NP-MRD: Showing NP-Card for 2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol (NP0155406)

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Record Information

Version

2.0

Created at

2022-09-02 12:27:28 UTC

Updated at

2022-09-02 12:27:28 UTC

NP-MRD ID

NP0155406

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol

Description

2-(Hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-1,2,3,4,4a,4b,5,6,7,8,10,10a-dodecahydrophenanthren-2-yl]oxy}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. 2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol is found in Isodon eriocalyx. 2-(Hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-1,2,3,4,4a,4b,5,6,7,8,10,10a-dodecahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171521442D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004171521442D          

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   -1.3480   -1.3480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1730   -1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5855   -0.6336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4105   -0.6336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8230   -1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1730    0.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5855    0.7954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3480    0.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355    0.7954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355   -0.6336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105   -0.6336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  2 18  1  0  0  0  0
  8 18  1  0  0  0  0
 13 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 19 23  1  0  0  0  0
 23 24  1  0  0  0  0
  5 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 28 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 26 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0155406

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(CO)C(CCC2(C)C3CCC(CC3=CCC12)C(O)(CO)CO)OC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H44O10/c1-24-8-7-19(36-23-22(33)21(32)20(31)17(10-27)35-23)25(2,11-28)18(24)6-3-14-9-15(4-5-16(14)24)26(34,12-29)13-30/h3,15-23,27-34H,4-13H2,1-2H3

> <INCHI_KEY>
BIPKKRGVQHIDKM-UHFFFAOYSA-N

> <FORMULA>
C26H44O10

> <MOLECULAR_WEIGHT>
516.628

> <EXACT_MASS>
516.293447617

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
56.53912910974124

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-1,2,3,4,4a,4b,5,6,7,8,10,10a-dodecahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.81

> <JCHEM_LOGP>
-1.6029468150000001

> <ALOGPS_LOGS>
-2.69

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.8525258108597

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.145383271971554

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7859615929073875

> <JCHEM_POLAR_SURFACE_AREA>
180.29999999999998

> <JCHEM_REFRACTIVITY>
129.197

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.06e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      -0.883  -5.710   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.564  -5.184   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.831  -6.700   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.349  -7.690   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.206  -3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.564  -2.516   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.104  -2.516   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.874  -3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.644  -2.516   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.414  -3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.184  -2.516   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.724  -2.516   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.494  -3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.724  -5.184   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.184  -5.184   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.414  -6.517   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.874  -6.517   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.104  -5.184   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.034  -3.850   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.034  -5.390   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      10.574  -3.850   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      11.344  -5.184   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       9.034  -2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      10.367  -1.540   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -1.746  -3.850   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -2.516  -2.516   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -4.056  -2.516   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -4.826  -1.183   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -6.366  -1.183   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -7.136  -2.516   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -4.056   0.151   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -4.826   1.485   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -2.516   0.151   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -1.746   1.485   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -1.746  -1.183   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -0.206  -1.183   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5   18                                             
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6   25                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   18                                             
CONECT    9    8                                                            
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   19                                                  
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17    2    8                                                  
CONECT   19   13   20   21   23                                             
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21                                                            
CONECT   23   19   24                                                       
CONECT   24   23                                                            
CONECT   25    5   26                                                       
CONECT   26   25   27   35                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31   28   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   26   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₄₄O₁₀

Average Mass

516.6280 Da

Monoisotopic Mass

516.29345 Da

IUPAC Name

2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-1,2,3,4,4a,4b,5,6,7,8,10,10a-dodecahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol

Traditional Name

2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

CC1(CO)C(CCC2(C)C3CCC(CC3=CCC12)C(O)(CO)CO)OC1OC(CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C26H44O10/c1-24-8-7-19(36-23-22(33)21(32)20(31)17(10-27)35-23)25(2,11-28)18(24)6-3-14-9-15(4-5-16(14)24)26(34,12-29)13-30/h3,15-23,27-34H,4-13H2,1-2H3

InChI Key

BIPKKRGVQHIDKM-UHFFFAOYSA-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
Isodon eriocalyx	LOTUS Database	35616633

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
Abietane diterpenoid
Diterpenoid
Steroid
Hydrophenanthrene
Phenanthrene
Glycosyl compound
O-glycosyl compound
Monosaccharide
Oxane
Tertiary alcohol
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Polyol
Alcohol
Hydrocarbon derivative
Primary alcohol
Organic oxygen compound
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	-0.81	ALOGPS
logP	-1.6	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	12.15	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	180.3 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	129.2 m³·mol⁻¹	ChemAxon
Polarizability	56.54 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol (NP0155406)

MOL for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)

3D MOL for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)

3D SDF for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)

3D-SDF for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)

PDB for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)

3D PDB for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)

SMILES for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)

INCHI for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)

Structure for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)

3D Structure for NP0155406 (2-(hydroxymethyl)-6-{[1-(hydroxymethyl)-1,4a-dimethyl-7-(1,2,3-trihydroxypropan-2-yl)-2,3,4,4b,5,6,7,8,10,10a-decahydrophenanthren-2-yl]oxy}oxane-3,4,5-triol)