NP-MRD: Showing NP-Card for (-)-Glabcensin D (NP0077599)

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Record Information

Version

2.0

Created at

2022-04-28 22:44:01 UTC

Updated at

2022-04-28 22:44:01 UTC

NP-MRD ID

NP0077599

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Glabcensin D

Description

(1R,2R,3R,4S,6R,7S,9R,10S,11S,13S)-3,7-bis(acetyloxy)-2,6-dihydroxy-5,5,9-trimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]Hexadecan-11-yl acetate belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D. (-)-Glabcensin D is found in Isodon angustifolius and Isodon angustifolius var. glabrescens. Based on a literature review very few articles have been published on (1R,2R,3R,4S,6R,7S,9R,10S,11S,13S)-3,7-bis(acetyloxy)-2,6-dihydroxy-5,5,9-trimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]Hexadecan-11-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292200442D          

 35 38  0  0  1  0            999 V2000
    3.3179    1.4304    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5667    0.6438    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0099    0.0351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2043    0.2129    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9555    0.9995    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5123    1.6083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1344    1.2014    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5353    0.5473    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8407   -0.2392    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6500   -0.4062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9084   -1.1897    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3591   -1.8052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.5514   -1.6373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0598    1.0801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4433    2.6571    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.1828    3.4345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  9 15  1  6  0  0  0
  8 16  1  1  0  0  0
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 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
  7 19  1  0  0  0  0
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  8 26  1  0  0  0  0
 26 27  2  0  0  0  0
  5 28  1  6  0  0  0
  3 29  1  0  0  0  0
  3 30  1  0  0  0  0
  2 31  1  6  0  0  0
  1 32  1  6  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292200442D          

 35 38  0  0  1  0            999 V2000
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 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
  8 26  1  0  0  0  0
 26 27  2  0  0  0  0
  5 28  1  6  0  0  0
  3 29  1  0  0  0  0
  3 30  1  0  0  0  0
  2 31  1  6  0  0  0
  1 32  1  6  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0077599

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@H]1C[C@]2(C)[C@@H]3[C@H](C[C@@H]4C[C@@]3([C@@H](O)[C@H](OC(C)=O)[C@@H]2C(C)(C)[C@H]1O)C(=O)C4=C)OC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H36O9/c1-11-15-8-16(33-12(2)27)19-25(7)10-17(34-13(3)28)22(31)24(5,6)20(25)18(35-14(4)29)23(32)26(19,9-15)21(11)30/h15-20,22-23,31-32H,1,8-10H2,2-7H3/t15-,16+,17+,18-,19+,20-,22+,23+,25-,26+/m1/s1

> <INCHI_KEY>
VLXREZYMAHAWAB-LPZADHOISA-N

> <FORMULA>
C26H36O9

> <MOLECULAR_WEIGHT>
492.565

> <EXACT_MASS>
492.235932739

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
50.773971106756086

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,3R,4S,6R,7S,9R,10S,11S,13S)-3,7-bis(acetyloxy)-2,6-dihydroxy-5,5,9-trimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-11-yl acetate

> <ALOGPS_LOGP>
1.59

> <JCHEM_LOGP>
0.9419249840000017

> <ALOGPS_LOGS>
-3.33

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.942400189890257

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.3148654009847

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3526198475045934

> <JCHEM_POLAR_SURFACE_AREA>
136.43

> <JCHEM_REFRACTIVITY>
121.11539999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.30e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,3R,4S,6R,7S,9R,10S,11S,13S)-3,7-bis(acetyloxy)-2,6-dihydroxy-5,5,9-trimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-11-yl acetate

