NP-MRD: Showing NP-Card for Gemmacolide C (NP0079059)

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Record Information

Version

2.0

Created at

2022-04-29 00:08:00 UTC

Updated at

2022-04-29 00:08:01 UTC

NP-MRD ID

NP0079059

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gemmacolide C

Description

(1'S,2R,2'R,3'R,4'R,7'S,8'S,12'R,13'R,14'S,16'R)-12',14',16'-tris(acetyloxy)-8'-chloro-3'-hydroxy-4',13'-dimethyl-9'-methylidene-5'-oxo-6'-oxaspiro[oxirane-2,17'-tricyclo[11.4.0.0³,⁷]Heptadecane]-2'-yl acetate belongs to the class of organic compounds known as diterpene lactones. These are diterpenoids containing a lactone moiety. Gemmacolide C is found in Ellisella sp. and Junceella juncea. Based on a literature review very few articles have been published on (1'S,2R,2'R,3'R,4'R,7'S,8'S,12'R,13'R,14'S,16'R)-12',14',16'-tris(acetyloxy)-8'-chloro-3'-hydroxy-4',13'-dimethyl-9'-methylidene-5'-oxo-6'-oxaspiro[oxirane-2,17'-tricyclo[11.4.0.0³,⁷]Heptadecane]-2'-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292202082D          

 41 44  0  0  1  0            999 V2000
    6.3045   -0.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 39 41  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292202082D          

 41 44  0  0  1  0            999 V2000
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    2.0921   -0.8124    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8568    0.3889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1008   -0.5583    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9093   -2.5955    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    6.1917   -2.7909    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1541   -3.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8490   -4.0596    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4215   -3.9945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2293   -1.9667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0529   -0.2157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4975    0.4792    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6472    0.9503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3797    1.3298    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4173    2.1540    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0746    0.8852    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
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  5 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
  4 19  1  0  0  0  0
 19 20  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 18 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 17 27  1  1  0  0  0
 24 28  1  6  0  0  0
 18 29  1  6  0  0  0
 16 30  1  6  0  0  0
 11 31  1  6  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
  5 35  1  6  0  0  0
  3 36  1  0  0  0  0
 36 37  1  0  0  0  0
  3 37  1  6  0  0  0
  2 38  1  6  0  0  0
 38 39  1  0  0  0  0
 39 40  2  0  0  0  0
 39 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0079059

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C(=O)O[C@@H]2[C@@H](Cl)C(=C)CC[C@@H](OC(C)=O)[C@]3(C)[C@H](C[C@@H](OC(C)=O)[C@]4(CO4)[C@@H]3[C@@H](OC(C)=O)[C@]12O)OC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C28H37ClO12/c1-12-8-9-18(37-14(3)30)26(7)19(38-15(4)31)10-20(39-16(5)32)27(11-36-27)22(26)24(40-17(6)33)28(35)13(2)25(34)41-23(28)21(12)29/h13,18-24,35H,1,8-11H2,2-7H3/t13-,18+,19-,20+,21-,22+,23+,24+,26+,27+,28-/m0/s1

> <INCHI_KEY>
MDILJZNWKHVGLR-WOCBMPHJSA-N

> <FORMULA>
C28H37ClO12

> <MOLECULAR_WEIGHT>
601.04

> <EXACT_MASS>
600.1973543

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
57.61755761837376

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'S,2R,2'R,3'R,4'R,7'S,8'S,12'R,13'R,14'S,16'R)-2',14',16'-tris(acetyloxy)-8'-chloro-3'-hydroxy-4',13'-dimethyl-9'-methylidene-5'-oxo-6'-oxaspiro[oxirane-2,17'-tricyclo[11.4.0.0^{3,7}]heptadecane]-12'-yl acetate

