarkChem[M-H]-193.34931661259
DeepCCS[M-2H]-238.02930932474
DeepCCS[M+Na]+213.45430932474
AllCCS[M+H]+208.432859911
AllCCS[M+H-H2O]+206.332859911
AllCCS[M+NH4]+210.432859911
AllCCS[M+Na]+211.032859911
AllCCS[M-H]-206.832859911
AllCCS[M+Na-2H]-208.932859911
AllCCS[M+HCOO]-211.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
SecalciferolCC(CC[C@@H](O)C(C)(C)O)C1CCC2\C(CCC[C@]12C)=C\C=C1/C[C@@H](O)CCC1=C3541.4Standard polar33892256
SecalciferolCC(CC[C@@H](O)C(C)(C)O)C1CCC2\C(CCC[C@]12C)=C\C=C1/C[C@@H](O)CCC1=C3313.3Standard non polar33892256
SecalciferolCC(CC[C@@H](O)C(C)(C)O)C1CCC2\C(CCC[C@]12C)=C\C=C1/C[C@@H](O)CCC1=C3577.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Secalciferol,1TMS,isomer #1C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O3479.1Semi standard non polar33892256
Secalciferol,1TMS,isomer #2C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C3516.1Semi standard non polar33892256
Secalciferol,1TMS,isomer #3C=C1CC[C@H](O[Si](C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O)C(C)(C)O3470.2Semi standard non polar33892256
Secalciferol,2TMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O3481.0Semi standard non polar33892256
Secalciferol,2TMS,isomer #2C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O[Si](C)(C)C3577.1Semi standard non polar33892256
Secalciferol,2TMS,isomer #3C=C1CC[C@H](O[Si](C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C3533.0Semi standard non polar33892256
Secalciferol,3TMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O[Si](C)(C)C3583.7Semi standard non polar33892256
Secalciferol,1TBDMS,isomer #1C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O3718.6Semi standard non polar33892256
Secalciferol,1TBDMS,isomer #2C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C(C)(C)C3751.9Semi standard non polar33892256
Secalciferol,1TBDMS,isomer #3C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O)C(C)(C)O3677.5Semi standard non polar33892256
Secalciferol,2TBDMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O3930.0Semi standard non polar33892256
Secalciferol,2TBDMS,isomer #2C=C1CC[C@H](O)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O[Si](C)(C)C(C)(C)C4049.7Semi standard non polar33892256
Secalciferol,2TBDMS,isomer #3C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C(C)(C)C3981.0Semi standard non polar33892256
Secalciferol,3TBDMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C\C=C1/CCC[C@@]2(C)C1CCC2C(C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O[Si](C)(C)C(C)(C)C4249.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Secalciferol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-7029200000-c84dd427774a8bd55bf42017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Secalciferol GC-MS (3 TMS) - 70eV, Positivesplash10-014i-1312049000-f6115b14a152464f5e1b2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Secalciferol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 10V, Positive-QTOFsplash10-00l2-0119200000-7bcd78fea8093a8230ae2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 20V, Positive-QTOFsplash10-0a5a-2369100000-04f3fb5d7d655a9ce4702017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 40V, Positive-QTOFsplash10-0zgi-4389100000-269c6b355710e7dcd9b82017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 10V, Negative-QTOFsplash10-014i-0004900000-7bbe3ea5eae60b2a20592017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 20V, Negative-QTOFsplash10-05mk-0009300000-4137913e2e1e7271894c2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 40V, Negative-QTOFsplash10-0079-9006000000-b2d6915fde38c349870a2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 10V, Positive-QTOFsplash10-00lr-0439300000-d0f3435842264a17a15a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 20V, Positive-QTOFsplash10-00rx-4579100000-2ffe9e7393dd492716a02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 40V, Positive-QTOFsplash10-0avi-2960000000-4329739a1dba4656972b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 10V, Negative-QTOFsplash10-014j-0007900000-764d7cf399a810ff092c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 20V, Negative-QTOFsplash10-0671-3109300000-5c39962acfb73b3f737d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Secalciferol 40V, Negative-QTOFsplash10-01ri-2129300000-7f78982c59e2cf08742c2021-10-12Wishart LabView Spectrum
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 IDNot Available
Good Scents IDNot Available
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

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