NP-MRD: Showing NP-Card for prasinoxanthin (NP0212564)

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Record Information

Version

2.0

Created at

2022-09-05 11:16:00 UTC

Updated at

2022-09-05 11:16:00 UTC

NP-MRD ID

NP0212564

Secondary Accession Numbers

None

Natural Product Identification

Common Name

prasinoxanthin

Description

Prasinoxanthin 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, prasinoxanthin is considered to be an isoprenoid. prasinoxanthin is found in Micromonas pusilla and Prasinococcus capsulatus. prasinoxanthin was first documented in 2012 (PMID: 22441568). Based on a literature review very few articles have been published on Prasinoxanthin (PMID: 27491971).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052213162D          

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M  END

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M  END


  Mrv1652309052213162D          

 44 45  0  0  1  0            999 V2000
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   -6.8176  -12.6909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.1064  -11.9157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1031  -12.2784    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -6.0532  -10.8504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2287  -10.8792    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4405  -10.1219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2650  -10.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0033   -9.4223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3907   -8.6939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9535   -7.9942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3408   -7.2658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1653   -7.2370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9036   -6.5661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2909   -5.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8537   -5.1381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2410   -4.4096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8039   -3.7100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9794   -3.7388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1912   -2.9816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7540   -2.2819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1413   -1.5535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7041   -0.8539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8796   -0.8827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0914   -0.1254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6543    0.5742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0416    1.3026    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.8661    1.3314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3033    0.6318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2534    2.0599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8162    2.7595    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.2035    3.4879    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9917    2.7307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6044    2.0023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8629    2.3639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8899    1.5898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
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  7  9  1  0  0  0  0
  7 10  1  0  0  0  0
  2 10  1  0  0  0  0
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 38 39  1  0  0  0  0
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 39 41  1  0  0  0  0
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 35 42  1  0  0  0  0
 42 43  1  0  0  0  0
 42 44  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0212564

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(\C=C\C=C(/C)\C=C\[C@H]1C(C)=C[C@H](O)CC1(C)C)=C/C=C/C=C(\C)/C=C/C=C(\C)C(=O)C[C@]1(O)C(=C)C[C@@H](O)CC1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C40H56O4/c1-28(17-13-18-30(3)21-22-36-32(5)23-34(41)25-38(36,7)8)15-11-12-16-29(2)19-14-20-31(4)37(43)27-40(44)33(6)24-35(42)26-39(40,9)10/h11-23,34-36,41-42,44H,6,24-27H2,1-5,7-10H3/b12-11+,17-13+,19-14+,22-21+,28-15+,29-16+,30-18+,31-20+/t34-,35+,36-,40-/m0/s1

> <INCHI_KEY>
WOJYJHBMWRNRJG-DTJZQRCSSA-N

> <FORMULA>
C40H56O4

> <MOLECULAR_WEIGHT>
600.884

> <EXACT_MASS>
600.417860283

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
100

> <JCHEM_AVERAGE_POLARIZABILITY>
74.39934764925361

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3E,5E,7E,9E,11E,13E,15E,17E)-1-[(1R,4S)-1,4-dihydroxy-2,2-dimethyl-6-methylidenecyclohexyl]-18-[(1R,4R)-4-hydroxy-2,6,6-trimethylcyclohex-2-en-1-yl]-3,7,12,16-tetramethyloctadeca-3,5,7,9,11,13,15,17-octaen-2-one

> <JCHEM_LOGP>
7.498954276000003

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.194914617026441

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.642078395511476

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3913432216953265

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
195.05420000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
prasinoxanthin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0     -14.060 -22.920   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -12.726 -23.690   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -12.726 -25.230   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -11.392 -26.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0     -11.392 -27.540   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0     -10.059 -25.230   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -10.059 -23.690   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -8.542 -23.957   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -9.532 -22.243   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -11.392 -22.920   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0     -10.669 -21.560   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0     -12.115 -21.560   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -11.299 -20.254   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -9.760 -20.308   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0     -12.022 -18.894   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -13.561 -18.841   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -11.206 -17.588   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -11.929 -16.229   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0     -11.113 -14.923   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0     -11.836 -13.563   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -13.375 -13.509   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -11.020 -12.257   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -11.743 -10.897   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -10.927  -9.591   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -11.650  -8.231   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -10.834  -6.925   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -9.295  -6.979   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -11.557  -5.566   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -10.741  -4.260   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -11.464  -2.900   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -10.648  -1.594   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -9.109  -1.648   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -11.371  -0.234   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -10.555   1.072   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -11.278   2.432   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -12.817   2.485   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -13.633   1.179   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -13.540   3.845   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -12.724   5.151   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0     -13.447   6.511   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0     -11.185   5.097   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -10.462   3.738   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -9.077   4.413   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -9.128   2.968   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7    2   11   12                                             
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36   42                                                  
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39                                                       
CONECT   39   38   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   42                                                       
CONECT   42   41   35   43   44                                             
CONECT   43   42                                                            
CONECT   44   42                                                            
MASTER        0    0    0    0    0    0    0    0   44    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₀H₅₆O₄