> <ALOGPS_LOGP>
2.44

> <JCHEM_LOGP>
0.7131929030000002

> <ALOGPS_LOGS>
-3.58

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.3681218247394

> <JCHEM_PKA_STRONGEST_BASIC>
-3.949983513858986

> <JCHEM_POLAR_SURFACE_AREA>
164.26

> <JCHEM_REFRACTIVITY>
136.8355

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.58e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1'S,2R,2'R,3'R,4'R,7'S,8'S,12'R,13'R,14'S,16'R)-2',14',16'-tris(acetyloxy)-8'-chloro-3'-hydroxy-4',13'-dimethyl-9'-methylidene-5'-oxo-6'-oxaspiro[oxirane-2,17'-tricyclo[11.4.0.0^{3,7}]heptadecane]-12'-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      11.768  -0.594   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.471   0.236   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.104  -0.473   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.034  -2.011   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.331  -2.841   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.698  -2.133   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      12.995  -2.963   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      14.363  -2.254   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      14.433  -0.716   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      15.660  -3.084   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.261  -4.380   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.893  -5.088   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.596  -4.258   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.229  -4.966   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.158  -6.505   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.931  -4.136   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.002  -2.598   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.369  -1.890   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.666  -2.720   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       8.030  -1.503   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       6.761  -0.058   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       5.251  -0.359   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       7.255   1.401   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.118  -0.370   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.595  -0.140   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       3.887   1.228   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       3.905  -1.516   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       7.199   0.726   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       7.655  -1.042   0.000  0.00  0.00           O+0
HETATM   30 Cl   UNK     0       3.564  -4.845   0.000  0.00  0.00          Cl+0
HETATM   31  O   UNK     0      11.558  -5.210   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      11.488  -6.748   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      12.785  -7.578   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      10.120  -7.456   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      11.628  -3.671   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.565  -0.403   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       8.395   0.895   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      10.541   1.774   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      11.909   2.482   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      11.979   4.021   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      13.206   1.652   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   38                                                  
CONECT    3    2    4   36   37                                             
CONECT    4    3    5   19                                                  
CONECT    5    4    6   11   35                                             
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    5   12   31                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   30                                                  
CONECT   17   16   18   27                                                  
CONECT   18   17   19   24   29                                             
CONECT   19   18    4   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   18   25   28                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   17                                                       
CONECT   28   24                                                            
CONECT   29   18                                                            
CONECT   30   16                                                            
CONECT   31   11   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35    5                                                            
CONECT   36    3   37                                                       
CONECT   37   36    3                                                       
CONECT   38    2   39                                                       
CONECT   39   38   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   88    0
END

View in JSmol

Synonyms

Value	Source
(1's,2R,2'r,3'r,4'r,7's,8's,12'r,13'r,14's,16'r)-12',14',16'-Tris(acetyloxy)-8'-chloro-3'-hydroxy-4',13'-dimethyl-9'-methylidene-5'-oxo-6'-oxaspiro[oxirane-2,17'-tricyclo[11.4.0.0,]heptadecane]-2'-yl acetic acid	Generator

Chemical Formula

C₂₈H₃₇ClO₁₂

Average Mass

601.0400 Da

Monoisotopic Mass

600.19735 Da

IUPAC Name

(1'S,2R,2'R,3'R,4'R,7'S,8'S,12'R,13'R,14'S,16'R)-2',14',16'-tris(acetyloxy)-8'-chloro-3'-hydroxy-4',13'-dimethyl-9'-methylidene-5'-oxo-6'-oxaspiro[oxirane-2,17'-tricyclo[11.4.0.0^{3,7}]heptadecane]-12'-yl acetate

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@H]1C(=O)O[C@@H]2[C@@H](Cl)C(=C)CC[C@@H](OC(C)=O)[C@]3(C)[C@H](C[C@@H](OC(C)=O)[C@]4(CO4)[C@@H]3[C@@H](OC(C)=O)[C@]12O)OC(C)=O

InChI Identifier

InChI=1S/C28H37ClO12/c1-12-8-9-18(37-14(3)30)26(7)19(38-15(4)31)10-20(39-16(5)32)27(11-36-27)22(26)24(40-17(6)33)28(35)13(2)25(34)41-23(28)21(12)29/h13,18-24,35H,1,8-11H2,2-7H3/t13-,18+,19-,20+,21-,22+,23+,24+,26+,27+,28-/m0/s1

InChI Key

MDILJZNWKHVGLR-WOCBMPHJSA-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
Ellisella sp.	-	KNApSAcK
Junceella juncea	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpene lactones. These are diterpenoids containing a lactone moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Diterpene lactones

Alternative Parents

Substituents

Briarane diterpenoid
Diterpenoid
Diterpene lactone
Pentacarboxylic acid or derivatives
Gamma butyrolactone
Tetrahydrofuran
Tertiary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organochloride
Organohalogen compound
Carbonyl group
Alkyl halide
Alkyl chloride
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	2.44	ALOGPS
logP	0.71	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	12.37	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	164.26 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	136.84 m³·mol⁻¹	ChemAxon
Polarizability	57.62 Å³	ChemAxon
Number of Rings	4	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

163060234

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Gemmacolide C (NP0079059)

MOL for NP0079059 (Gemmacolide C)

3D MOL for NP0079059 (Gemmacolide C)

3D SDF for NP0079059 (Gemmacolide C)

3D-SDF for NP0079059 (Gemmacolide C)

PDB for NP0079059 (Gemmacolide C)

3D PDB for NP0079059 (Gemmacolide C)

SMILES for NP0079059 (Gemmacolide C)

INCHI for NP0079059 (Gemmacolide C)

Structure for NP0079059 (Gemmacolide C)

3D Structure for NP0079059 (Gemmacolide C)