NP-MRD: Showing NP-Card for 25,26-dihydroxyvitamin D (NP0136756)

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Record Information

Version

2.0

Created at

2022-05-12 15:22:47 UTC

Updated at

2022-05-12 15:22:47 UTC

NP-MRD ID

NP0136756

Secondary Accession Numbers

None

Natural Product Identification

Common Name

25,26-dihydroxyvitamin D

Description

25,26-Dihydroxyvitamin D belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. 25,26-Dihydroxyvitamin D is an extremely weak basic (essentially neutral) compound (based on its pKa). However, rigorous examination has unambiguously excluded 25S,26-(OH)2D3, the naturally occurring form as a significant lactone precursor. 25,26-(OH)2D3 is a renal microsomal 25-OH-D3 metabolite, whose plasma concentration increases during vitamin D excess concomitantly with an increase in the concentration of lactone. This observation considered with the related structural features of 25,26-(OH)2D3 and lactone (both are oxidized at (C-26) suggested that 25,26(OH)2D3, a metabolite of unknown function, could be a precursor to lactone. 25,26-dihydroxyvitamin D was first documented in 1979 (PMID: 227368). In fact, it has been reported that functionalization of C-26 and subsequent lactone formation occurs exclusively in kidney.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304202019452D          

 32 34  0  0  1  0            999 V2000
   13.4497  -11.4854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4497  -12.3104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1642  -12.7229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8786  -12.3104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8786  -11.4854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1642  -11.0729    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.1642  -10.2479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1642  -13.5479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5932  -12.7229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5932  -13.5479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3076  -13.9604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3076  -14.7854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0221  -15.1979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7365  -14.7854    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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   17.0221  -13.5479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 17 32  1  1  0  0  0
M  END

     RDKit          3D

 74 76  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652304202019452D          

 32 34  0  0  1  0            999 V2000
   13.4497  -11.4854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4497  -12.3104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   14.8786  -11.4854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 14 30  1  6  0  0  0
 15 31  1  1  0  0  0
 17 32  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0136756

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12CC[C@]([H])([C@H](C)CCCC(C)(O)CO)[C@@]1(C)CC\C(C2)=C\C=C1\C[C@@H](O)CCC1=C

> <INCHI_IDENTIFIER>
InChI=1S/C27H44O3/c1-19-7-11-24(29)17-22(19)9-8-21-13-15-27(4)23(16-21)10-12-25(27)20(2)6-5-14-26(3,30)18-28/h8-9,20,23-25,28-30H,1,5-7,10-18H2,2-4H3/b21-8-,22-9-/t20-,23+,24+,25-,26?,27+/m1/s1

> <INCHI_KEY>
WWGCQHXFACVYPT-JKVVTCAUSA-N

> <FORMULA>
C27H44O3

> <MOLECULAR_WEIGHT>
416.6365

> <EXACT_MASS>
416.329045274

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
52.241966073050094

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6R)-6-[(1R,3aS,5Z,7aS)-5-{2-[(1Z,5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-1,2-diol

> <ALOGPS_LOGP>
5.14

> <JCHEM_LOGP>
4.607436103000002

> <ALOGPS_LOGS>
-4.73

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.48565163125678

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.03837592492842

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3184890847125637

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
126.60429999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.82e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
25,26-dihydroxyvitamin D

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0      25.106 -21.439   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      25.106 -22.979   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      26.440 -23.749   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.773 -22.979   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      27.773 -21.439   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      26.440 -20.669   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      26.440 -19.129   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      26.440 -25.289   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      29.107 -23.749   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      29.107 -25.289   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      30.441 -26.059   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      30.441 -27.599   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      31.775 -28.369   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      33.108 -27.599   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      33.108 -26.059   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      31.775 -25.289   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      34.573 -28.075   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      35.478 -26.829   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      34.573 -25.583   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      35.049 -29.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      34.018 -30.684   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      36.555 -29.860   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      37.031 -31.325   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      38.537 -31.645   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      39.013 -33.110   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      40.520 -33.430   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      40.996 -34.894   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      37.983 -34.254   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      37.507 -32.789   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      33.269 -29.131   0.000  0.00  0.00           C+0
HETATM   31  H   UNK     0      33.269 -24.528   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0      36.094 -28.316   0.000  0.00  0.00           H+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    3                                                            
CONECT    9    4   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   17   30                                             
CONECT   15   14   16   19   31                                             
CONECT   16   15   11                                                       
CONECT   17   14   18   20   32                                             
CONECT   18   17   19                                                       
CONECT   19   18   15                                                       
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   28   29                                             
CONECT   26   25   27                                                       
CONECT   27   26                                                            
CONECT   28   25                                                            
CONECT   29   25                                                            
CONECT   30   14                                                            
CONECT   31   15                                                            
CONECT   32   17                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

View in JSmol

Synonyms

Value	Source
25,26-Dihydroxycholecalciferol	HMDB
25,26-Dihydroxyvitamin D3	HMDB
9,10-Secocholesta-5,7,10(19)-triene-3b,25,26-triol	HMDB

Chemical Formula

C₂₇H₄₄O₃

Average Mass

416.6365 Da

Monoisotopic Mass

416.32905 Da

IUPAC Name

(6R)-6-[(1R,3aS,5Z,7aS)-5-{2-[(1Z,5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-1,2-diol

Traditional Name

25,26-dihydroxyvitamin D

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC[C@]([H])([C@H](C)CCCC(C)(O)CO)[C@@]1(C)CC\C(C2)=C\C=C1\C[C@@H](O)CCC1=C

InChI Identifier

InChI=1S/C27H44O3/c1-19-7-11-24(29)17-22(19)9-8-21-13-15-27(4)23(16-21)10-12-25(27)20(2)6-5-14-26(3,30)18-28/h8-9,20,23-25,28-30H,1,5-7,10-18H2,2-4H3/b21-8-,22-9-/t20-,23+,24+,25-,26?,27+/m1/s1

InChI Key

WWGCQHXFACVYPT-JKVVTCAUSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Sesquiterpenoid
Fatty alcohol
Fatty acyl
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
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	5.14	ALOGPS
logP	4.61	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	14.04	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	7	ChemAxon
Refractivity	126.6 m³·mol⁻¹	ChemAxon
Polarizability	52.24 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

HMDB0001420

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB021794

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

53477727

PDB ID

Not Available

ChEBI ID

89079

Good Scents ID

Not Available

References

General References

Shepard RM, Horst RL, Hamstra AJ, DeLuca HF: Determination of vitamin D and its metabolites in plasma from normal and anephric man. Biochem J. 1979 Jul 15;182(1):55-69. [PubMed:227368 ]

Showing NP-Card for 25,26-dihydroxyvitamin D (NP0136756)

MOL for NP0136756 (25,26-dihydroxyvitamin D)

3D MOL for NP0136756 (25,26-dihydroxyvitamin D)

3D SDF for NP0136756 (25,26-dihydroxyvitamin D)

3D-SDF for NP0136756 (25,26-dihydroxyvitamin D)

PDB for NP0136756 (25,26-dihydroxyvitamin D)

3D PDB for NP0136756 (25,26-dihydroxyvitamin D)

SMILES for NP0136756 (25,26-dihydroxyvitamin D)

INCHI for NP0136756 (25,26-dihydroxyvitamin D)

Structure for NP0136756 (25,26-dihydroxyvitamin D)

3D Structure for NP0136756 (25,26-dihydroxyvitamin D)