NP-MRD: Showing NP-Card for (-)-Petrosaspongiolide D (NP0081131)

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Record Information

Version

2.0

Created at

2022-04-29 02:05:53 UTC

Updated at

2022-04-29 02:05:53 UTC

NP-MRD ID

NP0081131

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Petrosaspongiolide D

Description

(1S,2R,4R,5S,8R,9S,13R,14S,17S,18S,20S)-9-(hydroxymethyl)-5,9,13-trimethyl-22-oxo-19,21,24-trioxahexacyclo[16.5.1.0¹,²⁰.0⁴,¹⁷.0⁵,¹⁴.0⁸,¹³]Tetracosan-2-yl acetate belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms. (-)-Petrosaspongiolide D is found in Petrosaspongia nigra and Spongia sp.. Based on a literature review very few articles have been published on (1S,2R,4R,5S,8R,9S,13R,14S,17S,18S,20S)-9-(hydroxymethyl)-5,9,13-trimethyl-22-oxo-19,21,24-trioxahexacyclo[16.5.1.0¹,²⁰.0⁴,¹⁷.0⁵,¹⁴.0⁸,¹³]Tetracosan-2-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292204052D          

 34 39  0  0  1  0            999 V2000
   -0.2024   -0.1854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9043    0.2481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1619   -1.0162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6469   -1.2093    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1301   -0.4708    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5547    0.1488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7139    0.2092    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5707    0.2327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  7 31  1  6  0  0  0
 31 32  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304292204052D          

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 18 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 16 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 20 25  1  0  0  0  0
 25 26  1  1  0  0  0
 26 27  1  0  0  0  0
 25 28  1  6  0  0  0
 21 29  1  1  0  0  0
 17 30  1  1  0  0  0
  7 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
M  END
> <DATABASE_ID>
NP0081131

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@@H]1C[C@@H]2[C@H](CC[C@H]3[C@@]2(C)CC[C@H]2[C@@](C)(CO)CCC[C@]32C)[C@@H]2O[C@H]3OC(=O)C[C@]13O2

> <INCHI_IDENTIFIER>
InChI=1S/C27H40O7/c1-15(29)31-20-12-17-16(22-33-23-27(20,34-22)13-21(30)32-23)6-7-19-25(17,3)11-8-18-24(2,14-28)9-5-10-26(18,19)4/h16-20,22-23,28H,5-14H2,1-4H3/t16-,17+,18-,19-,20+,22+,23+,24+,25-,26-,27-/m0/s1

> <INCHI_KEY>
XLOSRKDRMWLLGT-BBTNSOHDSA-N

> <FORMULA>
C27H40O7

> <MOLECULAR_WEIGHT>
476.61

> <EXACT_MASS>
476.277403628

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
52.45185509853511

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,4R,5S,8R,9S,13R,14S,17S,18S,20S)-9-(hydroxymethyl)-5,9,13-trimethyl-22-oxo-19,21,24-trioxahexacyclo[16.5.1.0^{1,20}.0^{4,17}.0^{5,14}.0^{8,13}]tetracosan-2-yl acetate

> <ALOGPS_LOGP>
3.02

> <JCHEM_LOGP>
3.7602038216666647

> <ALOGPS_LOGS>
-5.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.59234995508612

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.43608170168071

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2270155180903575

> <JCHEM_POLAR_SURFACE_AREA>
91.29000000000002

> <JCHEM_REFRACTIVITY>
121.17989999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.87e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,4R,5S,8R,9S,13R,14S,17S,18S,20S)-9-(hydroxymethyl)-5,9,13-trimethyl-22-oxo-19,21,24-trioxahexacyclo[16.5.1.0^{1,20}.0^{4,17}.0^{5,14}.0^{8,13}]tetracosan-2-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      -0.378  -0.346   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.688   0.463   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -0.302  -1.897   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.208  -2.257   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.110  -0.879   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.035   0.278   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.199   0.391   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.799   0.434   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.738  -0.843   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.264  -2.309   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.768  -3.042   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.220  -3.538   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.065  -1.869   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.296  -3.452   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.802  -3.130   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.276  -1.664   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.244  -0.521   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.718   0.944   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.224   1.266   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.256   0.123   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.782  -1.342   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.814  -2.486   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.320  -2.163   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      12.794  -0.698   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      11.762   0.445   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.869   1.516   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      12.494   3.010   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      11.493   1.961   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.308  -2.808   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.212   0.622   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       2.537   1.781   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.002   1.903   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       0.129   0.634   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.340   3.293   0.000  0.00  0.00           C+0
CONECT    1    2    3    6                                                  
CONECT    2    1                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6    7   13                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   31                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   17                                                  
CONECT   10    9   11   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11    4                                                       
CONECT   13   11    5                                                       
CONECT   14   10   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16    9   18   30                                             
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   16   22   29                                             
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   20   26   28                                             
CONECT   26   25   27                                                       
CONECT   27   26                                                            
CONECT   28   25                                                            
CONECT   29   21                                                            
CONECT   30   17                                                            
CONECT   31    7   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   78    0
END

