NP-MRD: Showing NP-Card for (1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid (NP0279094)

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Record Information

Version

2.0

Created at

2022-09-09 04:21:40 UTC

Updated at

2022-09-09 04:21:40 UTC

NP-MRD ID

NP0279094

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid

Description

CHEMBL293560 belongs to the class of organic compounds known as ophiobolane sesterterpenoids. These are sesterterpnoids with a structure based on the ophiobolane backbone. Ophiobolane is a tricyclic compound consisting of two cyclopentane rings joined by a cyclooctane ring, and carries a methyl group at the 1-, 4-, and 8-position, as well as a 6-methylheptane group at the 12-position. (1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid is found in Halorosellinia oceanica. Based on a literature review very few articles have been published on CHEMBL293560.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092206212D          

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M  END

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M  END


  Mrv1652309092206212D          

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  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 19 18  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  1  6  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 19 23  1  0  0  0  0
 23 24  1  6  0  0  0
 20 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 25 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 13  1  6  0  0  0
 16 31  1  0  0  0  0
  2 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0279094

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]([C@H]1OC(C)(C)OC1\C=C(/C)C(O)=O)C1=CC[C@@]2(C)C[C@@H]3[C@H](C)CC[C@@H]3\C(=C/C[C@H]12)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C28H40O6/c1-15-7-8-19-20(26(31)32)9-10-22-18(11-12-28(22,6)14-21(15)19)17(3)24-23(13-16(2)25(29)30)33-27(4,5)34-24/h9,11,13,15,17,19,21-24H,7-8,10,12,14H2,1-6H3,(H,29,30)(H,31,32)/b16-13+,20-9+/t15-,17-,19-,21-,22-,23?,24-,28+/m1/s1

> <INCHI_KEY>
KYAGGFDVLXQVAI-WNHGOZILSA-N

> <FORMULA>
C28H40O6

> <MOLECULAR_WEIGHT>
472.622

> <EXACT_MASS>
472.282489008

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
52.27665762728043

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3R,4R,7S,8E,11S)-12-[(1R)-1-[(4R)-5-[(1E)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0^{3,7}]tetradeca-8,12-diene-8-carboxylic acid

> <JCHEM_LOGP>
5.265607582333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.870011882407871

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.2597796070923595

> <JCHEM_PKA_STRONGEST_BASIC>
-4.087562589885838

> <JCHEM_POLAR_SURFACE_AREA>
93.06000000000002

> <JCHEM_REFRACTIVITY>
131.81449999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3R,4R,7S,8E,11S)-12-[(1R)-1-[(4R)-5-[(1E)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0^{3,7}]tetradeca-8,12-diene-8-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      -5.067  -6.970   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.644  -7.560   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.422  -6.622   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.623  -5.095   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.977  -4.361   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -3.696  -2.846   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.231  -2.725   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.736  -1.307   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.169  -2.645   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.506  -4.035   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.008  -4.316   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.522  -5.768   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.008  -3.145   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.649  -1.647   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.962  -0.843   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.133  -1.843   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.374  -0.322   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.556  -1.254   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.978  -1.843   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.568  -3.266   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.103  -3.145   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.462  -1.647   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.149  -0.843   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.028   0.692   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.978  -4.688   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.067  -5.777   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       6.669  -7.265   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       8.555  -5.379   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       4.556  -5.278   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.133  -4.688   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.543  -3.266   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.443  -9.086   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -2.020  -9.676   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -4.665 -10.024   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   32                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   31                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   31                                             
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20   23                                                  
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   19   24                                                  
CONECT   24   23                                                            
CONECT   25   20   26   29                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   25   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   13   16                                                  
CONECT   32    2   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₀O₆

Average Mass

472.6220 Da

Monoisotopic Mass

472.28249 Da

IUPAC Name

(1R,3R,4R,7S,8E,11S)-12-[(1R)-1-[(4R)-5-[(1E)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0^{3,7}]tetradeca-8,12-diene-8-carboxylic acid

Traditional Name

(1R,3R,4R,7S,8E,11S)-12-[(1R)-1-[(4R)-5-[(1E)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0^{3,7}]tetradeca-8,12-diene-8-carboxylic acid

CAS Registry Number

Not Available

SMILES

C[C@@H]([C@H]1OC(C)(C)OC1\C=C(/C)C(O)=O)C1=CC[C@@]2(C)C[C@@H]3[C@H](C)CC[C@@H]3\C(=C/C[C@H]12)C(O)=O

InChI Identifier

InChI=1S/C28H40O6/c1-15-7-8-19-20(26(31)32)9-10-22-18(11-12-28(22,6)14-21(15)19)17(3)24-23(13-16(2)25(29)30)33-27(4,5)34-24/h9,11,13,15,17,19,21-24H,7-8,10,12,14H2,1-6H3,(H,29,30)(H,31,32)/b16-13+,20-9+/t15-,17-,19-,21-,22-,23?,24-,28+/m1/s1

InChI Key

KYAGGFDVLXQVAI-WNHGOZILSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Halorosellinia oceanica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ophiobolane sesterterpenoids. These are sesterterpnoids with a structure based on the ophiobolane backbone. Ophiobolane is a tricyclic compound consisting of two cyclopentane rings joined by a cyclooctane ring, and carries a methyl group at the 1-, 4-, and 8-position, as well as a 6-methylheptane group at the 12-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesterterpenoids

Direct Parent

Ophiobolane sesterterpenoids

Alternative Parents

Substituents

Ophiobolane sesterterpenoid
Ketal
Dicarboxylic acid or derivatives
Meta-dioxolane
Oxacycle
Organoheterocyclic compound
Carboxylic acid
Carboxylic acid derivative
Acetal
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	5.27	ChemAxon
pKa (Strongest Acidic)	4.26	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.06 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	131.81 m³·mol⁻¹	ChemAxon
Polarizability	52.28 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	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

23152721

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44302014

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid (NP0279094)

MOL for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)

3D MOL for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)

3D SDF for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)

3D-SDF for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)

PDB for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)

3D PDB for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)

SMILES for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)

INCHI for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)

Structure for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)

3D Structure for NP0279094 ((1r,3r,4r,7s,8e,11s)-12-[(1r)-1-[(4r)-5-[(1e)-2-carboxy-2-methyleth-1-en-1-yl]-2,2-dimethyl-1,3-dioxolan-4-yl]ethyl]-1,4-dimethyltricyclo[9.3.0.0³,⁷]tetradeca-8,12-diene-8-carboxylic acid)