NP-MRD: Showing NP-Card for (-)-Garsubellin B (NP0078472)

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Record Information

Version

2.0

Created at

2022-04-28 23:32:45 UTC

Updated at

2022-04-28 23:32:45 UTC

NP-MRD ID

NP0078472

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Garsubellin B

Description

(1S,3S,8R,10S)-3-(2-hydroxypropan-2-yl)-9,9-dimethyl-6,10-bis(3-methylbut-2-en-1-yl)-8-[(2S)-2-methylbutanoyl]-4-oxatricyclo[6.3.1.0¹,⁵]Dodec-5-ene-7,12-dione belongs to the class of organic compounds known as monoterpenoids. Monoterpenoids are compounds containing a chain of two isoprene units. (-)-Garsubellin B is found in Garcinia subelliptica. Based on a literature review very few articles have been published on (1S,3S,8R,10S)-3-(2-hydroxypropan-2-yl)-9,9-dimethyl-6,10-bis(3-methylbut-2-en-1-yl)-8-[(2S)-2-methylbutanoyl]-4-oxatricyclo[6.3.1.0¹,⁵]Dodec-5-ene-7,12-dione.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292201322D          

 36 38  0  0  1  0            999 V2000
    3.5422    0.4268    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0637    1.1222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7827    1.9324    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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  5 17  1  0  0  0  0
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 33 36  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292201322D          

 36 38  0  0  1  0            999 V2000
    3.5422    0.4268    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    4.1991   -0.0723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9598    0.2471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954   -0.8907    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7523   -1.3898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6485   -2.2083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4706   -1.4295    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  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
  8  9  2  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  5 17  1  0  0  0  0
 16 18  1  6  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
  5 22  1  6  0  0  0
  1 22  1  0  0  0  0
 22 23  2  0  0  0  0
  3 24  1  6  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
  2 29  1  0  0  0  0
  2 30  1  0  0  0  0
  1 31  1  6  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 33 36  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0078472

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](C)C(=O)[C@@]12C(=O)C(CC=C(C)C)=C3O[C@@H](C[C@]3(C[C@H](CC=C(C)C)C1(C)C)C2=O)C(C)(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C31H46O5/c1-11-20(6)24(32)31-25(33)22(15-13-19(4)5)26-30(27(31)34,17-23(36-26)29(9,10)35)16-21(28(31,7)8)14-12-18(2)3/h12-13,20-21,23,35H,11,14-17H2,1-10H3/t20-,21-,23-,30-,31-/m0/s1

> <INCHI_KEY>
GCNDCAZIZCRBTJ-ZQDCLXQQSA-N

> <FORMULA>
C31H46O5

> <MOLECULAR_WEIGHT>
498.704

> <EXACT_MASS>
498.334524581

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
82

> <JCHEM_AVERAGE_POLARIZABILITY>
57.32534033246242

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,3S,8R,10S)-3-(2-hydroxypropan-2-yl)-9,9-dimethyl-6,10-bis(3-methylbut-2-en-1-yl)-8-[(2S)-2-methylbutanoyl]-4-oxatricyclo[6.3.1.0^{1,5}]dodec-5-ene-7,12-dione

> <ALOGPS_LOGP>
5.17

> <JCHEM_LOGP>
6.942178608333332

> <ALOGPS_LOGS>
-5.39

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.74546447162912

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.306628599173958

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1020799591613315

> <JCHEM_POLAR_SURFACE_AREA>
80.67

> <JCHEM_REFRACTIVITY>
146.3184

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.02e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3S,8R,10S)-3-(2-hydroxypropan-2-yl)-9,9-dimethyl-6,10-bis(3-methylbut-2-en-1-yl)-8-[(2S)-2-methylbutanoyl]-4-oxatricyclo[6.3.1.0^{1,5}]dodec-5-ene-7,12-dione

