NP-MRD: Showing NP-Card for Pycnolide (NP0058958)

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Record Information

Version

1.0

Created at

2022-04-28 04:15:12 UTC

Updated at

2022-04-28 04:15:12 UTC

NP-MRD ID

NP0058958

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pycnolide

Description

(1R,3E)-5-hydroxy-1-[(2S,3R)-2-[(1E)-3-hydroxy-2-methylprop-1-en-1-yl]-4-methylidene-5-oxooxolan-3-yl]-3-methylpent-3-en-1-yl (2Z)-2-methylbut-2-enoate belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. Pycnolide is found in Liatris pycnostachya. Based on a literature review very few articles have been published on (1R,3E)-5-hydroxy-1-[(2S,3R)-2-[(1E)-3-hydroxy-2-methylprop-1-en-1-yl]-4-methylidene-5-oxooxolan-3-yl]-3-methylpent-3-en-1-yl (2Z)-2-methylbut-2-enoate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282206152D          

 26 26  0  0  1  0            999 V2000
   -2.1356   -0.5619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3071    0.2451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819   -0.8974    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4681   -1.7179    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2751   -1.8894    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6876   -1.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5081   -1.0887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8551   -2.2699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0266   -3.0769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8112   -3.3318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4135   -3.6289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5850   -4.4359    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -0.4849    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6674    0.3401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    0.7526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    1.5776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0964    1.9901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8109    1.5776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1889    0.5811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -0.8974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615   -0.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615    0.3401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760   -0.8974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904   -0.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    0.3401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760   -1.7224    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  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  2  0  0  0  0
  4  8  1  6  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  3 13  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 15 19  1  0  0  0  0
 13 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
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
M  END


  Mrv1652304282206152D          

 26 26  0  0  1  0            999 V2000
   -2.1356   -0.5619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3071    0.2451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819   -0.8974    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4681   -1.7179    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2751   -1.8894    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6876   -1.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5081   -1.0887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8551   -2.2699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0266   -3.0769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8112   -3.3318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4135   -3.6289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5850   -4.4359    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -0.4849    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6674    0.3401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    0.7526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    1.5776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0964    1.9901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8109    1.5776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1889    0.5811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -0.8974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615   -0.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615    0.3401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760   -0.8974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904   -0.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    0.3401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760   -1.7224    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  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  2  0  0  0  0
  4  8  1  6  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  3 13  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 15 19  1  0  0  0  0
 13 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
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0058958

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C(\C)C(=O)O[C@H](C\C(C)=C\CO)[C@@H]1[C@@H](OC(=O)C1=C)\C=C(/C)CO

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O6/c1-6-14(4)19(23)25-16(9-12(2)7-8-21)18-15(5)20(24)26-17(18)10-13(3)11-22/h6-7,10,16-18,21-22H,5,8-9,11H2,1-4H3/b12-7+,13-10+,14-6-/t16-,17+,18-/m1/s1

> <INCHI_KEY>
GHEIESSKOYFMTB-CACSTRHPSA-N

> <FORMULA>
C20H28O6

> <MOLECULAR_WEIGHT>
364.438

> <EXACT_MASS>
364.188588622

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
38.66651198490925

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,3E)-5-hydroxy-1-[(2S,3R)-2-[(1E)-3-hydroxy-2-methylprop-1-en-1-yl]-4-methylidene-5-oxooxolan-3-yl]-3-methylpent-3-en-1-yl (2Z)-2-methylbut-2-enoate

> <ALOGPS_LOGP>
2.49

> <JCHEM_LOGP>
2.5861256706666667

> <ALOGPS_LOGS>
-3.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.358048794029294

