Bovine Metabolome Database: Showing metabocard for 24,25-Dihydroxyvitamin D (BMDB0000430)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (7) Show 7 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:30:37 UTC

Update Date

2020-06-04 20:45:48 UTC

BMDB ID

BMDB0000430

Secondary Accession Numbers

BMDB00430

Metabolite Identification

Common Name

24,25-Dihydroxyvitamin D

Description

24,25-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

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(3b,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,24,25-triol	HMDB
24,25-Dihydroxycholecalciferol	HMDB
24,25-Dihydroxyvitamin	HMDB
24,25-Dihydroxyvitamin D3	HMDB
24-Hydroxycalcidiol	HMDB
Vitamin D	HMDB
24,25 Dihydroxyvitamin D3	HMDB
(24R)-24,25-Dihydroxyvitamin D3	HMDB
24,25-Dihydroxyvitamin D 3, (3beta,5Z,7E,24R)-isomer	HMDB
24,25 Dihydroxycholecalciferol	HMDB
Dihydroxyvitamin D3, 24,25	HMDB
24R,25-Dihydroxycholecalciferol	HMDB
24,25 Dihydroxyvitamin D 3	HMDB
24,25-Dihydroxyvitamin D 3	HMDB
24,25-Dihydroxy-vitamin D	HMDB

Chemical Formula

C₂₇H₄₄O₃

Average Molecular Weight

416.6365

Monoisotopic Molecular Weight

416.329045274

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 Name

24,25-dihydroxyvitamin

CAS Registry Number

40013-87-4

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 Key

FCKJYANJHNLEEP-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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Vitamin D and derivatives

Direct Parent

Vitamin 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 Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Ontology

Status

Detected and Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
Membrane

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	5.47	ALOGPS
logP	4.58	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	13.85	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	60.69 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	126.42 m³·mol⁻¹	ChemAxon
Polarizability	50.98 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-7029200000-c84dd427774a8bd55bf4	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-014i-1312049000-f6115b14a152464f5e1b	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00l2-0119200000-7bcd78fea8093a8230ae	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a5a-2369100000-04f3fb5d7d655a9ce470	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0zgi-4389100000-269c6b355710e7dcd9b8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0004900000-7bbe3ea5eae60b2a2059	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-05mk-0009300000-4137913e2e1e7271894c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0079-9006000000-b2d6915fde38c349870a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00lr-0439300000-d0f3435842264a17a15a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00rx-4579100000-2ffe9e7393dd492716a0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0avi-2960000000-4329739a1dba4656972b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014j-0007900000-764d7cf399a810ff092c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0671-3109300000-5c39962acfb73b3f737d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-01ri-2129300000-7f78982c59e2cf08742c	View in MoNA

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Membrane

Biospecimen Locations

Milk

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Milk	Detected and Quantified	2 IU/100 g	Not Specified	Not Specified	Normal	Park, Y. W; Juáre...	details
Milk	Detected and Quantified	0.000065 uM	Not Specified	Not Specified	Normal	PMID: 6279806	details
Milk	Detected and Quantified	0.0001 +/- 0.00001 uM	Not Specified	Not Specified	Normal	PMID: 6788913	details
Milk	Detected and Quantified	0.00009 +/- 0.00002 uM	Not Specified	Not Specified	Normal	PMID: 6788913	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000430

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB112199

KNApSAcK ID

Not Available

Chemspider ID

17215953

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5419

PubChem Compound

12895043

PDB ID

Not Available

ChEBI ID

89324

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]
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 ]
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

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

Structure for BMDB0000430 (24,25-Dihydroxyvitamin D)

Enzymes