NP-MRD: Showing NP-Card for 2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one (NP0327690)

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Record Information

Version

2.0

Created at

2022-09-12 10:29:49 UTC

Updated at

2022-09-12 10:29:49 UTC

NP-MRD ID

NP0327690

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one

Description

2-(3,7-Dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)-9H-xanthen-9-one belongs to the class of organic compounds known as 4-prenylated xanthones. These are organic compounds containing a C5-isoprenoid group linked to a xanthone moiety at the 4-position. Xanthone is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring that carries a ketone group. 2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one is found in Cratoxylum cochinchinense. 2-(3,7-Dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)-9H-xanthen-9-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171522282D          

 33 35  0  0  0  0            999 V2000
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    0.0000   -4.1250    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


  Mrv1533004171522282D          

 33 35  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0327690

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCCC(C)=CCC1=C(O)C(CC=C(C)C)=C2OC3=CC=C(O)C=C3C(=O)C2=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O5/c1-16(2)7-6-8-18(5)10-13-20-25(30)21(12-9-17(3)4)28-24(26(20)31)27(32)22-15-19(29)11-14-23(22)33-28/h7,9-11,14-15,29-31H,6,8,12-13H2,1-5H3

> <INCHI_KEY>
KZDOPFMALKAMOV-UHFFFAOYSA-N

> <FORMULA>
C28H32O5

> <MOLECULAR_WEIGHT>
448.559

> <EXACT_MASS>
448.22497413

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
51.06450032406562

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)-9H-xanthen-9-one

> <ALOGPS_LOGP>
5.90

> <JCHEM_LOGP>
7.815792529000001

> <ALOGPS_LOGS>
-5.28

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.705334253274497

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.1897095554551465

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7665525185616526

> <JCHEM_POLAR_SURFACE_AREA>
86.99

> <JCHEM_REFRACTIVITY>
135.0472

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.37e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      -2.667 -13.860   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+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  -5.390   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   33                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   32                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   30                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   18                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   12   19   29                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   26                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   20   27                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   18   30                                                  
CONECT   30   29    9   31                                                  
CONECT   31   30                                                            
CONECT   32    6                                                            
CONECT   33    2                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₂O₅

Average Mass

448.5590 Da

Monoisotopic Mass

448.22497 Da

IUPAC Name

2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)-9H-xanthen-9-one

Traditional Name

2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one

CAS Registry Number

Not Available

SMILES

CC(C)=CCCC(C)=CCC1=C(O)C(CC=C(C)C)=C2OC3=CC=C(O)C=C3C(=O)C2=C1O

InChI Identifier

InChI=1S/C28H32O5/c1-16(2)7-6-8-18(5)10-13-20-25(30)21(12-9-17(3)4)28-24(26(20)31)27(32)22-15-19(29)11-14-23(22)33-28/h7,9-11,14-15,29-31H,6,8,12-13H2,1-5H3

InChI Key

KZDOPFMALKAMOV-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

Species Name	Source	Reference
Cratoxylum cochinchinense	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 4-prenylated xanthones. These are organic compounds containing a C5-isoprenoid group linked to a xanthone moiety at the 4-position. Xanthone is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring that carries a ketone group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

4-prenylated xanthones

Alternative Parents

Substituents

4-prenylated xanthone
2-prenylated xanthone
Chromone
Aromatic monoterpenoid
Monoterpenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Oxacycle
Polyol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen 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	5.9	ALOGPS
logP	7.82	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	7.19	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	135.05 m³·mol⁻¹	ChemAxon
Polarizability	51.06 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	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

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

85503167

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one (NP0327690)

MOL for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)

3D MOL for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)

3D SDF for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)

3D-SDF for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)

PDB for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)

3D PDB for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)

SMILES for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)

INCHI for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)

Structure for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)

3D Structure for NP0327690 (2-(3,7-dimethylocta-2,6-dien-1-yl)-1,3,7-trihydroxy-4-(3-methylbut-2-en-1-yl)xanthen-9-one)