NP-MRD: Showing NP-Card for [(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate (NP0255830)

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Record Information

Version

2.0

Created at

2022-09-07 20:27:41 UTC

Updated at

2022-09-07 20:27:41 UTC

NP-MRD ID

NP0255830

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate

Description

[(2R,3S,4S,5R,6R)-6-{[(4S)-5-[(3aR,4R,5R,6aR)-5-hydroxy-5-methyl-3-methylidene-2-oxo-hexahydro-2H-cyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. [(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate is found in Picradeniopsis woodhousei. Based on a literature review very few articles have been published on [(2R,3S,4S,5R,6R)-6-{[(4S)-5-[(3aR,4R,5R,6aR)-5-hydroxy-5-methyl-3-methylidene-2-oxo-hexahydro-2H-cyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072222272D          

 34 36  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072222272D          

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 32 33  1  1  0  0  0
 11 34  1  0  0  0  0
 34  2  1  6  0  0  0
  6 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0255830

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](CCCO[C@@H]1O[C@H](COC(C)=O)[C@@H](O)[C@H](O)[C@H]1O)C(=O)[C@@H]1[C@H]2[C@@H](C[C@@]1(C)O)OC(=O)C2=C

> <INCHI_IDENTIFIER>
InChI=1S/C23H34O11/c1-10(17(25)16-15-11(2)21(29)33-13(15)8-23(16,4)30)6-5-7-31-22-20(28)19(27)18(26)14(34-22)9-32-12(3)24/h10,13-16,18-20,22,26-28,30H,2,5-9H2,1,3-4H3/t10-,13+,14+,15+,16-,18+,19-,20+,22+,23+/m0/s1

> <INCHI_KEY>
DVXWVFXAXIIFHO-LZMFOXHKSA-N

> <FORMULA>
C23H34O11

> <MOLECULAR_WEIGHT>
486.514

> <EXACT_MASS>
486.210111915

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
49.66620059875406

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6R)-6-{[(4S)-5-[(3aR,4R,5R,6aR)-5-hydroxy-5-methyl-3-methylidene-2-oxo-hexahydro-2H-cyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate

> <JCHEM_LOGP>
-0.4298511336666663

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.187566454595174

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.209458419872478

> <JCHEM_PKA_STRONGEST_BASIC>
-3.018009377370272

> <JCHEM_POLAR_SURFACE_AREA>
169.04999999999998

> <JCHEM_REFRACTIVITY>
114.09620000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6R)-6-{[(4S)-5-[(3aR,4R,5R,6aR)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.308   1.258   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.934   2.665   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.441   2.985   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -6.585   1.955   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -5.601   4.517   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.195   5.143   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.425   6.477   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.918   6.157   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.757   7.688   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.378   6.157   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.757   4.625   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.424   3.855   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.424   2.315   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.910   4.625   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.910   6.165   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.244   3.855   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.577   4.625   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.911   3.855   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.245   4.625   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       7.578   3.855   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       8.912   4.625   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      10.246   3.855   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.579   4.625   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      11.579   6.165   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      12.913   6.935   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.913   8.475   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      14.247   6.165   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      10.246   2.315   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      11.579   1.545   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       8.912   1.545   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.912   0.005   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       7.578   2.315   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       6.245   1.545   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -3.164   3.999   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   34                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8   12   34                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   32                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   28                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   22   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   20   33                                                  
CONECT   33   32                                                            
CONECT   34   11    2    6                                                  
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Value	Source
[(2R,3S,4S,5R,6R)-6-{[(4S)-5-[(3ar,4R,5R,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-hexahydro-2H-cyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetic acid	Generator

Chemical Formula

C₂₃H₃₄O₁₁

Average Mass

486.5140 Da

Monoisotopic Mass

486.21011 Da

IUPAC Name

[(2R,3S,4S,5R,6R)-6-{[(4S)-5-[(3aR,4R,5R,6aR)-5-hydroxy-5-methyl-3-methylidene-2-oxo-hexahydro-2H-cyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate

Traditional Name

[(2R,3S,4S,5R,6R)-6-{[(4S)-5-[(3aR,4R,5R,6aR)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate

CAS Registry Number

Not Available

SMILES

C[C@@H](CCCO[C@@H]1O[C@H](COC(C)=O)[C@@H](O)[C@H](O)[C@H]1O)C(=O)[C@@H]1[C@H]2[C@@H](C[C@@]1(C)O)OC(=O)C2=C

InChI Identifier

InChI=1S/C23H34O11/c1-10(17(25)16-15-11(2)21(29)33-13(15)8-23(16,4)30)6-5-7-31-22-20(28)19(27)18(26)14(34-22)9-32-12(3)24/h10,13-16,18-20,22,26-28,30H,2,5-9H2,1,3-4H3/t10-,13+,14+,15+,16-,18+,19-,20+,22+,23+/m0/s1

InChI Key

DVXWVFXAXIIFHO-LZMFOXHKSA-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
Picradeniopsis woodhousei	LOTUS Database	35616633

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
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Glycosyl compound
O-glycosyl compound
Bicyclic monoterpenoid
Monoterpenoid
Dicarboxylic acid or derivatives
Fatty acyl
Gamma butyrolactone
Monosaccharide
Oxane
Cyclic alcohol
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Tertiary alcohol
Lactone
Ketone
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Carboxylic acid derivative
Polyol
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxygen compound
Organic oxide
Organooxygen compound
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	-0.43	ChemAxon
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	169.05 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	114.1 m³·mol⁻¹	ChemAxon
Polarizability	49.67 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

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

162970988

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate (NP0255830)

MOL for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)

3D MOL for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)

3D SDF for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)

3D-SDF for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)

PDB for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)

3D PDB for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)

SMILES for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)

INCHI for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)

Structure for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)

3D Structure for NP0255830 ([(2r,3s,4s,5r,6r)-6-{[(4s)-5-[(3ar,4r,5r,6ar)-5-hydroxy-5-methyl-3-methylidene-2-oxo-tetrahydrocyclopenta[b]furan-4-yl]-4-methyl-5-oxopentyl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl acetate)