NP-MRD: Showing NP-Card for 23S,25-Dihydroxyvitamin D3 (NP0087608)

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Record Information

Version

2.0

Created at

2022-05-11 16:54:20 UTC

Updated at

2022-05-11 16:54:20 UTC

NP-MRD ID

NP0087608

Secondary Accession Numbers

None

Natural Product Identification

Common Name

23S,25-Dihydroxyvitamin D3

Description

23S,25-dihydroxyvitamin D3, also known as 23,25-dihydroxycholecalciferol, 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. 23S,25-Dihydroxyvitamin D3 was first documented in 1982 (PMID: 6286629). 23S,25-dihydroxyvitamin D3 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02231220492D          

 31 33  0  0  1  0            999 V2000
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   20.1651   -3.0471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8866  -11.7258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7446   -6.7756    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.5253   -6.5241    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.7446   -7.6007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0068   -7.1881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5253   -7.8520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   16.0302   -8.0131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7446   -5.9506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3157   -6.7756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3157   -7.6007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   16.8319   -8.4209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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 31  6  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv0541 02231220492D          

 31 33  0  0  1  0            999 V2000
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   20.1651   -3.0471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0087608

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(C[C@@H](C)[C@H]1CCC2([H])\C(CCC[C@]12C)=C\C=C1\C[C@H](O)CCC1=C)CC(O)(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C27H44O3/c1-18-8-11-22(28)16-21(18)10-9-20-7-6-14-27(5)24(12-13-25(20)27)19(2)15-23(29)17-26(3,4)30/h9-10,19,22-25,28-30H,1,6-8,11-17H2,2-5H3/b20-9+,21-10-/t19-,22-,23?,24-,25?,27-/m1/s1

> <INCHI_KEY>
JVBPQHSRTHJMLM-UXHBOMOISA-N

> <FORMULA>
C27H44O3

> <MOLECULAR_WEIGHT>
416.6365

> <EXACT_MASS>
416.329045274

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
50.88471471401546

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6R)-6-[(1R,4E,7aR)-4-{2-[(1Z,5R)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,4-diol

> <ALOGPS_LOGP>
5.17

> <JCHEM_LOGP>
4.1948335366666685

> <ALOGPS_LOGS>
-4.62

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.645063728485919

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.929132732712148

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3184890847799178

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
126.68649999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.98e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
23,25-dihydroxyvitamin d3

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      34.149  -7.787   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      37.642  -5.688   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      25.922 -21.888   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      31.257 -12.648   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      32.714 -12.178   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      31.257 -14.188   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      33.613 -13.418   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      32.714 -14.657   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      29.923 -11.878   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      33.192 -10.715   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.923 -14.958   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      31.257 -11.108   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      28.589 -12.648   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      28.589 -14.188   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      34.699 -10.397   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      32.164  -9.568   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      29.923 -16.498   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      35.178  -8.933   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      36.685  -8.616   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      28.589 -17.268   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      37.163  -7.152   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      28.589 -18.808   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      35.699  -6.673   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      38.627  -7.630   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      27.255 -19.578   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      29.923 -19.578   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      27.255 -21.118   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      29.923 -21.118   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      28.589 -21.888   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      31.257 -18.808   0.000  0.00  0.00           C+0
HETATM   31  H   UNK     0      31.420 -15.719   0.000  0.00  0.00           H+0
CONECT    1   18                                                            
CONECT    2   21                                                            
CONECT    3   27                                                            
CONECT    4    5    6    9   12                                             
CONECT    5    4    7   10                                                  
CONECT    6    4    8   11   31                                             
CONECT    7    5    8                                                       
CONECT    8    6    7                                                       
CONECT    9    4   13                                                       
CONECT   10    5   15   16                                                  
CONECT   11    6   14   17                                                  
CONECT   12    4                                                            
CONECT   13    9   14                                                       
CONECT   14   11   13                                                       
CONECT   15   10   18                                                       
CONECT   16   10                                                            
CONECT   17   11   20                                                       
CONECT   18    1   15   19                                                  
CONECT   19   18   21                                                       
CONECT   20   17   22                                                       
CONECT   21    2   19   23   24                                             
CONECT   22   20   25   26                                                  
CONECT   23   21                                                            
CONECT   24   21                                                            
CONECT   25   22   27                                                       
CONECT   26   22   28   30                                                  
CONECT   27    3   25   29                                                  
CONECT   28   26   29                                                       
CONECT   29   27   28                                                       
CONECT   30   26                                                            
CONECT   31    6                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

