NP-MRD: Showing NP-Card for (2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one (NP0203472)

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Record Information

Version

2.0

Created at

2022-09-04 22:56:17 UTC

Updated at

2022-09-04 22:56:17 UTC

NP-MRD ID

NP0203472

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one

Description

(2R)-1-[(2R,3S)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H-1-benzopyran-8-yl]-2-methylbutan-1-one belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. (2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one is found in Hypericum prolificum. Based on a literature review very few articles have been published on (2R)-1-[(2R,3S)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H-1-benzopyran-8-yl]-2-methylbutan-1-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052200562D          

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M  END

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M  END


  Mrv1652309052200562D          

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    6.2398   -3.3113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  1  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
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
  7 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 16 29  1  0  0  0  0
 29 30  1  1  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 29 35  1  0  0  0  0
 13 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0203472

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@H](C)C(=O)C1=C(O)C=C(O)C2=C1O[C@](C)(CC\C=C(/C)CCC=C(C)C)[C@@H](CC=C(C)C)C2

> <INCHI_IDENTIFIER>
InChI=1S/C31H46O4/c1-9-23(7)29(34)28-27(33)19-26(32)25-18-24(16-15-21(4)5)31(8,35-30(25)28)17-11-14-22(6)13-10-12-20(2)3/h12,14-15,19,23-24,32-33H,9-11,13,16-18H2,1-8H3/b22-14+/t23-,24+,31-/m1/s1

> <INCHI_KEY>
KNWRSKBHVUABNU-GEPYNVQKSA-N

> <FORMULA>
C31H46O4

> <MOLECULAR_WEIGHT>
482.705

> <EXACT_MASS>
482.339609961

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
58.493138249237234

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-1-[(2R,3S)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H-1-benzopyran-8-yl]-2-methylbutan-1-one

> <JCHEM_LOGP>
9.26329179666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.236829082110948

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.18776101376801

> <JCHEM_PKA_STRONGEST_BASIC>
-4.612467142587989

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
148.85720000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-1-[(2R,3S)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one

> <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      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.528   0.677   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.518  -1.037   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.044  -2.485   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.561  -2.752   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.551  -1.572   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.024  -0.125   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.067  -1.840   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.594  -3.287   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      12.111  -3.554   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.637  -5.001   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      14.154  -5.269   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.648  -6.181   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   14                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   35                                                  
CONECT   14   13    7   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   18   29                                             
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   16   30   35                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   29   13                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₁H₄₆O₄

Average Mass

482.7050 Da

Monoisotopic Mass

482.33961 Da

IUPAC Name

(2R)-1-[(2R,3S)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H-1-benzopyran-8-yl]-2-methylbutan-1-one

Traditional Name

(2R)-1-[(2R,3S)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one

CAS Registry Number

Not Available

SMILES

CC[C@@H](C)C(=O)C1=C(O)C=C(O)C2=C1O[C@](C)(CC\C=C(/C)CCC=C(C)C)[C@@H](CC=C(C)C)C2

InChI Identifier

InChI=1S/C31H46O4/c1-9-23(7)29(34)28-27(33)19-26(32)25-18-24(16-15-21(4)5)31(8,35-30(25)28)17-11-14-22(6)13-10-12-20(2)3/h12,14-15,19,23-24,32-33H,9-11,13,16-18H2,1-8H3/b22-14+/t23-,24+,31-/m1/s1

InChI Key

KNWRSKBHVUABNU-GEPYNVQKSA-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
Hypericum prolificum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Sesquiterpenoid
Butyrophenone
Chromane
Benzopyran
1-benzopyran
Aryl alkyl ketone
Aryl ketone
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Benzenoid
Vinylogous acid
Ketone
Oxacycle
Ether
Organoheterocyclic compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
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	9.26	ChemAxon
pKa (Strongest Acidic)	8.19	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	148.86 m³·mol⁻¹	ChemAxon
Polarizability	58.49 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

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

163009636

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one (NP0203472)

MOL for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)

3D MOL for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)

3D SDF for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)

3D-SDF for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)

PDB for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)

3D PDB for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)

SMILES for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)

INCHI for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)

Structure for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)

3D Structure for NP0203472 ((2r)-1-[(2r,3s)-2-[(3e)-4,8-dimethylnona-3,7-dien-1-yl]-5,7-dihydroxy-2-methyl-3-(3-methylbut-2-en-1-yl)-3,4-dihydro-1-benzopyran-8-yl]-2-methylbutan-1-one)