NP-MRD: Showing NP-Card for (2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate (NP0246295)

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Record Information

Version

2.0

Created at

2022-09-07 07:42:54 UTC

Updated at

2022-09-07 07:42:54 UTC

NP-MRD ID

NP0246295

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate

Description

Verbenabraside A belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. (2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate is found in Verbena brasiliensis. Based on a literature review very few articles have been published on Verbenabraside A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072209422D          

 37 40  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072209422D          

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 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 22 29  1  0  0  0  0
 16 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 11 32  1  0  0  0  0
 32 33  1  1  0  0  0
 34  8  1  6  0  0  0
  4 34  1  0  0  0  0
 34 35  1  0  0  0  0
  2 35  1  0  0  0  0
 35 36  1  6  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0246295

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C[C@@H]2OC(=O)[C@@H](CO[C@@H]3O[C@H](CO)[C@@H](OC(=O)\C=C\C4=CC=C(O)C(O)=C4)[C@H](O)[C@H]3O)[C@@H]2[C@@H]1CO

> <INCHI_IDENTIFIER>
InChI=1S/C25H32O12/c1-11-6-17-20(13(11)8-26)14(24(33)35-17)10-34-25-22(32)21(31)23(18(9-27)36-25)37-19(30)5-3-12-2-4-15(28)16(29)7-12/h2-5,7,11,13-14,17-18,20-23,25-29,31-32H,6,8-10H2,1H3/b5-3+/t11-,13+,14-,17-,18+,20-,21+,22+,23+,25+/m0/s1

> <INCHI_KEY>
YLXHBUXEDMVNGL-KVWIEXSUSA-N

> <FORMULA>
C25H32O12

> <MOLECULAR_WEIGHT>
524.519

> <EXACT_MASS>
524.18937647

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
52.481415931740415

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5R,6R)-6-{[(3R,3aS,4R,5S,6aS)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydro-2H-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate

> <JCHEM_LOGP>
0.12334850566666745

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.10704506302042

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.208226929200718

> <JCHEM_PKA_STRONGEST_BASIC>
-2.602646795291049

> <JCHEM_POLAR_SURFACE_AREA>
192.44

> <JCHEM_REFRACTIVITY>
125.16120000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,5R,6R)-6-{[(3R,3aS,4R,5S,6aS)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate

> <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      -0.075  -0.476   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.834   0.294   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.299   0.770   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.744  -0.476   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.775  -3.186   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.281  -3.507   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.757  -4.971   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.264  -5.291   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.739  -6.756   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.246  -7.076   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.276  -5.932   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.709  -7.900   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       9.185  -9.365   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      10.691  -9.685   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      11.167 -11.150   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      11.722  -8.541   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.228  -8.861   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.258  -7.717   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      13.783  -6.252   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.813  -5.108   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      16.319  -5.428   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      17.350  -4.283   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      16.795  -6.892   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      18.302  -7.212   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      15.765  -8.037   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.203  -7.580   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.172  -8.725   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       6.727  -6.116   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.220  -5.795   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       1.894  -3.186   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       0.388  -3.507   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   35                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   34                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   34                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   32                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   30                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   29                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   22                                                       
CONECT   30   16   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   11   33                                                  
CONECT   33   32                                                            
CONECT   34    8    4   35                                                  
CONECT   35   34    2   36                                                  
CONECT   36   35   37                                                       
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₂O₁₂

Average Mass

524.5190 Da

Monoisotopic Mass

524.18938 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@H]1C[C@@H]2OC(=O)[C@@H](CO[C@@H]3O[C@H](CO)[C@@H](OC(=O)\C=C\C4=CC=C(O)C(O)=C4)[C@H](O)[C@H]3O)[C@@H]2[C@@H]1CO

InChI Identifier

InChI=1S/C25H32O12/c1-11-6-17-20(13(11)8-26)14(24(33)35-17)10-34-25-22(32)21(31)23(18(9-27)36-25)37-19(30)5-3-12-2-4-15(28)16(29)7-12/h2-5,7,11,13-14,17-18,20-23,25-29,31-32H,6,8-10H2,1H3/b5-3+/t11-,13+,14-,17-,18+,20-,21+,22+,23+,25+/m0/s1

InChI Key

YLXHBUXEDMVNGL-KVWIEXSUSA-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
Verbena brasiliensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Terpene lactone
Cinnamic acid or derivatives
Coumaric acid or derivatives
Hexose monosaccharide
Hydroxycinnamic acid or derivatives
Cinnamic acid ester
Glycosyl compound
O-glycosyl compound
Aromatic monoterpenoid
Monoterpenoid
Bicyclic monoterpenoid
Catechol
Styrene
Fatty acid ester
Phenol
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Oxane
Dicarboxylic acid or derivatives
Monosaccharide
Gamma butyrolactone
Monocyclic benzene moiety
Benzenoid
Fatty acyl
Oxolane
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Carboxylic acid ester
Lactone
Acetal
Carboxylic acid derivative
Organoheterocyclic compound
Oxacycle
Alcohol
Primary alcohol
Organic oxide
Carbonyl group
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00032479

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

101412294

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,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate (NP0246295)

MOL for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D MOL for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D SDF for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D-SDF for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

PDB for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D PDB for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

SMILES for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

INCHI for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

Structure for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D Structure for NP0246295 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4r,5s,6as)-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydrocyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(3,4-dihydroxyphenyl)prop-2-enoate)