NP-MRD: Showing NP-Card for 9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid (NP0207899)

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Record Information

Version

2.0

Created at

2022-09-05 04:41:03 UTC

Updated at

2022-09-05 04:41:03 UTC

NP-MRD ID

NP0207899

Secondary Accession Numbers

None

Natural Product Identification

Common Name

9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid

Description

9-(6-Hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid 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. 9-(6-Hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 04121516342D          

 31 32  0  0  0  0            999 V2000
   -6.6658    4.4168    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8533    4.2735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5712    3.4983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7587    3.3550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4765    2.5798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6641    2.4365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3819    1.6613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5694    1.5180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2873    0.7428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4748    0.5995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1926   -0.1757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3802   -0.3190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0980   -1.0942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4323   -2.0127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.3230    4.9055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
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  7  8  1  4  0  0  0
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  6 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
  2 31  1  0  0  0  0
M  END

     RDKit          3D

 69 70  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv0541 04121516342D          

 31 32  0  0  0  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
> <DATABASE_ID>
NP0207899

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCCC(=CCCC(C)=CCCC1(C)CCC2=CC(O)=CC(C)=C2O1)C(O)=O

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

> <INCHI_KEY>
CWYYWDRQIIFZHK-UHFFFAOYSA-N

> <FORMULA>
C27H38O4

> <MOLECULAR_WEIGHT>
426.597

> <EXACT_MASS>
426.277009704

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
50.99696135263562

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid

> <ALOGPS_LOGP>
6.12

> <JCHEM_LOGP>
7.455828636333333

> <ALOGPS_LOGS>
-5.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.141678936419815

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.135538408356064

> <JCHEM_PKA_STRONGEST_BASIC>
-4.852271747426285

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
129.55889999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.32e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-APR-15         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     -10.399   6.530   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -8.883   6.263   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -8.356   4.816   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.840   4.548   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.313   3.101   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.796   2.834   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.270   1.387   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.753   1.119   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.226  -0.328   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.710  -0.595   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.183  -2.043   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.807  -3.757   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.763   2.299   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -5.850   5.728   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -4.333   5.460   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -6.376   7.175   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -9.936   9.157   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   31                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   28                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   27                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   26                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   25                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   18   26                                                  
CONECT   26   25   14                                                       
CONECT   27   10                                                            
CONECT   28    6   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31    2                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

View in JSmol

Synonyms

Value	Source
9-(6-Hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoate	Generator

Chemical Formula

C₂₇H₃₈O₄

Average Mass

426.5970 Da

Monoisotopic Mass

426.27701 Da

IUPAC Name

9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid

Traditional Name

9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid

CAS Registry Number

Not Available

SMILES

CC(C)=CCCC(=CCCC(C)=CCCC1(C)CCC2=CC(O)=CC(C)=C2O1)C(O)=O

InChI Identifier

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

InChI Key

CWYYWDRQIIFZHK-UHFFFAOYSA-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

Not Available

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
Chromane
Benzopyran
1-benzopyran
Medium-chain fatty acid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Branched fatty acid
Hydroxy fatty acid
Heterocyclic fatty acid
Phenol
Methyl-branched fatty acid
Unsaturated fatty acid
Benzenoid
Fatty acid
Fatty acyl
Oxacycle
Carboxylic acid derivative
Carboxylic acid
Organoheterocyclic compound
Ether
Monocarboxylic acid or derivatives
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Carbonyl group
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	6.12	ALOGPS
logP	7.46	ChemAxon
logS	-5.8	ALOGPS
pKa (Strongest Acidic)	5.14	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	129.56 m³·mol⁻¹	ChemAxon
Polarizability	51 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

90830796

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid (NP0207899)

MOL for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)

3D MOL for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)

3D SDF for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)

3D-SDF for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)

PDB for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)

3D PDB for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)

SMILES for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)

INCHI for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)

Structure for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)

3D Structure for NP0207899 (9-(6-hydroxy-2,8-dimethyl-3,4-dihydro-1-benzopyran-2-yl)-6-methyl-2-(4-methylpent-3-en-1-yl)nona-2,6-dienoic acid)