NP-MRD: Showing NP-Card for (1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione (NP0206587)

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Record Information

Version

2.0

Created at

2022-09-05 02:53:21 UTC

Updated at

2022-09-05 02:53:21 UTC

NP-MRD ID

NP0206587

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione

Description

(1R,12S,13R,16R)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]Octadeca-3(8),4,6,10-tetraene-9,18-dione belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. (1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione is found in Garcinia bracteata. Based on a literature review very few articles have been published on (1R,12S,13R,16R)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]Octadeca-3(8),4,6,10-tetraene-9,18-dione.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052204532D          

 34 38  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309052204532D          

 34 38  0  0  1  0            999 V2000
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 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 23 29  1  0  0  0  0
 29 30  1  0  0  0  0
 17 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 23 33  1  0  0  0  0
 15 33  1  0  0  0  0
 33 34  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0206587

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CC[C@@]12OC(C)(C)[C@@H]3C[C@]4(OC5=C(C(O)=CC(O)=C5C(C)(C)C=C)C(=O)C4=C[C@H]13)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O6/c1-8-25(4,5)21-19(30)12-18(29)20-22(31)16-11-15-17-13-28(16,33-23(20)21)24(32)27(15,10-9-14(2)3)34-26(17,6)7/h8-9,11-12,15,17,29-30H,1,10,13H2,2-7H3/t15-,17+,27+,28+/m0/s1

> <INCHI_KEY>
WNZOVBCBFYFAQY-DPMNOVGYSA-N

> <FORMULA>
C28H32O6

> <MOLECULAR_WEIGHT>
464.558

> <EXACT_MASS>
464.21988875

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
49.86293264522526

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,12S,13R,16R)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0^{1,10}.0^{3,8}.0^{12,16}]octadeca-3(8),4,6,10-tetraene-9,18-dione

> <JCHEM_LOGP>
5.743734496000002

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.45894362215471

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.696524163717562

> <JCHEM_PKA_STRONGEST_BASIC>
-4.196680363933109

> <JCHEM_POLAR_SURFACE_AREA>
93.06

> <JCHEM_REFRACTIVITY>
130.57620000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,12S,13R,16R)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0^{1,10}.0^{3,8}.0^{12,16}]octadeca-3(8),4,6,10-tetraene-9,18-dione

> <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       6.308  -2.985   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.197  -1.918   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.566  -0.423   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.061  -0.791   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.071  -0.054   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.935   1.073   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.414   1.501   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.524   0.434   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.782   2.996   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.672   4.063   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       7.041   5.558   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.193   3.635   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.824   2.140   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.238   1.828   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.708   2.703   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.528   2.539   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.325   3.728   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.236   3.753   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.023   4.986   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.323   4.142   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.982   4.622   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.290   6.131   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.024   1.624   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.014   0.085   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.367  -0.652   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.405  -2.192   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.757  -2.929   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.090  -2.994   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -1.453   1.211   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -2.317   2.524   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.696   1.839   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.615   3.353   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.377   1.293   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       2.187  -0.017   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3    7   13                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   21                                                  
CONECT   13   12    6   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20   33                                             
CONECT   16   15   17                                                       
CONECT   17   16   18   30                                                  
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   15   21                                                  
CONECT   21   20   12   22                                                  
CONECT   22   21                                                            
CONECT   23   18   24   29   33                                             
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   23   30                                                       
CONECT   30   29   17   31   32                                             
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   23   15   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₂O₆

Average Mass

464.5580 Da

Monoisotopic Mass

464.21989 Da

IUPAC Name

(1R,12S,13R,16R)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0^{1,10}.0^{3,8}.0^{12,16}]octadeca-3(8),4,6,10-tetraene-9,18-dione

Traditional Name

(1R,12S,13R,16R)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0^{1,10}.0^{3,8}.0^{12,16}]octadeca-3(8),4,6,10-tetraene-9,18-dione

CAS Registry Number

Not Available

SMILES

CC(C)=CC[C@@]12OC(C)(C)[C@@H]3C[C@]4(OC5=C(C(O)=CC(O)=C5C(C)(C)C=C)C(=O)C4=C[C@H]13)C2=O

InChI Identifier

InChI=1S/C28H32O6/c1-8-25(4,5)21-19(30)12-18(29)20-22(31)16-11-15-17-13-28(16,33-23(20)21)24(32)27(15,10-9-14(2)3)34-26(17,6)7/h8-9,11-12,15,17,29-30H,1,10,13H2,2-7H3/t15-,17+,27+,28+/m0/s1

InChI Key

WNZOVBCBFYFAQY-DPMNOVGYSA-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
Garcinia bracteata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Xanthone
Chromone
Monoterpenoid
Aromatic monoterpenoid
Aryl ketone
1-hydroxy-2-unsubstituted benzenoid
Cyclohexenone
Oxepane
Alkyl aryl ether
Benzenoid
Vinylogous acid
Tetrahydrofuran
Ketone
Oxacycle
Ether
Dialkyl ether
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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	5.74	ChemAxon
pKa (Strongest Acidic)	7.7	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.06 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	130.58 m³·mol⁻¹	ChemAxon
Polarizability	49.86 Å³	ChemAxon
Number of Rings	5	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

163195542

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione (NP0206587)

MOL for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)

3D MOL for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)

3D SDF for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)

3D-SDF for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)

PDB for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)

3D PDB for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)

SMILES for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)

INCHI for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)

Structure for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)

3D Structure for NP0206587 ((1r,12s,13r,16r)-5,7-dihydroxy-15,15-dimethyl-13-(3-methylbut-2-en-1-yl)-4-(2-methylbut-3-en-2-yl)-2,14-dioxapentacyclo[11.4.1.0¹,¹⁰.0³,⁸.0¹²,¹⁶]octadeca-3(8),4,6,10-tetraene-9,18-dione)