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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2007-05-22 18:21:38 UTC
Update Date2022-03-07 02:49:30 UTC
HMDB IDHMDB0006226
Secondary Accession Numbers
  • HMDB06226
Metabolite Identification
Common Name24R,25-Dihydroxyvitamin D3
Description24R,25-Dihydroxyvitamin D3, also known as 24(R),25(OH)2D3, is a vitamin D metabolite; a dihydroxylated form of the seco-steroid. With the identification of a target cell, the growth plate resting zone (RC) chondrocyte, studies indicate that there are specific membrane-associated signal transduction pathways that mediate both rapid, nongenomic, and genomic responses of RC cells to 24(R),25(OH)2D3. These studies indicate that 24(R),25(OH)2D3 plays an important role in endochondral ossification by regulating less mature chondrocytes and promoting their maturation in the endochondral lineage. 24(R),25(OH)2D3 binds RC chondrocyte membranes with high specificity, increasing protein kinase C (PKC) activity. The effect is stereospecific; 24R,25(OH)2D3, but not 24S,25(OH)2D3, causes the increase, indicating a receptor-mediated response. Phospholipase D-2 (PLD2) activity is increased, resulting in increased production of diacylglycerol (DAG), which in turn activates PKC. 24(R),25(OH)2D3 does not cause translocation of PKC to the plasma membrane but activates existing PKCα. There is a rapid decrease in Ca2+ efflux, and the influx is stimulated. 24(R),25(OH)2D3 also reduces arachidonic acid release by decreasing phospholipase A2 (PLA2) activity, thereby decreasing the available substrate for prostaglandin production via the action of cyclooxygenase-1. PGE2 that is produced acts on the EP1 and EP2 receptors expressed by RC cells to downregulate PKC via protein kinase A, but the reduction in PGE2 decreases this negative feedback mechanism. Both pathways converge on MAP kinase, leading to new gene expression. One consequence of this is the production of new matrix vesicles containing PKCα and PKCγ, and an increase in PKC activity. The chondrocytes also produce 24(R),25(OH)2D3, and the secreted metabolite acts directly on the matrix vesicle membrane. Only PKCγ is directly affected by 24(R),25(OH)2D3 in the matrix vesicles, and activity of this isoform is inhibited. This effect may be involved in the control of matrix maturation and turnover. 24(R),25(OH)2D3 causes RC cells to mature along the endochondral developmental pathway, where they become responsive to 1α,25(OH)2D3 and lose responsiveness to 24(R),25(OH)2D3, a characteristic of more mature growth zone (GC) chondrocytes. 1α,25(OH)2D3 elicits its effects on GC through different signal transduction pathways than those used by 24(R),25(OH)2D3 (PMID: 11179745 ).
Structure
Data?1586446803
Synonyms
ValueSource
(24R)-24,25-DihydroxycholecalciferolChEBI
(24R)-24,25-Dihydroxyvitamin D3ChEBI
24(R),25-Dihydroxyvitamin D3ChEBI
24R,25(OH)2D3ChEBI
24R,25-DihydroxycholecalciferolChEBI
SecalciferolChEBI
Osteo DKegg
24,25-DihydroxycholecalciferolHMDB
24,25-Dihydroxyvitamin D3HMDB
Dihydroxyvitamin D3, 24,25HMDB
24,25 Dihydroxyvitamin D 3HMDB
24,25 Dihydroxyvitamin D3HMDB
24,25-Dihydroxyvitamin D 3, (3beta,5Z,7E,24R)-isomerHMDB
24,25 DihydroxycholecalciferolHMDB
24,25-Dihydroxyvitamin D 3HMDB
24R,25 DihydroxycholecalciferolHMDB
(24R)-HydroxycalcidiolHMDB
(3beta,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,24,25-triolHMDB
(3Β,5Z,7E)-9,10-secocholesta-5,7,10(19)-triene-3,24,25-triolHMDB
24(R),25-DihydroxycholecalciferolHMDB
24,25-Dihydroxyvitamin DHMDB
24-HydroxycalcidiolHMDB
24(R),25(OH)2D3HMDB
24R,25-Dihydroxyvitamin D3ChEBI
Chemical FormulaC27H44O3
Average Molecular Weight416.646
Monoisotopic Molecular Weight416.329045277
IUPAC Name(3R,6R)-6-[(1R,3aS,4E,7aR)-4-{2-[(1Z,5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol
Traditional Namesecalciferol
CAS Registry Number55721-11-4
SMILES
[H][C@@]1(CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C)[C@H](C)CC[C@@H](O)C(C)(C)O
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-/m1/s1
InChI KeyFCKJYANJHNLEEP-XRWYNYHCSA-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
DispositionNot Available
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 Solubility0.0084 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
Polarizability51.07 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
DeepCCS[M-2H]-246.48830932474
DeepCCS[M+Na]+221.24430932474
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
24R,25-Dihydroxyvitamin D3[H][C@@]1(CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C)[C@H](C)CC[C@@H](O)C(C)(C)O3595.9Standard polar33892256
