NP-MRD: Showing NP-Card for (3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate (NP0282687)

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Record Information

Version

2.0

Created at

2022-09-09 09:37:32 UTC

Updated at

2022-09-09 09:37:32 UTC

NP-MRD ID

NP0282687

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate

Description

(3R,5R)-2,5-dihydroxy-2-methyl-6-[(1R,2S,3S,4R,5S)-2,4,5-trihydroxy-4-methyl-3-{[(2Z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2Z)-2-methylbut-2-enoate belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. (3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate is found in Ligularia cymbulifera. Based on a literature review very few articles have been published on (3R,5R)-2,5-dihydroxy-2-methyl-6-[(1R,2S,3S,4R,5S)-2,4,5-trihydroxy-4-methyl-3-{[(2Z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2Z)-2-methylbut-2-enoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092211372D          

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M  END

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M  END


  Mrv1652309092211372D          

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  6 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 14 17  1  0  0  0  0
 18  2  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  1  0  0  0
 22 25  1  0  0  0  0
 25 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  2  0  0  0  0
 31 32  1  0  0  0  0
 25 33  1  0  0  0  0
 18 33  1  0  0  0  0
 33 34  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0282687

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C25H40O9/c1-9-13(3)22(29)33-19(24(6,7)31)12-17(26)15(5)16-11-18(27)25(8,32)21(20(16)28)34-23(30)14(4)10-2/h9-10,16-21,26-28,31-32H,5,11-12H2,1-4,6-8H3/b13-9-,14-10-/t16-,17-,18+,19-,20+,21+,25-/m1/s1

> <INCHI_KEY>
LGRBNEWZMTYTSW-FLEZKLDCSA-N

> <FORMULA>
C25H40O9

> <MOLECULAR_WEIGHT>
484.586

> <EXACT_MASS>
484.267232868

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
50.93120294498618

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,5R)-2,5-dihydroxy-2-methyl-6-[(1R,2S,3S,4R,5S)-2,4,5-trihydroxy-4-methyl-3-{[(2Z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2Z)-2-methylbut-2-enoate

> <JCHEM_LOGP>
1.7270189476666669

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.68572453722961

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.869213359875499

> <JCHEM_PKA_STRONGEST_BASIC>
-3.003988955955358

> <JCHEM_POLAR_SURFACE_AREA>
153.75

> <JCHEM_REFRACTIVITY>
126.67859999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,5R)-2,5-dihydroxy-2-methyl-6-[(1R,2S,3S,4R,5S)-2,4,5-trihydroxy-4-methyl-3-{[(2Z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2Z)-2-methylbut-2-enoate

> <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       0.564  -0.976   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.874  -2.310   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.644  -3.644   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.644  -0.976   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.184  -0.976   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.954   0.357   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       7.494   0.357   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.264  -0.976   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       8.264   1.691   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.804   1.691   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.494   3.025   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.954   3.025   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.954  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.620  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.287  -1.540   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.724  -3.644   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       0.564  -3.644   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334  -4.977   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.564  -6.311   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.334  -7.645   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.976  -6.311   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.709  -7.828   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -2.423  -6.838   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -1.746  -4.977   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -3.286  -4.977   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -4.056  -6.311   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -3.286  -7.645   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -5.596  -6.311   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -6.366  -4.977   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -6.366  -7.645   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -5.596  -8.978   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.976  -3.644   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -1.746  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   18                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   14                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12                                                            
CONECT   14    6   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14                                                            
CONECT   18    2   19   33                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24   25                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   22   26   33                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31                                                            
CONECT   33   25   18   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   68    0
END

View in JSmol

Synonyms

Value	Source
(3R,5R)-2,5-Dihydroxy-2-methyl-6-[(1R,2S,3S,4R,5S)-2,4,5-trihydroxy-4-methyl-3-{[(2Z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2Z)-2-methylbut-2-enoic acid	Generator

Chemical Formula

C₂₅H₄₀O₉

Average Mass

484.5860 Da

Monoisotopic Mass

484.26723 Da

IUPAC Name

(3R,5R)-2,5-dihydroxy-2-methyl-6-[(1R,2S,3S,4R,5S)-2,4,5-trihydroxy-4-methyl-3-{[(2Z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2Z)-2-methylbut-2-enoate

Traditional Name

(3R,5R)-2,5-dihydroxy-2-methyl-6-[(1R,2S,3S,4R,5S)-2,4,5-trihydroxy-4-methyl-3-{[(2Z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2Z)-2-methylbut-2-enoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C25H40O9/c1-9-13(3)22(29)33-19(24(6,7)31)12-17(26)15(5)16-11-18(27)25(8,32)21(20(16)28)34-23(30)14(4)10-2/h9-10,16-21,26-28,31-32H,5,11-12H2,1-4,6-8H3/b13-9-,14-10-/t16-,17-,18+,19-,20+,21+,25-/m1/s1

InChI Key

LGRBNEWZMTYTSW-FLEZKLDCSA-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
Ligularia cymbulifera	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Bisabolane sesquiterpenoid
Sesquiterpenoid
Cyclohexanol
Fatty acid ester
Cyclitol or derivatives
Fatty acyl
Dicarboxylic acid or derivatives
Cyclic alcohol
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Carboxylic acid derivative
Polyol
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
Organooxygen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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	1.73	ChemAxon
pKa (Strongest Acidic)	12.87	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	153.75 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	126.68 m³·mol⁻¹	ChemAxon
Polarizability	50.93 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

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

162847118

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate (NP0282687)

MOL for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)

3D MOL for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)

3D SDF for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)

3D-SDF for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)

PDB for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)

3D PDB for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)

SMILES for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)

INCHI for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)

Structure for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)

3D Structure for NP0282687 ((3r,5r)-2,5-dihydroxy-2-methyl-6-[(1r,2s,3s,4r,5s)-2,4,5-trihydroxy-4-methyl-3-{[(2z)-2-methylbut-2-enoyl]oxy}cyclohexyl]hept-6-en-3-yl (2z)-2-methylbut-2-enoate)