NP-MRD: Showing NP-Card for 1-a,24R,25-Trihydroxyvitamin D2 (NP0136771)

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Record Information

Version

2.0

Created at

2022-05-12 15:23:12 UTC

Updated at

2022-05-12 15:23:12 UTC

NP-MRD ID

NP0136771

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-a,24R,25-Trihydroxyvitamin D2

Description

1-A,24R,25-Trihydroxyvitamin D2, also known as 1,24,25-trihydroxyergocalciferol, 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. Thus, 1-a,24R,25-trihydroxyvitamin D2 is considered to be a secosteroid lipid molecule. 1-a,24R,25-Trihydroxyvitamin D2 was first documented in 1986 (PMID: 3490274). 1-A,24R,25-Trihydroxyvitamin D2 is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652304202020002D          

 34 36  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END

  Mrv1652304202020002D          

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 21 23  1  0  0  0  0
 22 24  1  0  0  0  0
 22 26  2  0  0  0  0
 23 25  1  0  0  0  0
 24 25  1  0  0  0  0
 29 19  1  0  0  0  0
 30 19  1  0  0  0  0
 19 31  1  6  0  0  0
 32 29  1  0  0  0  0
 33 29  1  0  0  0  0
 34 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0136771

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C28H44O4/c1-18(13-15-28(6,32)26(3,4)31)23-11-12-24-20(8-7-14-27(23,24)5)9-10-21-16-22(29)17-25(30)19(21)2/h9-10,13,15,18,22-25,29-32H,2,7-8,11-12,14,16-17H2,1,3-6H3/b15-13+,20-9+,21-10-/t18-,22-,23-,24+,25+,27-,28-/m1/s1

> <INCHI_KEY>
KRGCLKZOZQUAFK-ABEKVIRTSA-N

> <FORMULA>
C28H44O4

> <MOLECULAR_WEIGHT>
444.6466

> <EXACT_MASS>
444.323959896

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
52.94837340032535

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3S,5Z)-5-{2-[(1R,3aS,4E,7aR)-1-[(2R,3E,5R)-5,6-dihydroxy-5,6-dimethylhept-3-en-2-yl]-7a-methyl-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol

> <ALOGPS_LOGP>
4.40

> <JCHEM_LOGP>
3.350399861333333

> <ALOGPS_LOGS>
-4.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.323915753914449

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.370632167598409

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7596614720148134

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
133.49479999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.32e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3S,5Z)-5-{2-[(1R,3aS,4E,7aR)-1-[(2R,3E,5R)-5,6-dihydroxy-5,6-dimethylhept-3-en-2-yl]-7a-methyl-hexahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol

