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Showing NP-Card for (1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate (NP0235308)

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Record Information
Version2.0
Created at2022-09-06 17:51:30 UTC
Updated at2022-09-06 17:51:30 UTC
NP-MRD IDNP0235308
Secondary Accession NumbersNone
Natural Product Identification
Common Name(1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate
DescriptionTomenphantin A belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety. (1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate was first documented in 2020 (PMID: 32496057). Based on a literature review very few articles have been published on tomenphantin A.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0235308 ((1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate)


  Mrv1652309062219512D          

 25 27  0  0  1  0            999 V2000
    0.8462    2.4626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1590    1.6992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9765    1.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6542    1.0466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1633    1.1575    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9669    0.2832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7844    0.1723    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1425    0.9155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9600    0.8047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1072   -0.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4778   -0.5404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6866    1.1955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2828    0.6253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4300   -0.1865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0719   -0.9297    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8733   -1.1254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0471   -1.7544    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3453   -1.3206    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5278   -1.2097    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1698   -1.9529    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3522   -1.8420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7820   -2.4383    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2051   -1.0303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4618   -0.6722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9316   -0.6395    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 18 17  1  1  0  0  0
 15 18  1  0  0  0  0
 18 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
 23 24  2  0  0  0  0
 25 23  1  6  0  0  0
  7 25  1  0  0  0  0
 19 25  1  0  0  0  0
M  END
Download

3D MOL for NP0235308 ((1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate)

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3D SDF for NP0235308 ((1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate)

  Mrv1652309062219512D          

 25 27  0  0  1  0            999 V2000
    0.8462    2.4626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1590    1.6992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9765    1.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6542    1.0466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1633    1.1575    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9669    0.2832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7844    0.1723    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1425    0.9155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9600    0.8047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1072   -0.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4778   -0.5404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6866    1.1955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2828    0.6253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4300   -0.1865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0719   -0.9297    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8733   -1.1254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0471   -1.7544    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3453   -1.3206    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5278   -1.2097    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1698   -1.9529    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3522   -1.8420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7820   -2.4383    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2051   -1.0303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4618   -0.6722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9316   -0.6395    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 18 17  1  1  0  0  0
 15 18  1  0  0  0  0
 18 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
 23 24  2  0  0  0  0
 25 23  1  6  0  0  0
  7 25  1  0  0  0  0
 19 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0235308

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=C)C(=O)O[C@H]1C\C(CO)=C\CC[C@@]2(C)O[C@H]2[C@H]2OC(=O)C(=C)[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C19H24O6/c1-10(2)17(21)23-13-8-12(9-20)6-5-7-19(4)16(25-19)15-14(13)11(3)18(22)24-15/h6,13-16,20H,1,3,5,7-9H2,2,4H3/b12-6-/t13-,14+,15-,16-,19+/m0/s1

> <INCHI_KEY>
AFQQBXILQNQSCA-WSFMCSFISA-N

> <FORMULA>
C19H24O6

> <MOLECULAR_WEIGHT>
348.395

> <EXACT_MASS>
348.157288493

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
35.704596388403644

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,4R,7Z,10S,11R)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0^{2,4}]tetradec-7-en-10-yl 2-methylprop-2-enoate

> <JCHEM_LOGP>
2.2716618816666663

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.157355395673896

> <JCHEM_PKA_STRONGEST_BASIC>
-2.729972749932192

> <JCHEM_POLAR_SURFACE_AREA>
85.36000000000001

> <JCHEM_REFRACTIVITY>
90.05459999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,4R,7Z,10S,11R)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0^{2,4}]tetradec-7-en-10-yl 2-methylprop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0235308 ((1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate)
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PDB for NP0235308 ((1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate)
HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       1.580   4.597   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.163   3.172   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.689   2.965   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.221   1.954   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.305   2.161   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       1.805   0.529   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.331   0.322   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.999   1.709   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.525   1.502   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.800  -0.013   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.625  -1.009   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       6.882   2.232   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.995   1.167   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.269  -0.348   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.601  -1.735   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.097  -2.101   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       7.555  -3.275   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.245  -2.465   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.719  -2.258   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.050  -3.645   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.524  -3.438   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       1.460  -4.551   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.249  -1.923   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.862  -1.255   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.606  -1.194   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   25                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   15   19                                                  
CONECT   19   18   20   25                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23    7   19                                                  
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

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3D PDB for NP0235308 ((1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate)
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SMILES for NP0235308 ((1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate)
CC(=C)C(=O)O[C@H]1C\C(CO)=C\CC[C@@]2(C)O[C@H]2[C@H]2OC(=O)C(=C)[C@H]12
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INCHI for NP0235308 ((1s,2s,4r,7z,10s,11r)-8-(hydroxymethyl)-4-methyl-12-methylidene-13-oxo-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-en-10-yl 2-methylprop-2-enoate)
InChI=1S/C19H24O6/c1-10(2)17(21)23-13-8-12(9-20)6-5-7-19(4)16(25-19)15-14(13)11(3)18(22)24-15/h6,13-16,20H,1,3,5,7-9H2,2,4H3/b12-6-/t13-,14+,15-,16-,19+/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC19H24O6
Average Mass348.3950 Da
Monoisotopic Mass348.15729 Da
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry NumberNot Available
SMILES
CC(=C)C(=O)O[C@H]1C\C(CO)=C\CC[C@@]2(C)O[C@H]2[C@H]2OC(=O)C(=C)[C@H]12
InChI Identifier
InChI=1S/C19H24O6/c1-10(2)17(21)23-13-8-12(9-20)6-5-7-19(4)16(25-19)15-14(13)11(3)18(22)24-15/h6,13-16,20H,1,3,5,7-9H2,2,4H3/b12-6-/t13-,14+,15-,16-,19+/m0/s1
InChI KeyAFQQBXILQNQSCA-WSFMCSFISA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassTerpene lactones  
Direct ParentGermacranolides and derivatives  
Alternative Parents
Substituents
  • Germacranolide
    • 

  • Germacrane sesquiterpenoid
    • 

  • Sesquiterpenoid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Gamma butyrolactone
    • 

  • Oxolane
    • 

  • Enoate ester
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Lactone
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Ether
    • 

  • Oxirane
    • 

  • Dialkyl ether
    • 

  • Carboxylic acid derivative
    • 

  • Organoheterocyclic compound
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Organooxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00049404  
Chemspider ID8422629  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10247142  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Garcia Manzano MF, Joray MB, Laiolo J, Palacios SM, Carpinella MC: Cytotoxic Activity of Germacrane-Type Sesquiterpene Lactones from Dimerostemma aspilioides. J Nat Prod. 2020 Jun 26;83(6):1909-1918. doi: 10.1021/acs.jnatprod.0c00115. Epub  2020 Jun 4. [PubMed:32496057  ] 
  2. LOTUS database [Link]