NP-MRD: Showing NP-Card for (5s,6r)-β-carotene 5,6-epoxide (NP0286132)

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Record Information

Version

2.0

Created at

2022-09-09 14:34:51 UTC

Updated at

2022-09-09 14:34:51 UTC

NP-MRD ID

NP0286132

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(5s,6r)-β-carotene 5,6-epoxide

Description

(5S,6R)-beta-carotene 5,6-epoxide belongs to the class of organic compounds known as xanthophylls. These are carotenoids containing an oxygenated carotene backbone. Carotenes are characterized by the presence of two end-groups (mostly cyclohexene rings, but also cyclopentene rings or acyclic groups) linked by a long branched alkyl chain. Carotenes belonging form a subgroup of the carotenoids family. Xanthophylls arise by oxygenation of the carotene backbone. Thus, (5S,6R)-beta-carotene 5,6-epoxide is considered to be an isoprenoid. (5s,6r)-β-carotene 5,6-epoxide is found in Diospyros kaki. Based on a literature review very few articles have been published on (5S,6R)-beta-carotene 5,6-epoxide.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092216342D          

 41 43  0  0  1  0            999 V2000
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M  END

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M  END


  Mrv1652309092216342D          

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   -9.4237   -6.5408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8362   -5.8263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5987   -6.5408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1862   -5.8263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3612   -5.8263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9487   -5.1118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3612   -4.3974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1237   -5.1118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7112   -4.3974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8862   -4.3974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4737   -3.6829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6487   -3.6829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2362   -4.3974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2362   -2.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4112   -2.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9987   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1737   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7612   -2.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7612   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0638   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4763   -0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2382   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4763   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0638    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1908    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9053   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9053   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1908   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5781   -1.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8035   -1.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6612   -8.6842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0292   -8.1539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0292   -9.2145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0737   -9.3987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8987   -9.3987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3112   -8.6842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  2  0  0  0  0
 26 25  1  6  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 26 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
  3 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
 36 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
  2 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0286132

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C/C=C/C=C(\C)/C=C/C=C(\C)/C=C/[C@]12O[C@@]1(C)CCCC2(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C40H56O/c1-31(19-13-21-33(3)24-25-36-35(5)23-15-27-37(36,6)7)17-11-12-18-32(2)20-14-22-34(4)26-30-40-38(8,9)28-16-29-39(40,10)41-40/h11-14,17-22,24-26,30H,15-16,23,27-29H2,1-10H3/b12-11+,19-13+,20-14+,25-24+,30-26+,31-17+,32-18+,33-21+,34-22+/t39-,40+/m0/s1

> <INCHI_KEY>
RVCRIPILOFSMFG-MLLMWRMGSA-N

> <FORMULA>
C40H56O

> <MOLECULAR_WEIGHT>
552.887

> <EXACT_MASS>
552.433116423

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
97

> <JCHEM_AVERAGE_POLARIZABILITY>
72.64749864127013

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,6S)-2,2,6-trimethyl-1-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohex-1-en-1-yl)octadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl]-7-oxabicyclo[4.1.0]heptane

> <JCHEM_LOGP>
10.650283638333335

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.2822405371219325

> <JCHEM_POLAR_SURFACE_AREA>
12.53

> <JCHEM_REFRACTIVITY>
190.34350000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(5S,6R)-β-carotene 5,6-epoxide

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0     -22.981 -13.543   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -22.211 -14.877   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -20.671 -14.877   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -19.901 -13.543   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -18.361 -13.543   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -17.591 -12.209   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -18.361 -10.876   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -16.051 -12.209   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -15.281 -10.876   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -13.741 -10.876   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0     -12.971  -9.542   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -13.741  -8.208   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -11.431  -9.542   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -10.661  -8.208   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -9.121  -8.208   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -8.351  -6.875   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -6.811  -6.875   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.041  -8.208   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.041  -5.541   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.501  -5.541   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.731  -4.207   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.191  -4.207   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.421  -5.541   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.421  -2.874   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.119  -2.874   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.889  -1.540   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.445  -0.770   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       0.889  -0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.119   1.334   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.223   0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.556  -0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.556  -1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.223  -2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.946  -3.670   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.500  -3.670   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -19.901 -16.210   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -18.721 -15.221   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -18.721 -17.200   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -20.671 -17.544   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -22.211 -17.544   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -22.981 -16.210   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   41                                                  
CONECT    3    2    4   36                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28   33                                             
CONECT   27   26   28                                                       
CONECT   28   27   26   29   30                                             
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   26   34   35                                             
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36    3   37   38   39                                             
CONECT   37   36                                                            
CONECT   38   36                                                            
CONECT   39   36   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40    2                                                       
MASTER        0    0    0    0    0    0    0    0   41    0   86    0
END

View in JSmol

Synonyms

Value	Source
(5S,6R)-b-Carotene 5,6-epoxide	Generator
(5S,6R)-Β-carotene 5,6-epoxide	Generator

Chemical Formula

C₄₀H₅₆O

Average Mass

552.8870 Da

Monoisotopic Mass

552.43312 Da

IUPAC Name

(1R,6S)-2,2,6-trimethyl-1-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohex-1-en-1-yl)octadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl]-7-oxabicyclo[4.1.0]heptane

Traditional Name

(5S,6R)-β-carotene 5,6-epoxide

CAS Registry Number

Not Available

SMILES

C\C(\C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C/C=C/C=C(\C)/C=C/C=C(\C)/C=C/[C@]12O[C@@]1(C)CCCC2(C)C

InChI Identifier

InChI=1S/C40H56O/c1-31(19-13-21-33(3)24-25-36-35(5)23-15-27-37(36,6)7)17-11-12-18-32(2)20-14-22-34(4)26-30-40-38(8,9)28-16-29-39(40,10)41-40/h11-14,17-22,24-26,30H,15-16,23,27-29H2,1-10H3/b12-11+,19-13+,20-14+,25-24+,30-26+,31-17+,32-18+,33-21+,34-22+/t39-,40+/m0/s1

InChI Key

RVCRIPILOFSMFG-MLLMWRMGSA-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
Diospyros kaki	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthophylls. These are carotenoids containing an oxygenated carotene backbone. Carotenes are characterized by the presence of two end-groups (mostly cyclohexene rings, but also cyclopentene rings or acyclic groups) linked by a long branched alkyl chain. Carotenes belonging form a subgroup of the carotenoids family. Xanthophylls arise by oxygenation of the carotene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Tetraterpenoids

Direct Parent

Xanthophylls

Alternative Parents

Substituents

Xanthophyll
Oxepane
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

beta-carotene 5,6-epoxide (CHEBI:35309 )
C40 isoprenoids (tetraterpenes) (LMPR01070292 )

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	10.65	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	12.53 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	190.34 m³·mol⁻¹	ChemAxon
Polarizability	72.65 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

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

7827797

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9548874

PDB ID

Not Available

ChEBI ID

35309

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (5s,6r)-β-carotene 5,6-epoxide (NP0286132)

MOL for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)

3D MOL for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)

3D SDF for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)

3D-SDF for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)

PDB for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)

3D PDB for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)

SMILES for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)

INCHI for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)

Structure for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)

3D Structure for NP0286132 ((5s,6r)-β-carotene 5,6-epoxide)