NP-MRD: Showing NP-Card for (3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol (NP0250524)

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Record Information

Version

2.0

Created at

2022-09-07 13:22:00 UTC

Updated at

2022-09-07 13:22:01 UTC

NP-MRD ID

NP0250524

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol

Description

(3E,5R,7E)-1-(6-hydroxy-2,8-dimethyl-2H-chromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol belongs to the class of organic compounds known as tocotrienols. These are vitamin E derivatives containing an unsaturated trimethyltrideca-3,7,11-trien-1-yl chain attached to the carbon C6 atom of a benzopyran ring system. The differ from tocopherols that contain a saturated trimethyltridecyl chain. (3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol is found in Sargassum siliquastrum. Based on a literature review very few articles have been published on (3E,5R,7E)-1-(6-hydroxy-2,8-dimethyl-2H-chromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072215222D          

 31 32  0  0  1  0            999 V2000
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   -5.8533    4.2735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309072215222D          

 31 32  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0250524

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC\C(C)=C\C(O)[C@H](O)C(\C)=C\CCC1(C)OC2=C(C)C=C(O)C=C2C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C27H38O4/c1-18(2)9-7-10-19(3)15-24(29)25(30)20(4)11-8-13-27(6)14-12-22-17-23(28)16-21(5)26(22)31-27/h9,11-12,14-17,24-25,28-30H,7-8,10,13H2,1-6H3/b19-15+,20-11+/t24?,25-,27?/m1/s1

> <INCHI_KEY>
NLMRJUCJUFPPBR-JVOKAKCTSA-N

> <FORMULA>
C27H38O4

> <MOLECULAR_WEIGHT>
426.597

> <EXACT_MASS>
426.277009704

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
51.221395031547786

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3E,5R,7E)-1-(6-hydroxy-2,8-dimethyl-2H-chromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol

> <JCHEM_LOGP>
5.991014626666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.358506412132204

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.97151996163393

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3387106919383918

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
131.52729999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3E,5R,7E)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0     -12.443   8.245   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -10.926   7.977   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -9.936   9.157   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -10.399   6.530   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -8.883   6.263   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -8.356   4.816   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.840   4.548   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.850   5.728   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.313   3.101   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.796   2.834   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.806   4.013   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -4.270   1.387   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -5.259   0.207   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -2.753   1.119   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.763   2.299   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.226  -0.328   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.710  -0.595   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.183  -2.043   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.807  -3.757   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21   31                                             
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   30                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   23   31                                                  
CONECT   31   30   19                                                       
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₈O₄

Average Mass

426.5970 Da

Monoisotopic Mass

426.27701 Da

IUPAC Name

(3E,5R,7E)-1-(6-hydroxy-2,8-dimethyl-2H-chromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol

Traditional Name

(3E,5R,7E)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol

CAS Registry Number

Not Available

SMILES

CC(C)=CCC\C(C)=C\C(O)[C@H](O)C(\C)=C\CCC1(C)OC2=C(C)C=C(O)C=C2C=C1

InChI Identifier

InChI=1S/C27H38O4/c1-18(2)9-7-10-19(3)15-24(29)25(30)20(4)11-8-13-27(6)14-12-22-17-23(28)16-21(5)26(22)31-27/h9,11-12,14-17,24-25,28-30H,7-8,10,13H2,1-6H3/b19-15+,20-11+/t24?,25-,27?/m1/s1

InChI Key

NLMRJUCJUFPPBR-JVOKAKCTSA-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
Sargassum siliquastrum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tocotrienols. These are vitamin E derivatives containing an unsaturated trimethyltrideca-3,7,11-trien-1-yl chain attached to the carbon C6 atom of a benzopyran ring system. The differ from tocopherols that contain a saturated trimethyltridecyl chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Quinone and hydroquinone lipids

Direct Parent

Tocotrienols

Alternative Parents

Substituents

Tocotrienol
Diterpenoid
1-benzopyran
Benzopyran
Fatty alcohol
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Fatty acyl
Benzenoid
Secondary alcohol
1,2-diol
Oxacycle
Organoheterocyclic compound
Ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	5.99	ChemAxon
pKa (Strongest Acidic)	9.97	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.92 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	131.53 m³·mol⁻¹	ChemAxon
Polarizability	51.22 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	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

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

163001660

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol (NP0250524)

MOL for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)

3D MOL for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)

3D SDF for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)

3D-SDF for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)

PDB for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)

3D PDB for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)

SMILES for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)

INCHI for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)

Structure for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)

3D Structure for NP0250524 ((3e,5r,7e)-1-(6-hydroxy-2,8-dimethylchromen-2-yl)-4,8,12-trimethyltrideca-3,7,11-triene-5,6-diol)