View in JSmol

Synonyms

Value	Source
(3beta,5Z,7E)-9,10-Secocholesta-5,7,10(19)-triene-3,23,25-triol	HMDB
23,25-Dihydroxycholecalciferol	HMDB
23,25-Dihydroxyvitamin D3	HMDB
23S,25-Dihydroxyvitamin D	HMDB
23,25-Dihydroxyvitamin D3, (3beta,5Z,7E,23R)-isomer	HMDB
23S, 25 Dihydroxyvitamin D	HMDB
23,25-Dihydroxyvitamin D3, (3beta,5Z,7E,23S)-isomer	HMDB
23S,25-Dihydroxyvitamin D3	MeSH

Chemical Formula

C₂₇H₄₄O₃

Average Mass

416.6365 Da

Monoisotopic Mass

416.32905 Da

IUPAC Name

(6R)-6-[(1R,4E,7aR)-4-{2-[(1Z,5R)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,4-diol

Traditional Name

23,25-dihydroxyvitamin d3

CAS Registry Number

Not Available

SMILES

OC(C[C@@H](C)[C@H]1CCC2([H])\C(CCC[C@]12C)=C\C=C1\C[C@H](O)CCC1=C)CC(O)(C)C

InChI Identifier

InChI=1S/C27H44O3/c1-18-8-11-22(28)16-21(18)10-9-20-7-6-14-27(5)24(12-13-25(20)27)19(2)15-23(29)17-26(3,4)30/h9-10,19,22-25,28-30H,1,6-8,11-17H2,2-5H3/b20-9+,21-10-/t19-,22-,23?,24-,25?,27-/m1/s1

InChI Key

JVBPQHSRTHJMLM-UXHBOMOISA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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

Physical Properties

State

Not Available

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	5.17	ALOGPS
logP	4.19	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	14.93	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	126.69 m³·mol⁻¹	ChemAxon
Polarizability	50.88 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0006720

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB024038

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13072270

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Napoli JL, Pramanik BC, Partridge JJ, Uskokovic MR, Horst RL: 23S,25-dihydroxyvitamin D3 as a circulating metabolite of vitamin D3. Its role in 25-hydroxyvitamin D3-26,23-lactone biosynthesis. J Biol Chem. 1982 Aug 25;257(16):9634-9. [PubMed:6286629 ]

Showing NP-Card for 23S,25-Dihydroxyvitamin D3 (NP0087608)

MOL for NP0087608 (23S,25-Dihydroxyvitamin D3)

3D MOL for NP0087608 (23S,25-Dihydroxyvitamin D3)

3D SDF for NP0087608 (23S,25-Dihydroxyvitamin D3)

3D-SDF for NP0087608 (23S,25-Dihydroxyvitamin D3)

PDB for NP0087608 (23S,25-Dihydroxyvitamin D3)

3D PDB for NP0087608 (23S,25-Dihydroxyvitamin D3)

SMILES for NP0087608 (23S,25-Dihydroxyvitamin D3)

INCHI for NP0087608 (23S,25-Dihydroxyvitamin D3)

Structure for NP0087608 (23S,25-Dihydroxyvitamin D3)

3D Structure for NP0087608 (23S,25-Dihydroxyvitamin D3)