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.126526225666655

> <JCHEM_PKA_STRONGEST_BASIC>
-2.2170688008104094

> <JCHEM_POLAR_SURFACE_AREA>
93.06

> <JCHEM_REFRACTIVITY>
100.6985

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3E)-5-hydroxy-1-[(2S,3R)-2-[(1E)-3-hydroxy-2-methylprop-1-en-1-yl]-4-methylidene-5-oxooxolan-3-yl]-3-methylpent-3-en-1-yl (2Z)-2-methylbut-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -3.986  -1.049   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.307   0.458   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.580  -1.675   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.741  -3.207   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.247  -3.527   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -5.017  -2.193   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -6.548  -2.032   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.596  -4.237   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.916  -5.744   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.381  -6.219   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.772  -6.774   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.092  -8.280   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.246  -0.905   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.246   0.635   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.580   1.405   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.580   2.945   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.913   3.715   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -5.247   2.945   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -4.086   1.085   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.088  -1.675   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.421  -0.905   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       1.421   0.635   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.755  -1.675   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.089  -0.905   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.089   0.635   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.755  -3.215   0.000  0.00  0.00           C+0
CONECT    1    2    3    6                                                  
CONECT    2    1                                                            
CONECT    3    1    4   13                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    4    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11                                                            
CONECT   13    3   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   19                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   15                                                            
CONECT   20   13   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   23                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   52    0
END

View in JSmol

Synonyms

Value	Source
(1R,3E)-5-Hydroxy-1-[(2S,3R)-2-[(1E)-3-hydroxy-2-methylprop-1-en-1-yl]-4-methylidene-5-oxooxolan-3-yl]-3-methylpent-3-en-1-yl (2Z)-2-methylbut-2-enoic acid	Generator

Chemical Formula

C₂₀H₂₈O₆

Average Mass

364.4380 Da

Monoisotopic Mass

364.18859 Da

IUPAC Name

(1R,3E)-5-hydroxy-1-[(2S,3R)-2-[(1E)-3-hydroxy-2-methylprop-1-en-1-yl]-4-methylidene-5-oxooxolan-3-yl]-3-methylpent-3-en-1-yl (2Z)-2-methylbut-2-enoate

Traditional Name

(1R,3E)-5-hydroxy-1-[(2S,3R)-2-[(1E)-3-hydroxy-2-methylprop-1-en-1-yl]-4-methylidene-5-oxooxolan-3-yl]-3-methylpent-3-en-1-yl (2Z)-2-methylbut-2-enoate

CAS Registry Number

Not Available

SMILES

C\C=C(\C)C(=O)O[C@H](C\C(C)=C\CO)[C@@H]1[C@@H](OC(=O)C1=C)\C=C(/C)CO

InChI Identifier

InChI=1S/C20H28O6/c1-6-14(4)19(23)25-16(9-12(2)7-8-21)18-15(5)20(24)26-17(18)10-13(3)11-22/h6-7,10,16-18,21-22H,5,8-9,11H2,1-4H3/b12-7+,13-10+,14-6-/t16-,17+,18-/m1/s1

InChI Key

GHEIESSKOYFMTB-CACSTRHPSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Liatris pycnostachya	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Monoterpenoid
Monocyclic monoterpenoid
Fatty alcohol
Fatty acid ester
Fatty acyl
Gamma butyrolactone
Dicarboxylic acid or derivatives
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	2.49	ALOGPS
logP	2.59	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	15.13	ChemAxon
pKa (Strongest Basic)	-2.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.06 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	100.7 m³·mol⁻¹	ChemAxon
Polarizability	38.67 Å³	ChemAxon
Number of Rings	1	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

162955144

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pycnolide (NP0058958)

MOL for NP0058958 (Pycnolide)

3D MOL for NP0058958 (Pycnolide)

3D SDF for NP0058958 (Pycnolide)

3D-SDF for NP0058958 (Pycnolide)

PDB for NP0058958 (Pycnolide)

3D PDB for NP0058958 (Pycnolide)

SMILES for NP0058958 (Pycnolide)

INCHI for NP0058958 (Pycnolide)

Structure for NP0058958 (Pycnolide)

3D Structure for NP0058958 (Pycnolide)