NP-MRD: Showing NP-Card for 1,25-Dihydroxyvitamin D3-26,23-lactone (NP0086676)

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Record Information

Version

2.0

Created at

2022-05-11 16:27:52 UTC

Updated at

2022-05-11 16:27:52 UTC

NP-MRD ID

NP0086676

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1,25-Dihydroxyvitamin D3-26,23-lactone

Description

1,25-Dihydroxyvitamin D3-26,23-lactone 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. 1,25-Dihydroxyvitamin D3-26,23-lactone is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652305221920522D          

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M  END

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 26  3  1  1  0  0  0
 26 11  1  0  0  0  0
 26 22  1  0  0  0  0
 26 23  1  0  0  0  0
 27  4  1  6  0  0  0
 27 15  1  0  0  0  0
 27 25  1  0  0  0  0
 20 28  1  1  0  0  0
 24 29  1  6  0  0  0
 30 25  2  0  0  0  0
 27 31  1  1  0  0  0
 32 21  1  0  0  0  0
 32 25  1  0  0  0  0
 16 33  1  1  0  0  0
 20 34  1  6  0  0  0
 21 35  1  6  0  0  0
 22 36  1  6  0  0  0
 23 37  1  6  0  0  0
 24 38  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0086676

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@](C)(C[C@@]1([H])C[C@@](C)(O)C(=O)O1)[C@@]1([H])CC[C@@]2([H])C(CCC[C@]12C)=CC=C1C[C@@]([H])(O)C[C@]([H])(O)C1=C

> <INCHI_IDENTIFIER>
InChI=1S/C27H40O5/c1-16(12-21-15-27(4,31)25(30)32-21)22-9-10-23-18(6-5-11-26(22,23)3)7-8-19-13-20(28)14-24(29)17(19)2/h7-8,16,20-24,28-29,31H,2,5-6,9-15H2,1,3-4H3/t16-,20-,21+,22-,23+,24+,26-,27-/m1/s1

> <INCHI_KEY>
WMYIVSWWSRCZFA-CYLANSHFSA-N

> <FORMULA>
C27H40O5

> <MOLECULAR_WEIGHT>
444.6035

> <EXACT_MASS>
444.28757439

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
51.31806011347877

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,5S)-5-[(2R)-2-[(1R,3aS,7aR)-4-{2-[(3S,5R)-3,5-dihydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]propyl]-3-hydroxy-3-methyloxolan-2-one

> <ALOGPS_LOGP>
3.65

> <JCHEM_LOGP>
2.981253377333335

> <ALOGPS_LOGS>
-4.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.397718308932088

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.496968646145163

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7596614720148134

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
126.15239999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.06e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,5S)-5-[(2R)-2-[(1R,3aS,7aR)-4-{2-[(3S,5R)-3,5-dihydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1H-inden-1-yl]propyl]-3-hydroxy-3-methyloxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       2.680  -1.012   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   8.233   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.429   0.541   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.959  -5.551   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   5.923   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.590   6.693   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.257   9.003   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.590  11.313   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.573  -2.898   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.924   9.003   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.590   8.233   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.257  10.543   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.333  -1.652   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.924  10.543   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.797  -3.668   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.333  -4.144   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       0.923  11.313   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       6.258  11.313   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -3.043  -4.574   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       1.001  -4.914   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -1.797  -2.128   0.000  0.00  0.00           O+0
HETATM   33  H   UNK     0       1.174  -1.332   0.000  0.00  0.00           H+0
HETATM   34  H   UNK     0       2.257  12.083   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0      -1.421  -0.564   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0       0.605   1.356   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       3.429   5.144   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0       6.258   9.773   0.000  0.00  0.00           H+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3   26                                                            
CONECT    4   27                                                            
CONECT    5    6   11                                                       
CONECT    6    5   18                                                       
CONECT    7    8   18                                                       
CONECT    8    7   19                                                       
CONECT    9   10   22                                                       
CONECT   10    9   23                                                       
CONECT   11    5   26                                                       
CONECT   12   16   21                                                       
CONECT   13   19   20                                                       
CONECT   14   20   24                                                       
CONECT   15   21   27                                                       
CONECT   16    1   12   22   33                                             
CONECT   17    2   19   24                                                  
CONECT   18    6    7   23                                                  
CONECT   19    8   13   17                                                  
CONECT   20   13   14   28   34                                             
CONECT   21   12   15   32   35                                             
CONECT   22    9   16   26   36                                             
CONECT   23   10   18   26   37                                             
CONECT   24   14   17   29   38                                             
CONECT   25   27   30   32                                                  
CONECT   26    3   11   22   23                                             
CONECT   27    4   15   25   31                                             
CONECT   28   20                                                            
CONECT   29   24                                                            
CONECT   30   25                                                            
CONECT   31   27                                                            
CONECT   32   21   25                                                       
CONECT   33   16                                                            
CONECT   34   20                                                            
CONECT   35   21                                                            
CONECT   36   22                                                            
CONECT   37   23                                                            
CONECT   38   24                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₀O₅

Average Mass

444.6035 Da

Monoisotopic Mass

444.28757 Da

IUPAC Name

(3R,5S)-5-[(2R)-2-[(1R,3aS,7aR)-4-{2-[(3S,5R)-3,5-dihydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]propyl]-3-hydroxy-3-methyloxolan-2-one

Traditional Name

(3R,5S)-5-[(2R)-2-[(1R,3aS,7aR)-4-{2-[(3S,5R)-3,5-dihydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1H-inden-1-yl]propyl]-3-hydroxy-3-methyloxolan-2-one

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(C[C@@]1([H])C[C@@](C)(O)C(=O)O1)[C@@]1([H])CC[C@@]2([H])C(CCC[C@]12C)=CC=C1C[C@@]([H])(O)C[C@]([H])(O)C1=C

InChI Identifier

InChI=1S/C27H40O5/c1-16(12-21-15-27(4,31)25(30)32-21)22-9-10-23-18(6-5-11-26(22,23)3)7-8-19-13-20(28)14-24(29)17(19)2/h7-8,16,20-24,28-29,31H,2,5-6,9-15H2,1,3-4H3/t16-,20-,21+,22-,23+,24+,26-,27-/m1/s1

InChI Key

WMYIVSWWSRCZFA-CYLANSHFSA-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
Steroid lactone
Gamma butyrolactone
Cyclic alcohol
Tertiary alcohol
Tetrahydrofuran
Carboxylic acid ester
Lactone
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Carbonyl group
Organooxygen compound
Organic oxide
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	3.65	ALOGPS
logP	2.98	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	12.5	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	126.15 m³·mol⁻¹	ChemAxon
Polarizability	51.32 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022344

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

122285

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 1,25-Dihydroxyvitamin D3-26,23-lactone (NP0086676)

MOL for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)

3D MOL for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)

3D SDF for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)

3D-SDF for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)

PDB for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)

3D PDB for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)

SMILES for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)

INCHI for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)

Structure for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)

3D Structure for NP0086676 (1,25-Dihydroxyvitamin D3-26,23-lactone)