Showing metabocard for 24,25-Dihydroxyvitamin D (BMDB0000430)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (7) Show 7 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:30:37 UTC
Update Date2020-06-04 20:45:48 UTC
BMDB IDBMDB0000430
Secondary Accession Numbers
  • BMDB00430
Metabolite Identification
Common Name24,25-Dihydroxyvitamin D
Description24,25-Dihydroxyvitamin D, also known as vitamin D or 24-hydroxycalcidiol, 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. 24,25-Dihydroxyvitamin D is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(3b,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,24,25-triolHMDB
24,25-DihydroxycholecalciferolHMDB
24,25-DihydroxyvitaminHMDB
24,25-Dihydroxyvitamin D3HMDB
24-HydroxycalcidiolHMDB
Vitamin DHMDB
24,25 Dihydroxyvitamin D3HMDB
(24R)-24,25-Dihydroxyvitamin D3HMDB
24,25-Dihydroxyvitamin D 3, (3beta,5Z,7E,24R)-isomerHMDB
24,25 DihydroxycholecalciferolHMDB
Dihydroxyvitamin D3, 24,25HMDB
24R,25-DihydroxycholecalciferolHMDB
24,25 Dihydroxyvitamin D 3HMDB
24,25-Dihydroxyvitamin D 3HMDB
24,25-Dihydroxy-vitamin DHMDB
Chemical FormulaC27H44O3
Average Molecular Weight416.6365
Monoisotopic Molecular Weight416.329045274
IUPAC Name(6R)-6-[(1R,3aS,4E,7aR)-4-{2-[(1Z,5R)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol
Traditional Name24,25-dihydroxyvitamin
CAS Registry Number40013-87-4
SMILES
C[C@H](CCC(O)C(C)(C)O)[C@H]1CC[C@@]2([H])\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-/m1/s1
InChI KeyFCKJYANJHNLEEP-OIMXRAFZSA-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
StatusDetected and Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
Polarizability50.98 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Membrane
Biospecimen Locations
  • Milk
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
MilkDetected and Quantified2 IU/100 gNot SpecifiedNot SpecifiedNormal
    • Park, Y. W; Juáre...
 details
MilkDetected and Quantified0.000065 uMNot SpecifiedNot SpecifiedNormal details
MilkDetected and Quantified0.0001 +/- 0.00001 uMNot SpecifiedNot Specified
Normal		 details
MilkDetected and Quantified0.00009 +/- 0.00002 uMNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
HMDB IDHMDB0000430
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB112199
KNApSAcK IDNot Available
Chemspider ID17215953
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5419
PubChem Compound12895043
PDB IDNot Available
ChEBI ID89324
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Reeve LE, Jorgensen NA, DeLuca HF: Vitamin D compounds in cows' milk. J Nutr. 1982 Apr;112(4):667-72. doi: 10.1093/jn/112.4.667. [PubMed:6279806 ]
  2. Hollis BW, Roos BA, Draper HH, Lambert PW: Vitamin D and its metabolites in human and bovine milk. J Nutr. 1981 Jul;111(7):1240-8. doi: 10.1093/jn/111.7.1240. [PubMed:6788913 ]
  3. Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W. (2007). Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W.. Physico-chemical characteristics of goat and sheep milk. Small Ruminant Res.(2007) 68:88-113 doi: 10.1016/j.smallrumres.2006.09.013. Small Ruminant Research.

Enzymes

Enzyme Details
1. Vitamin D-binding protein
General function:
Involved in actin binding
Specific function:
Involved in vitamin D transport and storage, scavenging of extracellular G-actin, enhancement of the chemotactic activity of C5 alpha for neutrophils in inflammation and macrophage activation.
Gene Name:
GC
Uniprot ID:
Q3MHN5
Molecular weight:
53342.0
Enzyme Details
2. Chromatin assembly factor 1 subunit A
General function:
Not Available
Specific function:
Core component of the CAF-1 complex, a complex thought to mediate chromatin assembly in DNA replication and DNA repair. Assembles histone octamers onto replicating DNA in vitro. CAF-1 performs the first step of the nucleosome assembly process, bringing newly synthesized histones H3 and H4 to replicating DNA; histones H2A/H2B can bind to this chromatin precursor subsequent to DNA replication to complete the histone octamer. CHAF1A binds to histones H3 and H4. It may play a role in heterochromatin maintenance in proliferating cells by bringing newly synthesized cbx proteins to heterochromatic DNA replication foci.
Gene Name:
CHAF1A
Uniprot ID:
A6QLA6
Molecular weight:
107258.0
Enzyme Details
3. TOB2 protein
General function:
Involved in vitamin D receptor binding
Specific function:
Not Available
Gene Name:
TOB2
Uniprot ID:
A4FUY5
Molecular weight:
36529.0
Enzyme Details
4. Calbindin
General function:
Involved in calcium ion binding
Specific function:
Buffers cytosolic calcium. May stimulate a membrane Ca(2+)-ATPase and a 3',5'-cyclic nucleotide phosphodiesterase.
Gene Name:
CALB1
Uniprot ID:
P04467
Molecular weight:
29964.0
Enzyme Details
5. SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
General function:
Involved in cell cycle
Specific function:
Core component of the BAF (SWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of tumor formation. The BAF complex is able to create a stable, altered form of chromatin that constrains fewer negative supercoils than normal. This change in supercoiling would be due to the conversion of up to one-half of the nucleosomes on polynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2 histones octamers. Stimulates in vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Plays a key role in cell-cycle control and causes cell cycle arrest in G0/G1. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity).
Gene Name:
SMARCB1
Uniprot ID:
Q5BIN2
Molecular weight:
44111.0
Enzyme Details
6. SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
General function:
Involved in chromatin modification
Specific function:
Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner (By similarity). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Has a strong influence on vitamin D-mediated transcriptional activity from an enhancer vitamin D receptor element (VDRE). May be a link between mammalian SWI-SNF-like chromatin remodeling complexes and the vitamin D receptor (VDR) heterodimer. Mediates critical interactions between nuclear receptors and the BRG1/SMARCA4 chromatin-remodeling complex for transactivation (By similarity).
Gene Name:
SMARCD1
Uniprot ID:
Q2TBN1
Molecular weight:
58252.0
Enzyme Details
7. Protein S100-G
General function:
Involved in calcium ion binding
Specific function:
Not Available
Gene Name:
S100G
Uniprot ID:
P02633
Molecular weight:
8918.0