NP-MRD: Showing NP-Card for Podolactone E (NP0050246)

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Record Information

Version

2.0

Created at

2022-04-27 20:49:45 UTC

Updated at

2022-04-27 20:49:45 UTC

NP-MRD ID

NP0050246

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Podolactone E

Description

(1S,2S,4R,5R,6R,9S,12R,17R)-12-ethenyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0²,⁴.0⁶,¹⁷.0¹¹,¹⁶]Heptadeca-10,15-diene-7,14-dione belongs to the class of organic compounds known as naphthopyrans. Naphthopyrans are compounds containing a pyran ring fused to a naphthalene moiety. Furan is a 6 membered-ring non-aromatic ring with five carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings. Podolactone E is found in Podocarpus neriifolius . Based on a literature review very few articles have been published on (1S,2S,4R,5R,6R,9S,12R,17R)-12-ethenyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0²,⁴.0⁶,¹⁷.0¹¹,¹⁶]Heptadeca-10,15-diene-7,14-dione.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304272222492D          

 24 28  0  0  1  0            999 V2000
   -0.4633   -1.3639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6566   -0.5619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0613   -1.9324    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8680   -2.7344    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0767   -2.9680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1166   -3.7700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9078   -4.0037    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5057   -3.4352    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3124   -2.6332    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5212   -2.3996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3279   -1.5976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1864   -2.1789    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9118   -2.5719    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9341   -3.3966    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2311   -3.8283    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0815   -4.6396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6499   -5.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2636   -4.7480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9114   -4.2949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6595   -3.7896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8895   -1.7472    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2332   -1.8120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4659   -3.3028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2726   -4.1049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
  1 11  1  0  0  0  0
  9 12  1  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
  8 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
  7 18  1  1  0  0  0
 15 19  1  1  0  0  0
 14 20  1  6  0  0  0
 13 21  1  6  0  0  0
 12 21  1  6  0  0  0
  9 22  1  6  0  0  0
  4 23  1  1  0  0  0
 23 24  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0050246

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C18H18O6/c1-4-9-7-5-10-13-17(2,8(7)6-11(19)22-9)15-12(24-15)14(20)18(13,3)16(21)23-10/h4-6,9-10,12-15,20H,1H2,2-3H3/t9-,10+,12-,13-,14+,15-,17-,18-/m1/s1

> <INCHI_KEY>
GYGGJZCRRDXTBB-DPYVYZABSA-N

> <FORMULA>
C18H18O6

> <MOLECULAR_WEIGHT>
330.336

> <EXACT_MASS>
330.1103383

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
32.04095023610333

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,4R,5R,6R,9S,12R,17R)-12-ethenyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0^{2,4}.0^{6,17}.0^{11,16}]heptadeca-10,15-diene-7,14-dione

> <ALOGPS_LOGP>
1.03

> <JCHEM_LOGP>
0.8492755553333344

> <ALOGPS_LOGS>
-1.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.41240539678699

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4932138794453698

> <JCHEM_POLAR_SURFACE_AREA>
85.36000000000001

> <JCHEM_REFRACTIVITY>
81.9954

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.75e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,4R,5R,6R,9S,12R,17R)-12-ethenyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0^{2,4}.0^{6,17}.0^{11,16}]heptadeca-10,15-diene-7,14-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-22         0                                  
HETATM    1  C   UNK     0      -0.865  -2.546   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.226  -1.049   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -1.981  -3.607   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.620  -5.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.143  -5.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.218  -7.037   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.695  -7.474   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.811  -6.412   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.450  -4.915   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.973  -4.479   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.612  -2.982   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.081  -4.067   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.435  -4.801   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.477  -6.340   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.165  -7.146   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.885  -8.661   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.946  -9.777   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       2.359  -8.863   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.435  -8.017   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       6.831  -7.074   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       5.394  -3.261   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.302  -3.382   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -2.736  -6.165   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.376  -7.662   0.000  0.00  0.00           C+0
CONECT    1    2    3   11                                                  
CONECT    2    1                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5   23                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   18                                                  
CONECT    8    7    9   15                                                  
CONECT    9    8   10   12   22                                             
CONECT   10    9    5   11                                                  
CONECT   11   10    1                                                       
CONECT   12    9   13   21                                                  
CONECT   13   12   14   21                                                  
CONECT   14   13   15   20                                                  
CONECT   15   14    8   16   19                                             
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    7                                                       
CONECT   19   15                                                            
CONECT   20   14                                                            
CONECT   21   13   12                                                       
CONECT   22    9                                                            
CONECT   23    4   24                                                       
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₁₈O₆

Average Mass

330.3360 Da

Monoisotopic Mass

330.11034 Da

IUPAC Name

(1S,2S,4R,5R,6R,9S,12R,17R)-12-ethenyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0^{2,4}.0^{6,17}.0^{11,16}]heptadeca-10,15-diene-7,14-dione

Traditional Name

(1S,2S,4R,5R,6R,9S,12R,17R)-12-ethenyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0^{2,4}.0^{6,17}.0^{11,16}]heptadeca-10,15-diene-7,14-dione

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C18H18O6/c1-4-9-7-5-10-13-17(2,8(7)6-11(19)22-9)15-12(24-15)14(20)18(13,3)16(21)23-10/h4-6,9-10,12-15,20H,1H2,2-3H3/t9-,10+,12-,13-,14+,15-,17-,18-/m1/s1

InChI Key

GYGGJZCRRDXTBB-DPYVYZABSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Podocarpus neriifolius	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthopyrans. Naphthopyrans are compounds containing a pyran ring fused to a naphthalene moiety. Furan is a 6 membered-ring non-aromatic ring with five carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Naphthopyrans

Sub Class

Not Available

Direct Parent

Naphthopyrans

Alternative Parents

Substituents

Naphthopyran
Naphthalene
Oxepane
Dihydropyranone
Pyran
Gamma butyrolactone
Dicarboxylic acid or derivatives
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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	1.03	ALOGPS
logP	0.85	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	13.41	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	85.36 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	82 m³·mol⁻¹	ChemAxon
Polarizability	32.04 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

163011376

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Podolactone E (NP0050246)

MOL for NP0050246 (Podolactone E)

3D MOL for NP0050246 (Podolactone E)

3D SDF for NP0050246 (Podolactone E)

3D-SDF for NP0050246 (Podolactone E)

PDB for NP0050246 (Podolactone E)

3D PDB for NP0050246 (Podolactone E)

SMILES for NP0050246 (Podolactone E)

INCHI for NP0050246 (Podolactone E)

Structure for NP0050246 (Podolactone E)

3D Structure for NP0050246 (Podolactone E)