NP-MRD: Showing NP-Card for Schomburgdepsidone A (NP0086007)

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Record Information

Version

2.0

Created at

2022-04-29 06:24:24 UTC

Updated at

2022-04-29 06:24:24 UTC

NP-MRD ID

NP0086007

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Schomburgdepsidone A

Description

4,5,12,14-Tetrahydroxy-6,7,15-tris(3-methylbut-2-en-1-yl)-2,9-dioxatricyclo[9.4.0.0³,⁸]Pentadeca-1(15),3(8),4,6,11,13-hexaen-10-one belongs to the class of organic compounds known as depsides and depsidones. These are polycyclic compounds that is either a polyphenolic compound composed of two or more monocyclic aromatic units linked by an ester bond (depside), or a compound containing the depsidone structure (depsidone). Schomburgdepsidone A is found in Garcinia schomburgkiana. Based on a literature review very few articles have been published on 4,5,12,14-tetrahydroxy-6,7,15-tris(3-methylbut-2-en-1-yl)-2,9-dioxatricyclo[9.4.0.0³,⁸]Pentadeca-1(15),3(8),4,6,11,13-hexaen-10-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292208242D          

 35 37  0  0  0  0            999 V2000
    4.5741    3.0436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2162    2.3003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.5470    0.8510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.9682   -0.5145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5729   -1.0756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3893   -1.8799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.6010   -2.1231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  2 35  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292208242D          

 35 37  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0086007

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC1=C(O)C=C(O)C2=C1OC1=C(OC2=O)C(CC=C(C)C)=C(CC=C(C)C)C(O)=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O7/c1-14(2)7-10-17-18(11-8-15(3)4)26-27(24(32)23(17)31)34-25-19(12-9-16(5)6)20(29)13-21(30)22(25)28(33)35-26/h7-9,13,29-32H,10-12H2,1-6H3

> <INCHI_KEY>
FMDBJBGIUXBZGO-UHFFFAOYSA-N

> <FORMULA>
C28H32O7

> <MOLECULAR_WEIGHT>
480.557

> <EXACT_MASS>
480.21480337

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
52.256666912345224

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5,12,14-tetrahydroxy-6,7,15-tris(3-methylbut-2-en-1-yl)-2,9-dioxatricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,12,14-hexaen-10-one

> <ALOGPS_LOGP>
5.29

> <JCHEM_LOGP>
7.583162307

> <ALOGPS_LOGS>
-5.03

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.3450211169175

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.740207890775569

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8496388047509424

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
138.69570000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.52e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5,12,14-tetrahydroxy-6,7,15-tris(3-methylbut-2-en-1-yl)-2,9-dioxatricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,12,14-hexaen-10-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  O   UNK     0       8.538   5.681   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.870   4.294   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.830   3.090   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.488   1.588   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.617   0.541   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.274  -0.960   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.403  -2.008   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.060  -3.509   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.189  -4.557   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.589  -3.963   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.088   0.995   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      12.217  -0.053   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      11.431   2.496   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.302   3.544   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      10.645   5.045   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.100   0.920   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.713   1.588   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.370   3.090   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.898   3.544   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.556   5.045   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.084   5.499   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.741   7.000   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.870   8.048   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.270   7.454   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.770   2.496   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.298   2.950   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.169   1.903   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.303   2.357   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.431   1.309   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.645   3.858   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.112   0.995   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       1.983  -0.053   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       4.584   0.541   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       4.926  -0.960   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       6.330   4.294   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   35                                                  
CONECT    3    2    4   14                                                  
CONECT    4    3    5   16                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    5   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    3   15                                                  
CONECT   15   14                                                            
CONECT   16    4   17                                                       
CONECT   17   16   18   33                                                  
CONECT   18   17   19   35                                                  
CONECT   19   18   20   25                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   19   26   31                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   25   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   17   34                                                  
CONECT   34   33                                                            
CONECT   35   18    2                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₂O₇

Average Mass

480.5570 Da

Monoisotopic Mass

480.21480 Da

IUPAC Name

4,5,12,14-tetrahydroxy-6,7,15-tris(3-methylbut-2-en-1-yl)-2,9-dioxatricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,12,14-hexaen-10-one

Traditional Name

4,5,12,14-tetrahydroxy-6,7,15-tris(3-methylbut-2-en-1-yl)-2,9-dioxatricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,12,14-hexaen-10-one

CAS Registry Number

Not Available

SMILES

CC(C)=CCC1=C(O)C=C(O)C2=C1OC1=C(OC2=O)C(CC=C(C)C)=C(CC=C(C)C)C(O)=C1O

InChI Identifier

InChI=1S/C28H32O7/c1-14(2)7-10-17-18(11-8-15(3)4)26-27(24(32)23(17)31)34-25-19(12-9-16(5)6)20(29)13-21(30)22(25)28(33)35-26/h7-9,13,29-32H,10-12H2,1-6H3

InChI Key

FMDBJBGIUXBZGO-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Garcinia schomburgkiana	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as depsides and depsidones. These are polycyclic compounds that is either a polyphenolic compound composed of two or more monocyclic aromatic units linked by an ester bond (depside), or a compound containing the depsidone structure (depsidone).

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Depsides and depsidones

Sub Class

Not Available

Direct Parent

Depsides and depsidones

Alternative Parents

Substituents

Depsidone
Dihydroxybenzoic acid
Diaryl ether
1-hydroxy-2-unsubstituted benzenoid
Dioxepine
1,4-dioxepine
Benzenoid
Vinylogous acid
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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	5.29	ALOGPS
logP	7.58	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	7.74	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	138.7 m³·mol⁻¹	ChemAxon
Polarizability	52.26 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

C00056106

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

163184025

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Schomburgdepsidone A (NP0086007)

MOL for NP0086007 (Schomburgdepsidone A)

3D MOL for NP0086007 (Schomburgdepsidone A)

3D SDF for NP0086007 (Schomburgdepsidone A)

3D-SDF for NP0086007 (Schomburgdepsidone A)

PDB for NP0086007 (Schomburgdepsidone A)

3D PDB for NP0086007 (Schomburgdepsidone A)

SMILES for NP0086007 (Schomburgdepsidone A)

INCHI for NP0086007 (Schomburgdepsidone A)

Structure for NP0086007 (Schomburgdepsidone A)

3D Structure for NP0086007 (Schomburgdepsidone A)