NP-MRD: Showing NP-Card for cochinchinone A (NP0031818)

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Record Information

Version

2.0

Created at

2021-06-19 22:47:31 UTC

Updated at

2021-06-30 00:00:38 UTC

NP-MRD ID

NP0031818

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cochinchinone A

Provided By

JEOL Database JEOL Logo

Description

Cochinchinone A 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. Cochinchinone A is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. cochinchinone A is found in Cratoxylum cochinchinense and Cratoxylum formosum. cochinchinone A was first documented in 2011 (PMID: 21428375). Based on a literature review very few articles have been published on cochinchinone A.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202100473D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306202100473D          

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  9  7  2  0  0  0  0
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M  END
> <DATABASE_ID>
NP0031818

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C2=C(OC3=C(C2=O)C(O[H])=C(C(O[H])=C3C([H])([H])C(\[H])=C(/C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O5/c1-16(2)7-6-8-18(5)10-13-21-25(30)20(12-9-17(3)4)26(31)24-27(32)22-15-19(29)11-14-23(22)33-28(21)24/h7,9-11,14-15,29-31H,6,8,12-13H2,1-5H3/b18-10+

> <INCHI_KEY>
ZHJQVNDLFGICFY-VCHYOVAHSA-N

> <FORMULA>
C28H32O5

> <MOLECULAR_WEIGHT>
448.559

> <EXACT_MASS>
448.22497413

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
50.03991817058446

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
5.91

> <JCHEM_LOGP>
7.815792529000001

> <ALOGPS_LOGS>
-5.28

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.705334994800396

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.189709692703025

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7665525483126614

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
135.04719999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.33e-03 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 65 67  0  0  0  0  0  0  0  0999 V2000
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M  END