View in JSmol

Synonyms

Value	Source
(1S,2R,4R,5S,8R,9S,13R,14S,17S,18S,20S)-9-(Hydroxymethyl)-5,9,13-trimethyl-22-oxo-19,21,24-trioxahexacyclo[16.5.1.0,.0,.0,.0,]tetracosan-2-yl acetic acid	Generator

Chemical Formula

C₂₇H₄₀O₇

Average Mass

476.6100 Da

Monoisotopic Mass

476.27740 Da

IUPAC Name

(1S,2R,4R,5S,8R,9S,13R,14S,17S,18S,20S)-9-(hydroxymethyl)-5,9,13-trimethyl-22-oxo-19,21,24-trioxahexacyclo[16.5.1.0^{1,20}.0^{4,17}.0^{5,14}.0^{8,13}]tetracosan-2-yl acetate

Traditional Name

(1S,2R,4R,5S,8R,9S,13R,14S,17S,18S,20S)-9-(hydroxymethyl)-5,9,13-trimethyl-22-oxo-19,21,24-trioxahexacyclo[16.5.1.0^{1,20}.0^{4,17}.0^{5,14}.0^{8,13}]tetracosan-2-yl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@@H]1C[C@@H]2[C@H](CC[C@H]3[C@@]2(C)CC[C@H]2[C@@](C)(CO)CCC[C@]32C)[C@@H]2O[C@H]3OC(=O)C[C@]13O2

InChI Identifier

InChI=1S/C27H40O7/c1-15(29)31-20-12-17-16(22-33-23-27(20,34-22)13-21(30)32-23)6-7-19-25(17,3)11-8-18-24(2,14-28)9-5-10-26(18,19)4/h16-20,22-23,28H,5-14H2,1-4H3/t16-,17+,18-,19-,20+,22+,23+,24+,25-,26-,27-/m0/s1

InChI Key

XLOSRKDRMWLLGT-BBTNSOHDSA-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
Petrosaspongia nigra	LOTUS Database	35616633
Spongia sp.	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxepanes

Sub Class

Not Available

Direct Parent

Oxepanes

Alternative Parents

Substituents

Oxepane
Dicarboxylic acid or derivatives
Gamma butyrolactone
Meta-dioxolane
Tetrahydrofuran
Carboxylic acid ester
Lactone
Acetal
Carboxylic acid derivative
Oxacycle
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Alcohol
Primary 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	3.02	ALOGPS
logP	3.76	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	17.44	ChemAxon
pKa (Strongest Basic)	-1.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	91.29 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	121.18 m³·mol⁻¹	ChemAxon
Polarizability	52.45 Å³	ChemAxon
Number of Rings	6	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

29216930

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162934414

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Petrosaspongiolide D (NP0081131)

MOL for NP0081131 ((-)-Petrosaspongiolide D)

3D MOL for NP0081131 ((-)-Petrosaspongiolide D)

3D SDF for NP0081131 ((-)-Petrosaspongiolide D)

3D-SDF for NP0081131 ((-)-Petrosaspongiolide D)

PDB for NP0081131 ((-)-Petrosaspongiolide D)

3D PDB for NP0081131 ((-)-Petrosaspongiolide D)

SMILES for NP0081131 ((-)-Petrosaspongiolide D)

INCHI for NP0081131 ((-)-Petrosaspongiolide D)

Structure for NP0081131 ((-)-Petrosaspongiolide D)

3D Structure for NP0081131 ((-)-Petrosaspongiolide D)