24R,25-Dihydroxyvitamin D3[H][C@@]1(CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C)[C@H](C)CC[C@@H](O)C(C)(C)O3431.7Standard non polar33892256
24R,25-Dihydroxyvitamin D3[H][C@@]1(CC[C@@]2([H])\C(CCC[C@]12C)=C\C=C1\C[C@@H](O)CCC1=C)[C@H](C)CC[C@@H](O)C(C)(C)O3555.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
24R,25-Dihydroxyvitamin D3,1TMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O3434.0Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,1TMS,isomer #2C=C1CC[C@H](O)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O3482.0Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,1TMS,isomer #3C=C1CC[C@H](O)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C3515.6Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,2TMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O3435.4Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,2TMS,isomer #2C=C1CC[C@H](O[Si](C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C3486.0Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,2TMS,isomer #3C=C1CC[C@H](O)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O[Si](C)(C)C3532.1Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,3TMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C)C(C)(C)O[Si](C)(C)C3503.3Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,1TBDMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O3629.6Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,1TBDMS,isomer #2C=C1CC[C@H](O)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O3709.8Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,1TBDMS,isomer #3C=C1CC[C@H](O)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C(C)(C)C3741.1Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,2TBDMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O3877.9Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,2TBDMS,isomer #2C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O)C(C)(C)O[Si](C)(C)C(C)(C)C3927.1Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,2TBDMS,isomer #3C=C1CC[C@H](O)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O[Si](C)(C)C(C)(C)C3984.1Semi standard non polar33892256
24R,25-Dihydroxyvitamin D3,3TBDMS,isomer #1C=C1CC[C@H](O[Si](C)(C)C(C)(C)C)C/C1=C/C=C1\CCC[C@@]2(C)[C@H]1CC[C@@H]2[C@H](C)CC[C@@H](O[Si](C)(C)C(C)(C)C)C(C)(C)O[Si](C)(C)C(C)(C)C4180.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 24R,25-Dihydroxyvitamin D3 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 - 24R,25-Dihydroxyvitamin D3 10V, Positive-QTOFsplash10-00l2-0119200000-9408ca86b83bf63d853f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 20V, Positive-QTOFsplash10-0a5a-1469100000-15967532fe6b0b27c09c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 40V, Positive-QTOFsplash10-0zmi-6396100000-3000f5727d0dad4b23512016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 10V, Negative-QTOFsplash10-014i-0005900000-c4be780e228f40b4d0fb2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 20V, Negative-QTOFsplash10-066s-1009300000-fd3202f74d1a84dfae952016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 40V, Negative-QTOFsplash10-0079-9005000000-fa0288a9145c4ccb232e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 10V, Positive-QTOFsplash10-00m0-0339300000-e33d06b378a97923b97d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 20V, Positive-QTOFsplash10-0kml-6494000000-48fa9e19701bee3495272021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 40V, Positive-QTOFsplash10-066u-4961000000-5fb8b17537725cdef3c82021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 10V, Negative-QTOFsplash10-014j-0006900000-7d1124e362f13b9eb6962021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 20V, Negative-QTOFsplash10-0670-1009400000-968d45c08ce476c374062021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 24R,25-Dihydroxyvitamin D3 40V, Negative-QTOFsplash10-08fr-4623900000-daa2c5a17d980b09964f2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
  • Mitochondria
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 IDFDB023846
KNApSAcK IDNot Available
Chemspider ID4446837
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5283748
PDB IDNot Available
ChEBI ID28818
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceSeki, Masao; Koizumi, Naoyuki; Morisaki, Masuo; Ikekawa, Nobuo. Synthesis of active forms of vitamin D. VI. Synthesis of (24R)- and (24S)-24,25-dihydroxyvitamin D3. Tetrahedron Letters (1975), (1), 15-18.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Boyan BD, Sylvia VL, Dean DD, Schwartz Z: 24,25-(OH)(2)D(3) regulates cartilage and bone via autocrine and endocrine mechanisms. Steroids. 2001 Mar-May;66(3-5):363-74. [PubMed:11179745 ]