Average Mass

600.8840 Da

Monoisotopic Mass

600.41786 Da

IUPAC Name

(3E,5E,7E,9E,11E,13E,15E,17E)-1-[(1R,4S)-1,4-dihydroxy-2,2-dimethyl-6-methylidenecyclohexyl]-18-[(1R,4R)-4-hydroxy-2,6,6-trimethylcyclohex-2-en-1-yl]-3,7,12,16-tetramethyloctadeca-3,5,7,9,11,13,15,17-octaen-2-one

Traditional Name

prasinoxanthin

CAS Registry Number

Not Available

SMILES

C\C(\C=C\C=C(/C)\C=C\[C@H]1C(C)=C[C@H](O)CC1(C)C)=C/C=C/C=C(\C)/C=C/C=C(\C)C(=O)C[C@]1(O)C(=C)C[C@@H](O)CC1(C)C

InChI Identifier

InChI=1S/C40H56O4/c1-28(17-13-18-30(3)21-22-36-32(5)23-34(41)25-38(36,7)8)15-11-12-16-29(2)19-14-20-31(4)37(43)27-40(44)33(6)24-35(42)26-39(40,9)10/h11-23,34-36,41-42,44H,6,24-27H2,1-5,7-10H3/b12-11+,17-13+,19-14+,22-21+,28-15+,29-16+,30-18+,31-20+/t34-,35+,36-,40-/m0/s1

InChI Key

WOJYJHBMWRNRJG-DTJZQRCSSA-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
Micromonas pusilla	LOTUS Database	35616633
Prasinococcus capsulatus	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
B'-hydroxy-alpha,beta-unsaturated-ketone
Beta-hydroxy ketone
Alpha-branched alpha,beta-unsaturated-ketone
Acryloyl-group
Cyclic alcohol
Alpha,beta-unsaturated ketone
Tertiary alcohol
Enone
Secondary alcohol
Ketone
Organic oxygen compound
Hydrocarbon derivative
Carbonyl group
Organic oxide
Alcohol
Organooxygen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

C40 isoprenoids (tetraterpenes) (LMPR01070200 )

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	7.5	ChemAxon
pKa (Strongest Acidic)	13.64	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	195.05 m³·mol⁻¹	ChemAxon
Polarizability	74.4 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

Not Available

KNApSAcK ID

C00023034

Chemspider ID

24823161

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15223585

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Jiang T, Chen F, Yu Z, Lu L, Wang Z: Size-dependent depletion and community disturbance of phytoplankton under intensive oyster mariculture based on HPLC pigment analysis in Daya Bay, South China Sea. Environ Pollut. 2016 Dec;219:804-814. doi: 10.1016/j.envpol.2016.07.058. Epub 2016 Aug 1. [PubMed:27491971 ]
Matsumoto T, Kawachi M, Miyashita H, Inagaki Y: Prasinoxanthin is absent in the green-colored dinoflagellate Lepidodinium chlorophorum strain NIES-1868: pigment composition and 18S rRNA phylogeny. J Plant Res. 2012 Nov;125(6):705-11. doi: 10.1007/s10265-012-0486-6. Epub 2012 Mar 23. [PubMed:22441568 ]
LOTUS database [Link]

Showing NP-Card for prasinoxanthin (NP0212564)

MOL for NP0212564 (prasinoxanthin)

3D MOL for NP0212564 (prasinoxanthin)

3D SDF for NP0212564 (prasinoxanthin)

3D-SDF for NP0212564 (prasinoxanthin)

PDB for NP0212564 (prasinoxanthin)

3D PDB for NP0212564 (prasinoxanthin)

SMILES for NP0212564 (prasinoxanthin)

INCHI for NP0212564 (prasinoxanthin)

Structure for NP0212564 (prasinoxanthin)

3D Structure for NP0212564 (prasinoxanthin)