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0       1.079  -0.253  -2.841  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.733  -1.671  -2.466  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.870  -2.436  -1.849  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.506  -2.152  -2.691  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.047  -3.525  -2.383  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.326  -3.489  -1.528  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.141  -2.860  -0.157  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.333  -3.674   0.815  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.680  -1.651   0.104  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.573  -0.818   1.353  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.757   0.438   1.105  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.377   1.624   0.664  0.00  0.00           C+0
HETATM   13  O   UNK     0      -3.743   1.605   0.544  0.00  0.00           O+0
HETATM   14  C   UNK     0      -1.640   2.781   0.347  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.309   4.036  -0.179  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.959   4.838   0.919  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.240   5.249   1.015  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.694   6.051   2.208  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.322   4.997   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.247   2.736   0.518  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.470   3.872   0.231  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.386   1.566   0.963  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.848   1.506   1.123  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.547   2.484   0.881  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.430   0.240   1.576  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.812   0.104   1.736  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.319  -1.116   2.167  0.00  0.00           C+0
HETATM   28  O   UNK     0       5.657  -1.308   2.341  0.00  0.00           O+0
HETATM   29  C   UNK     0       3.472  -2.187   2.437  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.093  -2.040   2.273  0.00  0.00           C+0
HETATM   31  C   UNK     0       1.569  -0.821   1.838  0.00  0.00           C+0
HETATM   32  O   UNK     0       0.210  -0.754   1.692  0.00  0.00           O+0
HETATM   33  C   UNK     0      -0.359   0.422   1.253  0.00  0.00           C+0
HETATM   34  H   UNK     0       0.229   0.283  -3.278  0.00  0.00           H+0
HETATM   35  H   UNK     0       1.401   0.306  -1.957  0.00  0.00           H+0
HETATM   36  H   UNK     0       1.892  -0.243  -3.575  0.00  0.00           H+0
HETATM   37  H   UNK     0       1.591  -3.430  -1.496  0.00  0.00           H+0
HETATM   38  H   UNK     0       2.677  -2.558  -2.579  0.00  0.00           H+0
HETATM   39  H   UNK     0       2.269  -1.889  -0.990  0.00  0.00           H+0
HETATM   40  H   UNK     0      -1.236  -1.488  -3.155  0.00  0.00           H+0
HETATM   41  H   UNK     0      -1.290  -4.008  -3.338  0.00  0.00           H+0
HETATM   42  H   UNK     0      -0.306  -4.168  -1.903  0.00  0.00           H+0
HETATM   43  H   UNK     0      -2.699  -4.513  -1.398  0.00  0.00           H+0
HETATM   44  H   UNK     0      -3.111  -2.962  -2.088  0.00  0.00           H+0
HETATM   45  H   UNK     0      -0.292  -3.741   0.486  0.00  0.00           H+0
HETATM   46  H   UNK     0      -1.333  -3.267   1.828  0.00  0.00           H+0
HETATM   47  H   UNK     0      -1.739  -4.689   0.883  0.00  0.00           H+0
HETATM   48  H   UNK     0      -3.252  -1.162  -0.686  0.00  0.00           H+0
HETATM   49  H   UNK     0      -3.584  -0.556   1.688  0.00  0.00           H+0
HETATM   50  H   UNK     0      -2.151  -1.371   2.197  0.00  0.00           H+0
HETATM   51  H   UNK     0      -4.074   2.516   0.617  0.00  0.00           H+0
HETATM   52  H   UNK     0      -1.584   4.681  -0.689  0.00  0.00           H+0
HETATM   53  H   UNK     0      -3.013   3.743  -0.964  0.00  0.00           H+0
HETATM   54  H   UNK     0      -2.268   5.117   1.716  0.00  0.00           H+0
HETATM   55  H   UNK     0      -5.064   7.030   1.889  0.00  0.00           H+0
HETATM   56  H   UNK     0      -5.501   5.527   2.731  0.00  0.00           H+0
HETATM   57  H   UNK     0      -3.887   6.219   2.929  0.00  0.00           H+0
HETATM   58  H   UNK     0      -5.739   5.947  -0.348  0.00  0.00           H+0
HETATM   59  H   UNK     0      -4.976   4.454  -0.881  0.00  0.00           H+0
HETATM   60  H   UNK     0      -6.129   4.411   0.452  0.00  0.00           H+0
HETATM   61  H   UNK     0       1.424   3.685   0.389  0.00  0.00           H+0
HETATM   62  H   UNK     0       4.466   0.945   1.525  0.00  0.00           H+0
HETATM   63  H   UNK     0       6.126  -0.485   2.122  0.00  0.00           H+0
HETATM   64  H   UNK     0       3.885  -3.135   2.773  0.00  0.00           H+0
HETATM   65  H   UNK     0       1.431  -2.876   2.482  0.00  0.00           H+0
CONECT    1    2   34   35   36                                             
CONECT    2    4    1    3                                                  
CONECT    3    2   37   38   39                                             
CONECT    4    5    2   40                                                  
CONECT    5    6    4   41   42                                             
CONECT    6    7    5   43   44                                             
CONECT    7    9    6    8                                                  
CONECT    8    7   45   46   47                                             
CONECT    9   10    7   48                                                  
CONECT   10   11    9   49   50                                             
CONECT   11   10   12   33                                                  
CONECT   12   13   11   14                                                  
CONECT   13   12   51                                                       
CONECT   14   20   12   15                                                  
CONECT   15   14   16   52   53                                             
CONECT   16   15   17   54                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17   55   56   57                                             
CONECT   19   17   58   59   60                                             
CONECT   20   21   14   22                                                  
CONECT   21   20   61                                                       
CONECT   22   23   20   33                                                  
CONECT   23   22   25   24                                                  
CONECT   24   23                                                            
CONECT   25   23   31   26                                                  
CONECT   26   25   27   62                                                  
CONECT   27   28   26   29                                                  
CONECT   28   27   63                                                       
CONECT   29   27   30   64                                                  
CONECT   30   31   29   65                                                  
CONECT   31   32   25   30                                                  
CONECT   32   33   31                                                       
CONECT   33   32   22   11                                                  
CONECT   34    1                                                            
CONECT   35    1                                                            
CONECT   36    1                                                            
CONECT   37    3                                                            
CONECT   38    3                                                            
CONECT   39    3                                                            
CONECT   40    4                                                            
CONECT   41    5                                                            
CONECT   42    5                                                            
CONECT   43    6                                                            
CONECT   44    6                                                            
CONECT   45    8                                                            
CONECT   46    8                                                            
CONECT   47    8                                                            
CONECT   48    9                                                            
CONECT   49   10                                                            
CONECT   50   10                                                            
CONECT   51   13                                                            
CONECT   52   15                                                            
CONECT   53   15                                                            
CONECT   54   16                                                            
CONECT   55   18                                                            
CONECT   56   18                                                            
CONECT   57   18                                                            
CONECT   58   19                                                            
CONECT   59   19                                                            
CONECT   60   19                                                            
CONECT   61   21                                                            
CONECT   62   26                                                            
CONECT   63   28                                                            
CONECT   64   29                                                            
CONECT   65   30                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  134    0
END

