NP-MRD: Showing NP-Card for (1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol (NP0228248)

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Record Information

Version

1.0

Created at

2022-09-06 07:49:37 UTC

Updated at

2022-09-06 07:49:37 UTC

NP-MRD ID

NP0228248

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol

Description

(24R)-1alpha,24-dihydroxy-22-oxavitamin D3, also known as (24R)-1alpha,24-dihydroxy-22-oxacholecalciferol, 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, (24R)-1alpha,24-dihydroxy-22-oxavitamin D3 is considered to be a secosteroid. (1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol is found in Trypanosoma brucei. Based on a literature review very few articles have been published on (24R)-1alpha,24-dihydroxy-22-oxavitamin D3.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062209492D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309062209492D          

 30 32  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0228248

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C26H42O4/c1-16(2)25(29)15-30-18(4)22-10-11-23-19(7-6-12-26(22,23)5)8-9-20-13-21(27)14-24(28)17(20)3/h8-9,16,18,21-25,27-29H,3,6-7,10-15H2,1-2,4-5H3/b19-8+,20-9-/t18-,21+,22+,23-,24-,25-,26+/m0/s1

> <INCHI_KEY>
QBLPQGCPHVNTFS-KJWIQCNYSA-N

> <FORMULA>
C26H42O4

> <MOLECULAR_WEIGHT>
418.618

> <EXACT_MASS>
418.308309832

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
49.990713241526294

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3S,5Z)-5-{2-[(1S,3aS,4E,7aS)-1-[(1S)-1-[(2R)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-octahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol

> <JCHEM_LOGP>
3.3399190396666665

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.569957101109164

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.976762682594178

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7596614720148134

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
123.32260000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3S,5Z)-5-{2-[(1S,3aS,4E,7aS)-1-[(1S)-1-[(2R)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.255  -1.241   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.761  -0.921   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.237   0.544   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.206   1.688   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.700   1.368   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.669   2.513   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.145   3.977   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.115   5.122   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.391   4.802   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.867   3.337   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.012   4.367   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.274   2.711   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.608   3.481   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.608   5.021   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.942   2.711   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       7.275   3.481   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.609   2.711   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       8.609   1.171   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       9.943   3.481   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.276   2.711   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.943   5.021   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.113   1.179   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.607   0.859   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.837   2.192   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -5.743   0.864   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -6.774  -0.280   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -8.280   0.040   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -6.298  -1.745   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -4.791  -2.065   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -4.315  -3.530   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   29                                                  
CONECT    3    2    4   25                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   24                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12   24                                             
CONECT   11   10                                                            
CONECT   12   10   13   22                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   12   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23    6   10                                                  
CONECT   25    3   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28    2   30                                                  
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   64    0
END

View in JSmol

Synonyms

Value	Source
(24R)-1alpha,24-Dihydroxy-22-oxacholecalciferol	ChEBI
(5Z,7E)-(1S,3R,24R)-22-Oxa-9,10-seco-5,7,10(19)-cholestatriene-1,3,24-triol	ChEBI
(24R)-1a,24-Dihydroxy-22-oxacholecalciferol	Generator
(24R)-1Α,24-dihydroxy-22-oxacholecalciferol	Generator
(24R)-1a,24-Dihydroxy-22-oxavitamin D3	Generator
(24R)-1Α,24-dihydroxy-22-oxavitamin D3	Generator

Chemical Formula

C₂₆H₄₂O₄

Average Mass

418.6180 Da

Monoisotopic Mass

418.30831 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C26H42O4/c1-16(2)25(29)15-30-18(4)22-10-11-23-19(7-6-12-26(22,23)5)8-9-20-13-21(27)14-24(28)17(20)3/h8-9,16,18,21-25,27-29H,3,6-7,10-15H2,1-2,4-5H3/b19-8+,20-9-/t18-,21+,22+,23-,24-,25-,26+/m0/s1

InChI Key

QBLPQGCPHVNTFS-KJWIQCNYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Trypanosoma brucei	LOTUS Database	35616633

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
Cyclic alcohol
Secondary alcohol
Ether
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

ether (CHEBI:73923 )
triol (CHEBI:73923 )
hydroxy seco-steroid (CHEBI:73923 )
Vitamin D3 and derivatives (LMST03020056 )

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

7826251

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9547311

PDB ID

Not Available

ChEBI ID

73923

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol (NP0228248)

MOL for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)

3D MOL for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)

3D SDF for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)

3D-SDF for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)

PDB for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)

3D PDB for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)

SMILES for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)

INCHI for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)

Structure for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)

3D Structure for NP0228248 ((1r,3s,5z)-5-{2-[(1s,3as,4e,7as)-1-[(1s)-1-[(2r)-2-hydroxy-3-methylbutoxy]ethyl]-7a-methyl-hexahydro-1h-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol)