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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2007-05-22 18:20:36 UTC
Update Date2022-03-07 02:49:30 UTC
HMDB IDHMDB0006225
Secondary Accession Numbers
  • HMDB06225
Metabolite Identification
Common NameErcalcitriol
DescriptionErcalcitriol 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 1.14.13.13). 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 1.14.13.13), 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 , 17867378 , 17197173 ).
Structure
Data?1582752375
Synonyms
ValueSource
1,25-DihydroxycalciferolChEBI
1,25-DihydroxyergocalciferolChEBI
1,25-Dihydroxyvitamin D2ChEBI
1alpha,25-DihydroxycalciferolChEBI
1alpha,25-DihydroxyergocalciferolChEBI
1a,25-DihydroxycalciferolGenerator
1Α,25-dihydroxycalciferolGenerator
1a,25-DihydroxyergocalciferolGenerator
1Α,25-dihydroxyergocalciferolGenerator
1a,25-Dihydroxyvitamin D2 / 1a,,25-dihydroxyergocalciferolHMDB
1Α,25-dihydroxyvitamin D2 / 1α,,25-dihydroxyergocalciferolHMDB
1 alpha,25-Dihydroxyvitamin D2HMDB
1,25-Dihydroxyergocalciferol, (1alpha,3beta,5Z,7E,22E)-isomerHMDB
1,25-(OH)2D2HMDB
ErcalcitriolChEBI
1a,25-Dihydroxyvitamin D2Generator
1Α,25-dihydroxyvitamin D2Generator
Chemical FormulaC28H44O3
Average Molecular Weight428.6472
Monoisotopic Molecular Weight428.329045274
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 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 Number60133-18-8
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
InChI KeyZGLHBRQAEXKACO-XJRQOBMKSA-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 Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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 Solubility0.007 g/LALOGPS
logP5.45ALOGPS
logP4.35ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)14.39ChemAxon
pKa (Strongest Basic)-1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area60.69 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity132.12 m³·mol⁻¹ChemAxon
Polarizability52.28 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+204.47731661259
DarkChem[M-H]-203.84631661259
DeepCCS[M-2H]-244.9330932474
DeepCCS[M+Na]+219.01330932474
AllCCS[M+H]+210.432859911
AllCCS[M+H-H2O]+208.332859911
AllCCS[M+NH4]+212.432859911
AllCCS[M+Na]+212.932859911
AllCCS[M-H]-209.732859911
AllCCS[M+Na-2H]-211.932859911
AllCCS[M+HCOO]-214.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ErcalcitriolC[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=C4013.9Standard polar33892256
ErcalcitriolC[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=C3399.5Standard non polar33892256
ErcalcitriolC[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=C3582.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Ercalcitriol,1TMS,isomer #1C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O[Si](C)(C)C)C[C@@H](O)C[C@@H]1O3549.8Semi standard non polar33892256
Ercalcitriol,1TMS,isomer #2C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O)C[C@@H](O[Si](C)(C)C)C[C@@H]1O3486.2Semi standard non polar33892256
Ercalcitriol,1TMS,isomer #3C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O)C[C@@H](O)C[C@@H]1O[Si](C)(C)C3487.7Semi standard non polar33892256
Ercalcitriol,2TMS,isomer #1C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O[Si](C)(C)C)C[C@@H](O[Si](C)(C)C)C[C@@H]1O3495.7Semi standard non polar33892256
Ercalcitriol,2TMS,isomer #2C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O[Si](C)(C)C)C[C@@H](O)C[C@@H]1O[Si](C)(C)C3485.5Semi standard non polar33892256
Ercalcitriol,2TMS,isomer #3C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O)C[C@@H](O[Si](C)(C)C)C[C@@H]1O[Si](C)(C)C3403.8Semi standard non polar33892256
Ercalcitriol,3TMS,isomer #1C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O[Si](C)(C)C)C[C@@H](O[Si](C)(C)C)C[C@@H]1O[Si](C)(C)C3419.3Semi standard non polar33892256
Ercalcitriol,1TBDMS,isomer #1C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O[Si](C)(C)C(C)(C)C)C[C@@H](O)C[C@@H]1O3780.4Semi standard non polar33892256