RDKit          3D

65 67  0  0  0  0  0  0  0  0999 V2000
    1.0787   -0.2525   -2.8415 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7328   -1.6708   -2.4664 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.9756    4.4537   -0.8812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1291    4.4107    0.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4238    3.6853    0.3885 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.1263   -0.4854    2.1220 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8847   -3.1346    2.7730 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4312   -2.8761    2.4818 H   0  0  0  0  0  0  0  0  0  0  0  0
 33 32  1  0
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  1 34  1  0
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  8 45  1  0
  8 46  1  0
  8 47  1  0
M  END

View in JSmol

Synonyms

Value	Source
1,3,7-Trihydroxy-2-(3-methyl-2-butenyl)-4-(3,7-dimethyl-2,6-octadienyl)xanthone	ChEBI

Chemical Formula

C₂₈H₃₂O₅

Average Mass

448.5590 Da

Monoisotopic Mass

448.22497 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H]OC1=C([H])C2=C(OC3=C(C2=O)C(O[H])=C(C(O[H])=C3C([H])([H])C(\[H])=C(/C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C1[H]

InChI Identifier

InChI=1S/C28H32O5/c1-16(2)7-6-8-18(5)10-13-21-25(30)20(12-9-17(3)4)26(31)24-27(32)22-15-19(29)11-14-23(22)33-28(21)24/h7,9-11,14-15,29-31H,6,8,12-13H2,1-5H3/b18-10+

InChI Key

ZHJQVNDLFGICFY-VCHYOVAHSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, NULL, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cratoxylum cochinchinense	JEOL database	Mahabusarakam, W., et al, Phytochemistry 67, 470 (2006)
Cratoxylum formosum	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

2-prenylated xanthone
4-prenylated xanthone
Chromone
Aromatic monoterpenoid
Monoterpenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Vinylogous acid
Polyol
Oxacycle
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

polyphenol (CHEBI:65646 )
xanthones (CHEBI:65646 )

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	5.91	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	50.04 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

C00029995

Chemspider ID

9808485

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

65646

Good Scents ID

Not Available

References

General References

Ren Y, Matthew S, Lantvit DD, Ninh TN, Chai H, Fuchs JR, Soejarto DD, de Blanco EJ, Swanson SM, Kinghorn AD: Cytotoxic and NF-kappaB inhibitory constituents of the stems of Cratoxylum cochinchinense and their semisynthetic analogues. J Nat Prod. 2011 May 27;74(5):1117-25. doi: 10.1021/np200051j. Epub 2011 Mar 23. [PubMed:21428375 ]
Mahabusarakam, W., et al. (2006). Mahabusarakam, W., et al, Phytochemistry 67, 470 (2006) . Phytochem..

Showing NP-Card for cochinchinone A (NP0031818)

MOL for NP0031818 (cochinchinone A)

3D MOL for NP0031818 (cochinchinone A)

3D SDF for NP0031818 (cochinchinone A)

3D-SDF for NP0031818 (cochinchinone A)

PDB for NP0031818 (cochinchinone A)

3D PDB for NP0031818 (cochinchinone A)

SMILES for NP0031818 (cochinchinone A)

INCHI for NP0031818 (cochinchinone A)

Structure for NP0031818 (cochinchinone A)

3D Structure for NP0031818 (cochinchinone A)