NP-MRD: Showing NP-Card for Orbiculin A (NP0080794)

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Record Information

Version

2.0

Created at

2022-04-29 01:47:14 UTC

Updated at

2022-04-29 01:47:14 UTC

NP-MRD ID

NP0080794

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Orbiculin A

Description

Orbiculin A belongs to the class of organic compounds known as agarofurans. These are organic compounds containing an agarofuran moiety( a three-ring system, with core fragment oxatricyclo[7.2.1.0^{1,6}]Dodec-2-ene). Orbiculin A is found in Celastrus orbiculatus . Based on a literature review very few articles have been published on orbiculin A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292203472D          

 42 46  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304292203472D          

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    4.5813   -0.3795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0724   -1.3077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8262   -0.3392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1313    0.6729    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4244   -0.0522    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1172   -0.8988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4252   -1.6684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7584   -1.1586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0538   -1.9289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8686   -2.0583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3880   -1.4173    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0927   -0.6470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2779   -0.5176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5910    1.2396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0877    1.9815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 11 16  1  0  0  0  0
  6 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
  5 20  1  0  0  0  0
 20 21  1  6  0  0  0
 18 22  1  6  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 17 26  1  6  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
  6 30  1  6  0  0  0
  5 31  1  0  0  0  0
  2 31  1  0  0  0  0
 31 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
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 38 39  1  0  0  0  0
 39 40  2  0  0  0  0
 35 40  1  0  0  0  0
  3 41  1  0  0  0  0
  3 42  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0080794

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C[C@H](OC(C)=O)[C@H](OC(C)=O)[C@@]2(C)[C@H](C[C@@H]3[C@@H](OC(=O)C4=CC=CC=C4)[C@]12OC3(C)C)OC(=O)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C33H38O9/c1-19-17-25(38-20(2)34)28(39-21(3)35)32(6)26(40-29(36)22-13-9-7-10-14-22)18-24-27(33(19,32)42-31(24,4)5)41-30(37)23-15-11-8-12-16-23/h7-16,19,24-28H,17-18H2,1-6H3/t19-,24-,25+,26+,27-,28+,32-,33-/m1/s1

> <INCHI_KEY>
KYEKMLQQOXNBSD-HJJCBLRASA-N

> <FORMULA>
C33H38O9

> <MOLECULAR_WEIGHT>
578.658

> <EXACT_MASS>
578.251582804

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
61.31298528573076

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,4S,5R,6R,7S,9R,12R)-4,5-bis(acetyloxy)-12-(benzoyloxy)-2,6,10,10-tetramethyl-11-oxatricyclo[7.2.1.0^{1,6}]dodecan-7-yl benzoate

> <ALOGPS_LOGP>
5.05

> <JCHEM_LOGP>
5.262709163333334

> <ALOGPS_LOGS>
-5.73

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.230838868107164

> <JCHEM_POLAR_SURFACE_AREA>
114.43

> <JCHEM_REFRACTIVITY>
150.1272

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.09e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,4S,5R,6R,7S,9R,12R)-4,5-bis(acetyloxy)-12-(benzoyloxy)-2,6,10,10-tetramethyl-11-oxatricyclo[7.2.1.0^{1,6}]dodecan-7-yl benzoate

> <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      -0.230  -0.789   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.985   0.639   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   2.214   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.048   3.069   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.365   2.029   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.138   0.565   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.365  -0.862   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.774  -2.590   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.734  -4.155   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.424  -5.315   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.524  -5.405   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.063  -5.444   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.799  -6.797   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.995  -8.111   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.455  -8.072   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.720  -6.719   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.689   0.422   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.578   1.683   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.943   3.097   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.395   3.252   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.286   4.864   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.083   2.414   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       7.331   3.491   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       7.369   5.078   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       8.927   3.338   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       5.342  -0.331   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.962  -0.931   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       8.552  -0.708   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       7.602  -2.441   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.409  -0.633   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.245   1.256   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       0.792  -0.098   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.219  -1.678   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       0.794  -3.114   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -1.416  -2.163   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -1.967  -3.601   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -3.488  -3.842   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -4.458  -2.646   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -3.906  -1.208   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -2.385  -0.966   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -2.970   2.314   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -2.030   3.699   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    3   31                                                  
CONECT    3    2    4   41   42                                             
CONECT    4    3    5                                                       
CONECT    5    4    6   20   31                                             
CONECT    6    5    7   17   30                                             
CONECT    7    6    1    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   11                                                       
CONECT   17    6   18   26                                                  
CONECT   18   17   19   22                                                  
CONECT   19   18   20                                                       
CONECT   20   19    5   21                                                  
CONECT   21   20                                                            
CONECT   22   18   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   17   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30    6                                                            
CONECT   31    5    2   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   40                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   35                                                       
CONECT   41    3                                                            
CONECT   42    3                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   92    0
END