> <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  C   UNK     0       6.612   0.797   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.586   2.095   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.061   3.607   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.470   3.767   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.404   2.510   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.469   1.170   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.042  -0.339   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.625  -0.486   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.241  -1.897   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.109  -1.565   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.705  -2.985   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.773  -4.211   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.368  -5.631   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.245  -4.017   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.977   1.566   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.886   3.111   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.326   3.677   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.588   3.941   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.709   4.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.418   5.238   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.241   2.643   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       5.522   1.665   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       6.466   2.882   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       8.016   4.815   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.447   6.246   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.401   7.455   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.832   8.886   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.925   7.232   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.825   1.181   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       9.045   2.588   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.838  -0.135   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       9.258   0.461   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       7.645  -1.663   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.871  -2.594   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.677  -4.122   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.478  -2.668   0.000  0.00  0.00           C+0
CONECT    1    2    8   22   31                                             
CONECT    2    1    3   29   30                                             
CONECT    3    2    4   24                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   17   22                                             
CONECT    6    5    7   15                                                  
CONECT    7    6    8   10                                                  
CONECT    8    7    1    9                                                  
CONECT    9    8                                                            
CONECT   10    7   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    6   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16    5                                                       
CONECT   18   16   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18                                                            
CONECT   22    5    1   23                                                  
CONECT   23   22                                                            
CONECT   24    3   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29    2                                                            
CONECT   30    2                                                            
CONECT   31    1   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   36                                                  
CONECT   34   33   35                                                       
CONECT   35   34                                                            
CONECT   36   33                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₁H₄₆O₅

Average Mass

498.7040 Da

Monoisotopic Mass

498.33452 Da

IUPAC Name

(1S,3S,8R,10S)-3-(2-hydroxypropan-2-yl)-9,9-dimethyl-6,10-bis(3-methylbut-2-en-1-yl)-8-[(2S)-2-methylbutanoyl]-4-oxatricyclo[6.3.1.0^{1,5}]dodec-5-ene-7,12-dione

Traditional Name

(1S,3S,8R,10S)-3-(2-hydroxypropan-2-yl)-9,9-dimethyl-6,10-bis(3-methylbut-2-en-1-yl)-8-[(2S)-2-methylbutanoyl]-4-oxatricyclo[6.3.1.0^{1,5}]dodec-5-ene-7,12-dione

CAS Registry Number

Not Available

SMILES

CC[C@H](C)C(=O)[C@@]12C(=O)C(CC=C(C)C)=C3O[C@@H](C[C@]3(C[C@H](CC=C(C)C)C1(C)C)C2=O)C(C)(C)O

InChI Identifier

InChI=1S/C31H46O5/c1-11-20(6)24(32)31-25(33)22(15-13-19(4)5)26-30(27(31)34,17-23(36-26)29(9,10)35)16-21(28(31,7)8)14-12-18(2)3/h12-13,20-21,23,35H,11,14-17H2,1-10H3/t20-,21-,23-,30-,31-/m0/s1

InChI Key

GCNDCAZIZCRBTJ-ZQDCLXQQSA-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 subelliptica	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monoterpenoids. Monoterpenoids are compounds containing a chain of two isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Monoterpenoids

Alternative Parents

Substituents

Monoterpenoid
Cyclohexenone
Vinylogous ester
Tetrahydrofuran
Tertiary alcohol
Ketone
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	5.17	ALOGPS
logP	6.94	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	14.31	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	80.67 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	146.32 m³·mol⁻¹	ChemAxon
Polarizability	57.33 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

163047985

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Garsubellin B (NP0078472)

MOL for NP0078472 ((-)-Garsubellin B)

3D MOL for NP0078472 ((-)-Garsubellin B)

3D SDF for NP0078472 ((-)-Garsubellin B)

3D-SDF for NP0078472 ((-)-Garsubellin B)

PDB for NP0078472 ((-)-Garsubellin B)

3D PDB for NP0078472 ((-)-Garsubellin B)

SMILES for NP0078472 ((-)-Garsubellin B)

INCHI for NP0078472 ((-)-Garsubellin B)

Structure for NP0078472 ((-)-Garsubellin B)

3D Structure for NP0078472 ((-)-Garsubellin B)