NP-MRD: Showing NP-Card for (2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0307442)

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Record Information

Version

2.0

Created at

2022-09-11 00:34:04 UTC

Updated at

2022-09-11 00:34:04 UTC

NP-MRD ID

NP0307442

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

Stemodinoside B belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. (2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol is found in Rhizopus oryzae and Stemodia maritima. Based on a literature review very few articles have been published on Stemodinoside B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112202342D          

 33 37  0  0  1  0            999 V2000
    4.6464    0.4601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8242    0.5275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9006   -0.2940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0332    1.3255    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4466    1.9056    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6557    2.7037    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6509    1.6877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 32 33  1  1  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309112202342D          

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 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 17 16  1  1  0  0  0
 13 17  1  0  0  0  0
  8 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  1  0  0  0
 23 22  1  6  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  6  0  0  0
 26 27  1  0  0  0  0
 25 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 23 32  1  0  0  0  0
 32 33  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0307442

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)C[C@H](O)C[C@@]2(C)[C@H]1CC[C@H]1C[C@H]3C[C@@]21CC[C@]3(C)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H44O7/c1-23(2)11-16(28)12-24(3)18(23)6-5-14-9-15-10-26(14,24)8-7-25(15,4)33-22-21(31)20(30)19(29)17(13-27)32-22/h14-22,27-31H,5-13H2,1-4H3/t14-,15-,16-,17+,18-,19+,20-,21+,22-,24-,25-,26+/m0/s1

> <INCHI_KEY>
ZMCHBXFQGYGBOK-PRKLWXFASA-N

> <FORMULA>
C26H44O7

> <MOLECULAR_WEIGHT>
468.631

> <EXACT_MASS>
468.308703757

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
52.389399678147825

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(1R,2S,4S,7S,10S,12S,13S)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0^{1,10}.0^{2,7}]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
1.4910225786666664

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.199934454054208

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210163216266274

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9018029550271759

> <JCHEM_POLAR_SURFACE_AREA>
119.61000000000001

> <JCHEM_REFRACTIVITY>
121.63380000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(1R,2S,4S,7S,10S,12S,13S)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0^{1,10}.0^{2,7}]hexadecan-13-yl]oxy}-6-(hydroxymethyl)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       8.673   0.859   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.138   0.985   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.281  -0.549   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.529   2.474   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.434   3.557   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.824   5.047   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.948   3.150   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.558   1.661   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.511   2.790   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.653   0.578   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.257  -0.936   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.769  -1.343   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.679  -0.249   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.092  -0.585   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.280   0.828   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.589   1.217   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.963   1.370   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.534   2.999   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.021   3.571   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.098   2.420   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.222   3.473   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.603   2.092   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -2.640   3.231   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -4.144   2.903   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -5.181   4.042   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -6.685   3.714   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -7.153   2.247   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -4.712   5.509   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -5.749   6.648   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -3.208   5.837   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -2.740   7.304   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -2.171   4.698   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -0.667   5.026   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4   10                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10   17                                             
CONECT    9    8                                                            
CONECT   10    8    2   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   13    8   18                                             
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15   21   22                                             
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   32                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   28                                                  
CONECT   26   25   27                                                       
CONECT   27   26                                                            
CONECT   28   25   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   23   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₄₄O₇

Average Mass

468.6310 Da

Monoisotopic Mass

468.30870 Da

IUPAC Name

(2S,3R,4S,5S,6R)-2-{[(1R,2S,4S,7S,10S,12S,13S)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0^{1,10}.0^{2,7}]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2S,3R,4S,5S,6R)-2-{[(1R,2S,4S,7S,10S,12S,13S)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0^{1,10}.0^{2,7}]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

CC1(C)C[C@H](O)C[C@@]2(C)[C@H]1CC[C@H]1C[C@H]3C[C@@]21CC[C@]3(C)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C26H44O7/c1-23(2)11-16(28)12-24(3)18(23)6-5-14-9-15-10-26(14,24)8-7-25(15,4)33-22-21(31)20(30)19(29)17(13-27)32-22/h14-22,27-31H,5-13H2,1-4H3/t14-,15-,16-,17+,18-,19+,20-,21+,22-,24-,25-,26+/m0/s1

InChI Key

ZMCHBXFQGYGBOK-PRKLWXFASA-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
Rhizopus oryzae	LOTUS Database	35616633
Stemodia maritima	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
Aphidicolane or stemodane diterpenoid
Diterpenoid
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Oxane
Monosaccharide
Cyclic alcohol
Secondary alcohol
Polyol
Organoheterocyclic compound
Acetal
Oxacycle
Organooxygen compound
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Primary alcohol
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	1.49	ChemAxon
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-0.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	119.61 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	121.63 m³·mol⁻¹	ChemAxon
Polarizability	52.39 Å³	ChemAxon
Number of Rings	5	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

24716744

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44576035

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,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0307442)

MOL for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0307442 ((2s,3r,4s,5s,6r)-2-{[(1r,2s,4s,7s,10s,12s,13s)-4-hydroxy-2,6,6,13-tetramethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecan-13-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)