View in JSmol

Synonyms

Value	Source
(1S,2R,4S,5R,6R,7S,9R,12R)-4,5-Diacetoxy-2,6,10,10-tetramethyl-11-oxatricyclo[7.2.1.0(1,6)]dodecane-7,12-diyl dibenzoate	ChEBI
1beta,2beta-Diacetoxy-6alpha,9alpha-bis(benzoyloxy)dihydro-beta-agarofuran	ChEBI
(1S,2R,4S,5R,6R,7S,9R,12R)-4,5-Diacetoxy-2,6,10,10-tetramethyl-11-oxatricyclo[7.2.1.0(1,6)]dodecane-7,12-diyl dibenzoic acid	Generator
1b,2b-Diacetoxy-6a,9a-bis(benzoyloxy)dihydro-b-agarofuran	Generator
1Β,2β-diacetoxy-6α,9α-bis(benzoyloxy)dihydro-β-agarofuran	Generator

Chemical Formula

C₃₃H₃₈O₉

Average Mass

578.6580 Da

Monoisotopic Mass

578.25158 Da

IUPAC Name

(1S,2R,4S,5R,6R,7S,9R,12R)-4,5-bis(acetyloxy)-12-(benzoyloxy)-2,6,10,10-tetramethyl-11-oxatricyclo[7.2.1.0^{1,6}]dodecan-7-yl benzoate

Traditional Name

(1S,2R,4S,5R,6R,7S,9R,12R)-4,5-bis(acetyloxy)-12-(benzoyloxy)-2,6,10,10-tetramethyl-11-oxatricyclo[7.2.1.0^{1,6}]dodecan-7-yl benzoate

CAS Registry Number

Not Available

SMILES

C[C@@H]1C[C@H](OC(C)=O)[C@H](OC(C)=O)[C@@]2(C)[C@H](C[C@@H]3[C@@H](OC(=O)C4=CC=CC=C4)[C@]12OC3(C)C)OC(=O)C1=CC=CC=C1

InChI Identifier

InChI=1S/C33H38O9/c1-19-17-25(38-20(2)34)28(39-21(3)35)32(6)26(40-29(36)22-13-9-7-10-14-22)18-24-27(33(19,32)42-31(24,4)5)41-30(37)23-15-11-8-12-16-23/h7-16,19,24-28H,17-18H2,1-6H3/t19-,24-,25+,26+,27-,28+,32-,33-/m1/s1

InChI Key

KYEKMLQQOXNBSD-HJJCBLRASA-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
Celastrus orbiculatus	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as agarofurans. These are organic compounds containing an agarofuran moiety( a three-ring system, with core fragment oxatricyclo[7.2.1.0^{1,6}]Dodec-2-ene).

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Agarofurans

Alternative Parents

Substituents

Agarofuran
Tetracarboxylic acid or derivatives
Benzoate ester
Benzoic acid or derivatives
Benzoyl
Oxepane
Monocyclic benzene moiety
Benzenoid
Tetrahydrofuran
Carboxylic acid ester
Organoheterocyclic compound
Ether
Dialkyl ether
Carboxylic acid derivative
Oxacycle
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic heterotricyclic compound (CHEBI:66824 )
acetate ester (CHEBI:66824 )
bridged compound (CHEBI:66824 )
benzoate ester (CHEBI:66824 )
cyclic ether (CHEBI:66824 )
dihydroagarofuran sesquiterpenoid (CHEBI:66824 )

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	5.05	ALOGPS
logP	5.26	ChemAxon
logS	-5.7	ALOGPS
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	114.43 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	150.13 m³·mol⁻¹	ChemAxon
Polarizability	61.31 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	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

C00046246

Chemspider ID

8802395

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10627032

PDB ID

Not Available

ChEBI ID

66824

Good Scents ID

Not Available

References

General References

Showing NP-Card for Orbiculin A (NP0080794)

MOL for NP0080794 (Orbiculin A)

3D MOL for NP0080794 (Orbiculin A)

3D SDF for NP0080794 (Orbiculin A)

3D-SDF for NP0080794 (Orbiculin A)

PDB for NP0080794 (Orbiculin A)

3D PDB for NP0080794 (Orbiculin A)

SMILES for NP0080794 (Orbiculin A)

INCHI for NP0080794 (Orbiculin A)

Structure for NP0080794 (Orbiculin A)

3D Structure for NP0080794 (Orbiculin A)