> <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  O   UNK     0      25.718 -21.521   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      31.053 -21.521   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      31.053 -12.281   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      32.510 -11.812   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      31.053 -13.821   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      33.409 -13.051   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      32.510 -14.291   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      29.719 -11.511   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      32.988 -10.348   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      29.719 -14.591   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      31.053 -10.741   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      28.386 -12.281   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      28.386 -13.821   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      31.960  -9.202   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      34.495 -10.031   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      29.719 -16.131   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      34.974  -8.567   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      28.386 -16.901   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      36.481  -8.249   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      28.386 -18.441   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      27.052 -19.211   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      29.719 -19.211   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      27.052 -20.751   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      29.719 -20.751   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      28.386 -21.521   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      31.053 -18.441   0.000  0.00  0.00           C+0
HETATM   27  H   UNK     0      33.727 -11.621   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0      31.183 -15.046   0.000  0.00  0.00           H+0
HETATM   29  C   UNK     0      36.959  -6.786   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      37.509  -9.396   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      35.452  -7.103   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      35.931  -5.639   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      38.466  -6.468   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      38.047  -7.875   0.000  0.00  0.00           C+0
CONECT    1   23                                                            
CONECT    2   24                                                            
CONECT    3    4    5    8   11                                             
CONECT    4    3    6    9   27                                             
CONECT    5    3    7   10   28                                             
CONECT    6    4    7                                                       
CONECT    7    5    6                                                       
CONECT    8    3   12                                                       
CONECT    9    4   14   15                                                  
CONECT   10    5   13   16                                                  
CONECT   11    3                                                            
CONECT   12    8   13                                                       
CONECT   13   10   12                                                       
CONECT   14    9                                                            
CONECT   15    9   17                                                       
CONECT   16   10   18                                                       
CONECT   17   15   19                                                       
CONECT   18   16   20                                                       
CONECT   19   17   29   30   31                                             
CONECT   20   18   21   22                                                  
CONECT   21   20   23                                                       
CONECT   22   20   24   26                                                  
CONECT   23    1   21   25                                                  
CONECT   24    2   22   25                                                  
CONECT   25   23   24                                                       
CONECT   26   22                                                            
CONECT   27    4                                                            
CONECT   28    5                                                            
CONECT   29   19   32   33   34                                             
CONECT   30   19                                                            
CONECT   31   19                                                            
CONECT   32   29                                                            
CONECT   33   29                                                            
CONECT   34   29                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Value	Source
(24R)-1alpha,24,25-Trihydroxyergocalciferol	HMDB
(24R)-1alpha,24,25-Trihydroxyvitamin D2	HMDB
(5Z,7E,22E)-(1S,3R,24R)-9,10-Seco-5,7,10(19),22-ergostatetraene-1,3,24,25-tetrol	HMDB
1-alpha,24R,25-Trihydroxyvitamin D2	HMDB
1,24,25-Trihydroxyergocalciferol	HMDB
1,24,25-Trihydroxyvitamin D2	HMDB
(24R)-1a,24,25-Trihydroxyvitamin D2 / (24R)-1a,24,25-trihydroxyergocalciferol	HMDB
(24R)-1Α,24,25-trihydroxyvitamin D2 / (24R)-1α,24,25-trihydroxyergocalciferol	HMDB

Chemical Formula

C₂₈H₄₄O₄

Average Mass

444.6466 Da

Monoisotopic Mass

444.32396 Da

IUPAC Name

(1R,3S,5Z)-5-{2-[(1R,3aS,4E,7aR)-1-[(2R,3E,5R)-5,6-dihydroxy-5,6-dimethylhept-3-en-2-yl]-7a-methyl-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol

Traditional Name

(1R,3S,5Z)-5-{2-[(1R,3aS,4E,7aR)-1-[(2R,3E,5R)-5,6-dihydroxy-5,6-dimethylhept-3-en-2-yl]-7a-methyl-hexahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C28H44O4/c1-18(13-15-28(6,32)26(3,4)31)23-11-12-24-20(8-7-14-27(23,24)5)9-10-21-16-22(29)17-25(30)19(21)2/h9-10,13,15,18,22-25,29-32H,2,7-8,11-12,14,16-17H2,1,3-6H3/b15-13+,20-9+,21-10-/t18-,22-,23-,24+,25+,27-,28-/m1/s1

InChI Key

KRGCLKZOZQUAFK-ABEKVIRTSA-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 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

Vitamin D2 and derivatives (LMST03010051 )

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	4.4	ALOGPS
logP	3.35	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	13.37	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	133.49 m³·mol⁻¹	ChemAxon
Polarizability	52.95 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	No	ChemAxon

External Links

HMDB ID

HMDB0006227

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023847

KNApSAcK ID

Not Available

Chemspider ID

7826193

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

2290317

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9547253

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Reddy GS, Tserng KY: Isolation and identification of 1,24,25-trihydroxyvitamin D2, 1,24,25,28-tetrahydroxyvitamin D2, and 1,24,25,26-tetrahydroxyvitamin D2: new metabolites of 1,25-dihydroxyvitamin D2 produced in rat kidney. Biochemistry. 1986 Sep 9;25(18):5328-36. doi: 10.1021/bi00366a051. [PubMed:3490274 ]

Showing NP-Card for 1-a,24R,25-Trihydroxyvitamin D2 (NP0136771)

MOL for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)

3D MOL for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)

3D SDF for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)

3D-SDF for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)

PDB for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)

3D PDB for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)

SMILES for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)

INCHI for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)

Structure for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)

3D Structure for NP0136771 (1-a,24R,25-Trihydroxyvitamin D2)