NP-MRD: Showing NP-Card for (2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol (NP0306813)

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Record Information

Version

2.0

Created at

2022-09-10 23:31:54 UTC

Updated at

2022-09-10 23:31:54 UTC

NP-MRD ID

NP0306813

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol

Description

(2S,3R,4S,5S)-2-{[(1S,4aS,6R,8S,8aR)-6-hydroxy-4-[(3E)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Based on a literature review very few articles have been published on (2S,3R,4S,5S)-2-{[(1S,4aS,6R,8S,8aR)-6-hydroxy-4-[(3E)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112201312D          

 34 36  0  0  1  0            999 V2000
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.2868    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  8 33  1  0  0  0  0
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 33 34  1  1  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309112201312D          

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  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 15 14  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 15 22  1  0  0  0  0
 22 23  1  6  0  0  0
 24 13  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  1  0  0  0
 27 28  1  0  0  0  0
 25 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
  8 33  1  0  0  0  0
 24 33  1  0  0  0  0
 33 34  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0306813

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CCC1=C(CO)C[C@H](O[C@@H]2OC[C@H](O)[C@H](O)[C@H]2O)[C@H]2[C@@](C)(CO)C[C@H](O)C[C@]12C)=C/CO

> <INCHI_IDENTIFIER>
InChI=1S/C25H42O9/c1-14(6-7-26)4-5-17-15(11-27)8-19(34-23-21(32)20(31)18(30)12-33-23)22-24(2,13-28)9-16(29)10-25(17,22)3/h6,16,18-23,26-32H,4-5,7-13H2,1-3H3/b14-6+/t16-,18-,19-,20-,21+,22-,23-,24+,25+/m0/s1

> <INCHI_KEY>
ODUBMYSXJWMARF-PXGCCCARSA-N

> <FORMULA>
C25H42O9

> <MOLECULAR_WEIGHT>
486.602

> <EXACT_MASS>
486.282882932

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
52.948473937332814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S)-2-{[(1S,4aS,6R,8S,8aR)-6-hydroxy-4-[(3E)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol

> <JCHEM_LOGP>
-1.3398073896666673

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.381542371285907

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.24459685353204

> <JCHEM_PKA_STRONGEST_BASIC>
-2.2170474255008905

> <JCHEM_POLAR_SURFACE_AREA>
160.07

> <JCHEM_REFRACTIVITY>
126.12190000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S)-2-{[(1S,4aS,6R,8S,8aR)-6-hydroxy-4-[(3E)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.334 -10.010   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       8.002   4.620   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.345   1.180   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.325   1.180   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       7.841   0.912   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.001  -3.850   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    2    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   33                                                  
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14   24                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   15   23                                                  
CONECT   23   22                                                            
CONECT   24   13   25   33                                                  
CONECT   25   24   26   27   29                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27                                                            
CONECT   29   25   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32    8   24   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

C₂₅H₄₂O₉

Average Mass

486.6020 Da

Monoisotopic Mass

486.28288 Da

IUPAC Name

(2S,3R,4S,5S)-2-{[(1S,4aS,6R,8S,8aR)-6-hydroxy-4-[(3E)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol

Traditional Name

(2S,3R,4S,5S)-2-{[(1S,4aS,6R,8S,8aR)-6-hydroxy-4-[(3E)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

C\C(CCC1=C(CO)C[C@H](O[C@@H]2OC[C@H](O)[C@H](O)[C@H]2O)[C@H]2[C@@](C)(CO)C[C@H](O)C[C@]12C)=C/CO

InChI Identifier

InChI=1S/C25H42O9/c1-14(6-7-26)4-5-17-15(11-27)8-19(34-23-21(32)20(31)18(30)12-33-23)22-24(2,13-28)9-16(29)10-25(17,22)3/h6,16,18-23,26-32H,4-5,7-13H2,1-3H3/b14-6+/t16-,18-,19-,20-,21+,22-,23-,24+,25+/m0/s1

InChI Key

ODUBMYSXJWMARF-PXGCCCARSA-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 diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Labdane diterpenoid
Diterpenoid
Glycosyl compound
O-glycosyl compound
Pentose monosaccharide
Fatty alcohol
Fatty acyl
Monosaccharide
Oxane
Cyclic alcohol
Secondary alcohol
Polyol
Acetal
Organoheterocyclic compound
Oxacycle
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
logP	-1.3	ChemAxon
pKa (Strongest Acidic)	12.24	ChemAxon
pKa (Strongest Basic)	-2.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	160.07 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	126.12 m³·mol⁻¹	ChemAxon
Polarizability	52.95 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

15705453

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol (NP0306813)

MOL for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)

3D MOL for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)

3D SDF for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)

3D-SDF for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)

PDB for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)

3D PDB for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)

SMILES for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)

INCHI for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)

Structure for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)

3D Structure for NP0306813 ((2s,3r,4s,5s)-2-{[(1s,4as,6r,8s,8ar)-6-hydroxy-4-[(3e)-5-hydroxy-3-methylpent-3-en-1-yl]-3,8-bis(hydroxymethyl)-4a,8-dimethyl-1,2,5,6,7,8a-hexahydronaphthalen-1-yl]oxy}oxane-3,4,5-triol)