NP-MRD: Showing NP-Card for (2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0296361)

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Record Information

Version

2.0

Created at

2022-09-10 05:53:31 UTC

Updated at

2022-09-10 05:53:32 UTC

NP-MRD ID

NP0296361

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

(2R,3R,4R,5S,6S)-2-{[(1S,2R,4aS,8aR)-1-[(3Z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. Based on a literature review very few articles have been published on (2R,3R,4R,5S,6S)-2-{[(1S,2R,4aS,8aR)-1-[(3Z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102207532D          

 34 36  0  0  1  0            999 V2000
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309102207532D          

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   -0.1203   -4.5637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 10 19  1  0  0  0  0
 19 20  1  6  0  0  0
  7 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
  6 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 29 33  1  0  0  0  0
 33 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0296361

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CC[C@]2(CO[C@@H]3O[C@@H](CO)[C@@H](O)[C@@H](O)[C@H]3O)[C@H](CCC=C2C)[C@@]1(C)CC\C(CO)=C\CO

> <INCHI_IDENTIFIER>
InChI=1S/C26H44O8/c1-16-7-11-26(15-33-24-23(32)22(31)21(30)19(14-29)34-24)17(2)5-4-6-20(26)25(16,3)10-8-18(13-28)9-12-27/h5,9,16,19-24,27-32H,4,6-8,10-15H2,1-3H3/b18-9-/t16-,19+,20-,21-,22-,23-,24-,25+,26-/m1/s1

> <INCHI_KEY>
NRZBODCTCGUFOH-GXNXPDBFSA-N

> <FORMULA>
C26H44O8

> <MOLECULAR_WEIGHT>
484.63

> <EXACT_MASS>
484.303618377

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
53.452681254432434

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5S,6S)-2-{[(1S,2R,4aS,8aR)-1-[(3Z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
0.7689988169999988

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.194417410471814

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210274928264212

> <JCHEM_PKA_STRONGEST_BASIC>
-2.5275413290004973

> <JCHEM_POLAR_SURFACE_AREA>
139.84

> <JCHEM_REFRACTIVITY>
129.089

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R,5S,6S)-2-{[(1S,2R,4aS,8aR)-1-[(3Z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.001   5.390   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.335   7.700   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.667   7.700   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.334   5.390   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.000   6.160   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.000   3.080   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.390  -4.440   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.944  -4.440   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.405  -4.493   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.318  -5.853   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.857  -5.907   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -2.580  -7.267   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -1.764  -8.573   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.498  -7.159   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -0.225  -8.519   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   25                                                  
CONECT    7    6    2    8   21                                             
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   19                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   10   20                                                  
CONECT   20   19                                                            
CONECT   21    7   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23    6   26   27                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   33                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31                                                            
CONECT   33   29   34                                                       
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₄₄O₈

Average Mass

484.6300 Da

Monoisotopic Mass

484.30362 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@@H]1CC[C@]2(CO[C@@H]3O[C@@H](CO)[C@@H](O)[C@@H](O)[C@H]3O)[C@H](CCC=C2C)[C@@]1(C)CC\C(CO)=C\CO

InChI Identifier

InChI=1S/C26H44O8/c1-16-7-11-26(15-33-24-23(32)22(31)21(30)19(14-29)34-24)17(2)5-4-6-20(26)25(16,3)10-8-18(13-28)9-12-27/h5,9,16,19-24,27-32H,4,6-8,10-15H2,1-3H3/b18-9-/t16-,19+,20-,21-,22-,23-,24-,25+,26-/m1/s1

InChI Key

NRZBODCTCGUFOH-GXNXPDBFSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Diterpene glycosides

Alternative Parents

Substituents

Diterpene glycoside
Diterpenoid
Clerodane diterpenoid
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Hexose monosaccharide
Alkyl glycoside
O-glycosyl compound
Glycosyl compound
Fatty alcohol
Fatty acyl
Oxane
Monosaccharide
Secondary alcohol
Oxacycle
Polyol
Organoheterocyclic compound
Acetal
Primary alcohol
Hydrocarbon derivative
Organic oxygen compound
Alcohol
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

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

552374

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

636631

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0296361)

MOL for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0296361 ((2r,3r,4r,5s,6s)-2-{[(1s,2r,4as,8ar)-1-[(3z)-5-hydroxy-3-(hydroxymethyl)pent-3-en-1-yl]-1,2,5-trimethyl-2,3,4,7,8,8a-hexahydronaphthalen-4a-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)