Ercalcitriol,1TBDMS,isomer #2C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O)C[C@@H](O[Si](C)(C)C(C)(C)C)C[C@@H]1O3708.1Semi standard non polar33892256
Ercalcitriol,1TBDMS,isomer #3C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O)C[C@@H](O)C[C@@H]1O[Si](C)(C)C(C)(C)C3689.0Semi standard non polar33892256
Ercalcitriol,2TBDMS,isomer #1C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O[Si](C)(C)C(C)(C)C)C[C@@H](O[Si](C)(C)C(C)(C)C)C[C@@H]1O3956.4Semi standard non polar33892256
Ercalcitriol,2TBDMS,isomer #2C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O[Si](C)(C)C(C)(C)C)C[C@@H](O)C[C@@H]1O[Si](C)(C)C(C)(C)C3918.1Semi standard non polar33892256
Ercalcitriol,2TBDMS,isomer #3C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O)C[C@@H](O[Si](C)(C)C(C)(C)C)C[C@@H]1O[Si](C)(C)C(C)(C)C3820.8Semi standard non polar33892256
Ercalcitriol,3TBDMS,isomer #1C=C1/C(=C\C=C2/CCC[C@@]3(C)[C@H]2CC[C@@H]3[C@H](C)/C=C/[C@H](C)C(C)(C)O[Si](C)(C)C(C)(C)C)C[C@@H](O[Si](C)(C)C(C)(C)C)C[C@@H]1O[Si](C)(C)C(C)(C)C4077.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Ercalcitriol GC-MS (Non-derivatized) - 70eV, Positivesplash10-08fr-4029600000-dbfa8697870ebd6830252017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ercalcitriol GC-MS (3 TMS) - 70eV, Positivesplash10-003r-1400149000-b8a11d6c4c1ad554146e2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ercalcitriol 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 - Ercalcitriol 10V, Positive-QTOFsplash10-03dl-0119800000-7dd9f14f9a8c59dc34da2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 20V, Positive-QTOFsplash10-0gvx-1329200000-0a0f4f399ef35e7f80392017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 40V, Positive-QTOFsplash10-03dr-4449200000-6bc7143e80424071bd592017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 10V, Negative-QTOFsplash10-004i-0001900000-01f91a65a26969417dc32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 20V, Negative-QTOFsplash10-0a6r-0004900000-35bc1dcb432dd5b316862017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 40V, Negative-QTOFsplash10-0i09-7109200000-c0e2fe47359423d7eee02017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 10V, Negative-QTOFsplash10-004i-0000900000-be3d96e63cee98d539bf2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 20V, Negative-QTOFsplash10-004i-1402900000-1f6915f21eef2875a0712021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 40V, Negative-QTOFsplash10-002f-2319300000-299bc94defd194cd6fac2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 10V, Positive-QTOFsplash10-014r-0193200000-a4d6e13ad596312a24b22021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 20V, Positive-QTOFsplash10-014r-1094000000-5a9b3afb3048a2dde8d92021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ercalcitriol 40V, Positive-QTOFsplash10-03y0-4982000000-9e151864bb3f37c456272021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
  • Mitochondria
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothInflammatory bowel disease details
Associated Disorders and Diseases
Disease References
Inflammatory bowel disease
  1. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023845
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9547243
PDB IDNot Available
ChEBI ID86320
Food Biomarker OntologyNot Available
VMH ID1A25DHVITD2
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceSicinski, 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 ]
  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 ]
  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 ]

Enzymes

General function:
Involved in monooxygenase activity
Specific function:
Catalyzes the conversion of 25-hydroxyvitamin D3 (25(OH)D) to 1-alpha,25-dihydroxyvitamin D3 (1,25(OH)2D) plays an important role in normal bone growth, calcium metabolism, and tissue differentiation.
Gene Name:
CYP27B1
Uniprot ID:
O15528
Molecular weight:
56503.475
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