> <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       6.193   2.670   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.658   1.202   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.618   0.065   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.115   0.397   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.650   1.866   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.690   3.002   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.118   2.243   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.999   1.022   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.569  -0.447   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.080  -0.758   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.562  -2.221   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.537  -3.370   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.019  -4.832   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.029  -3.056   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.575  -1.623   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.112   2.016   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.964   2.885   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.081   4.116   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.659   3.819   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.694   4.960   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.224   6.426   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.719   6.752   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.258   7.567   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.675   1.439   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.193   1.177   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.512   0.307   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.766  -1.212   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       3.203   3.340   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.339  -1.449   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.718  -1.013   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.162   0.870   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       7.233   3.806   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       6.768   5.275   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       5.265   5.607   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       7.808   6.411   0.000  0.00  0.00           C+0
CONECT    1    2    6   32                                                  
CONECT    2    1    3   31                                                  
CONECT    3    2    4   29   30                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   28                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   19                                                  
CONECT    8    7    9   16   26                                             
CONECT    9    8   10   15                                                  
CONECT   10    9    4   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    9                                                            
CONECT   16    8   17                                                       
CONECT   17   16   18   24                                                  
CONECT   18   17   19                                                       
CONECT   19   18    7   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   17   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24    8   27                                                  
CONECT   27   26                                                            
CONECT   28    5                                                            
CONECT   29    3                                                            
CONECT   30    3                                                            
CONECT   31    2                                                            
CONECT   32    1   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
(1R,2R,3R,4S,6R,7S,9R,10S,11S,13S)-3,7-Bis(acetyloxy)-2,6-dihydroxy-5,5,9-trimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0,.0,]hexadecan-11-yl acetic acid	Generator

Chemical Formula

C₂₆H₃₆O₉

Average Mass

492.5650 Da

Monoisotopic Mass

492.23593 Da

IUPAC Name

(1R,2R,3R,4S,6R,7S,9R,10S,11S,13S)-3,7-bis(acetyloxy)-2,6-dihydroxy-5,5,9-trimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-11-yl acetate

Traditional Name

(1R,2R,3R,4S,6R,7S,9R,10S,11S,13S)-3,7-bis(acetyloxy)-2,6-dihydroxy-5,5,9-trimethyl-14-methylidene-15-oxotetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-11-yl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@H]1C[C@]2(C)[C@@H]3[C@H](C[C@@H]4C[C@@]3([C@@H](O)[C@H](OC(C)=O)[C@@H]2C(C)(C)[C@H]1O)C(=O)C4=C)OC(C)=O

InChI Identifier

InChI=1S/C26H36O9/c1-11-15-8-16(33-12(2)27)19-25(7)10-17(34-13(3)28)22(31)24(5,6)20(25)18(35-14(4)29)23(32)26(19,9-15)21(11)30/h15-20,22-23,31-32H,1,8-10H2,2-7H3/t15-,16+,17+,18-,19+,20-,22+,23+,25-,26+/m1/s1

InChI Key

VLXREZYMAHAWAB-LPZADHOISA-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
Isodon angustifolius	LOTUS Database	35616633
Isodon angustifolius var. glabrescens	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Kaurane diterpenoids

Alternative Parents

Substituents

Kaurane diterpenoid
Tricarboxylic acid or derivatives
Cyclic alcohol
Secondary alcohol
Ketone
Carboxylic acid ester
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	1.59	ALOGPS
logP	0.94	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	13.31	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	136.43 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	121.12 m³·mol⁻¹	ChemAxon
Polarizability	50.77 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

162999411

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Glabcensin D (NP0077599)

MOL for NP0077599 ((-)-Glabcensin D)

3D MOL for NP0077599 ((-)-Glabcensin D)

3D SDF for NP0077599 ((-)-Glabcensin D)

3D-SDF for NP0077599 ((-)-Glabcensin D)

PDB for NP0077599 ((-)-Glabcensin D)

3D PDB for NP0077599 ((-)-Glabcensin D)

SMILES for NP0077599 ((-)-Glabcensin D)

INCHI for NP0077599 ((-)-Glabcensin D)

Structure for NP0077599 ((-)-Glabcensin D)

3D Structure for NP0077599 ((-)-Glabcensin D)