NP-MRD: Showing NP-Card for Spongianolide D (NP0077191)

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Record Information

Version

2.0

Created at

2022-04-28 22:20:10 UTC

Updated at

2022-04-28 22:20:10 UTC

NP-MRD ID

NP0077191

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Spongianolide D

Description

[(1S,2R,7S,10S,11R,13S,15S)-13-[(2R)-2-hydroxy-5-oxo-2,5-dihydrofuran-3-yl]-2,6,6,10-tetramethyl-14-oxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadecan-15-yl]methyl acetate belongs to the class of organic compounds known as cheilanthane sesterterpenoids. These are sesterterpnoids with a structure based on the cheilanthane backbone. Cheilanthane is a tricyclic compound consisting of a tetradecahydrophenanthrene ring system that carries two methyl groups at the 1-position, one methyl group at the 4a-,7-, and 8a-positions, as well as a 3-methylpentyl group at the 8-position. Spongianolide D is found in Spongia sp. Based on a literature review very few articles have been published on [(1S,2R,7S,10S,11R,13S,15S)-13-[(2R)-2-hydroxy-5-oxo-2,5-dihydrofuran-3-yl]-2,6,6,10-tetramethyl-14-oxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadecan-15-yl]methyl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292200202D          

 33 37  0  0  1  0            999 V2000
    4.2475    2.1537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304292200202D          

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 27 29  1  0  0  0  0
  8 30  1  1  0  0  0
  5 31  1  1  0  0  0
  3 32  1  0  0  0  0
  3 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0077191

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)OC[C@]12CC[C@@H]3[C@](C)(CC[C@H]4C(C)(C)CCC[C@@]34C)[C@H]1C[C@H](O2)C1=CC(=O)O[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C27H40O6/c1-16(28)31-15-27-12-8-20-25(4)10-6-9-24(2,3)19(25)7-11-26(20,5)21(27)14-18(33-27)17-13-22(29)32-23(17)30/h13,18-21,23,30H,6-12,14-15H2,1-5H3/t18-,19-,20-,21+,23+,25+,26-,27+/m0/s1

> <INCHI_KEY>
VSNRQJCSNGQROZ-KEEHIVELSA-N

> <FORMULA>
C27H40O6

> <MOLECULAR_WEIGHT>
460.611

> <EXACT_MASS>
460.282489008

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
50.909634734539196

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1S,2R,7S,10S,11R,13S,15S)-13-[(2R)-2-hydroxy-5-oxo-2,5-dihydrofuran-3-yl]-2,6,6,10-tetramethyl-14-oxatetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-15-yl]methyl acetate

> <ALOGPS_LOGP>
3.75

> <JCHEM_LOGP>
4.389437618999999

> <ALOGPS_LOGS>
-5.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.732484913822454

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.524342954509342

> <JCHEM_PKA_STRONGEST_BASIC>
-4.235616441553268

> <JCHEM_POLAR_SURFACE_AREA>
82.06

> <JCHEM_REFRACTIVITY>
122.81089999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.38e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1S,2R,7S,10S,11R,13S,15S)-13-[(2R)-2-hydroxy-5-oxo-2H-furan-3-yl]-2,6,6,10-tetramethyl-14-oxatetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-15-yl]methyl 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       7.929   4.020   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.452   2.572   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.459   1.394   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.943   1.666   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.420   3.114   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.413   4.291   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.904   3.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.911   2.208   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.434   0.759   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.950   0.488   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.395   2.479   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.872   3.927   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.865   5.104   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.381   4.833   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.667   3.877   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.095   2.398   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.179   1.534   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.544   1.875   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.972   0.395   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.511   0.345   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -5.375  -0.929   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -5.034   1.794   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -3.818   2.739   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -3.868   4.278   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.200   5.313   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.065   6.588   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       0.393   7.973   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -1.143   8.084   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.257   9.248   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.919   1.030   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.897   4.562   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.601   0.361   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       7.241  -0.130   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   32   33                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   31                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14                                                  
CONECT    8    7    9   11   30                                             
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12   17                                                  
CONECT   12   11   13   15   25                                             
CONECT   13   12   14                                                       
CONECT   14   13    7                                                       
CONECT   15   12   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16   11                                                       
CONECT   18   16   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   18   24                                                  
CONECT   24   23                                                            
CONECT   25   12   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30    8                                                            
CONECT   31    5                                                            
CONECT   32    3                                                            
CONECT   33    3                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   74    0
END

View in JSmol

Synonyms

Value	Source
[(1S,2R,7S,10S,11R,13S,15S)-13-[(2R)-2-Hydroxy-5-oxo-2,5-dihydrofuran-3-yl]-2,6,6,10-tetramethyl-14-oxatetracyclo[8.7.0.0,.0,]heptadecan-15-yl]methyl acetic acid	Generator

Chemical Formula

C₂₇H₄₀O₆

Average Mass

460.6110 Da

Monoisotopic Mass

460.28249 Da

IUPAC Name

[(1S,2R,7S,10S,11R,13S,15S)-13-[(2R)-2-hydroxy-5-oxo-2,5-dihydrofuran-3-yl]-2,6,6,10-tetramethyl-14-oxatetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-15-yl]methyl acetate

Traditional Name

[(1S,2R,7S,10S,11R,13S,15S)-13-[(2R)-2-hydroxy-5-oxo-2H-furan-3-yl]-2,6,6,10-tetramethyl-14-oxatetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-15-yl]methyl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)OC[C@]12CC[C@@H]3[C@](C)(CC[C@H]4C(C)(C)CCC[C@@]34C)[C@H]1C[C@H](O2)C1=CC(=O)O[C@H]1O

InChI Identifier

InChI=1S/C27H40O6/c1-16(28)31-15-27-12-8-20-25(4)10-6-9-24(2,3)19(25)7-11-26(20,5)21(27)14-18(33-27)17-13-22(29)32-23(17)30/h13,18-21,23,30H,6-12,14-15H2,1-5H3/t18-,19-,20-,21+,23+,25+,26-,27+/m0/s1

InChI Key

VSNRQJCSNGQROZ-KEEHIVELSA-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
Spongia sp.	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cheilanthane sesterterpenoids. These are sesterterpnoids with a structure based on the cheilanthane backbone. Cheilanthane is a tricyclic compound consisting of a tetradecahydrophenanthrene ring system that carries two methyl groups at the 1-position, one methyl group at the 4a-,7-, and 8a-positions, as well as a 3-methylpentyl group at the 8-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesterterpenoids

Direct Parent

Cheilanthane sesterterpenoids

Alternative Parents

Substituents

Cheilanthane sesterterpenoid
Steroid
17-oxasteroid
Naphthofuran
Dicarboxylic acid or derivatives
2-furanone
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Dihydrofuran
Lactone
Hemiacetal
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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	3.75	ALOGPS
logP	4.39	ChemAxon
logS	-5.5	ALOGPS
pKa (Strongest Acidic)	5.52	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	82.06 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	122.81 m³·mol⁻¹	ChemAxon
Polarizability	50.91 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

162960717

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Spongianolide D (NP0077191)

MOL for NP0077191 (Spongianolide D)

3D MOL for NP0077191 (Spongianolide D)

3D SDF for NP0077191 (Spongianolide D)

3D-SDF for NP0077191 (Spongianolide D)

PDB for NP0077191 (Spongianolide D)

3D PDB for NP0077191 (Spongianolide D)

SMILES for NP0077191 (Spongianolide D)

INCHI for NP0077191 (Spongianolide D)

Structure for NP0077191 (Spongianolide D)

3D Structure for NP0077191 (Spongianolide D)