NP-MRD: Showing NP-Card for 2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol (NP0324348)

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Record Information

Version

2.0

Created at

2022-09-12 04:22:28 UTC

Updated at

2022-09-12 04:22:28 UTC

NP-MRD ID

NP0324348

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol

Description

2-(Hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1H,4aH,5H,7aH-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton. 2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol is found in Verbascum phlomoides and Verbascum sinuatum. 2-(Hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1H,4aH,5H,7aH-cyclopenta[c]pyran-1-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


  Mrv1533004251512452D          

 33 36  0  0  0  0            999 V2000
    6.8513    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.7079    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.2789    1.2375    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


  Mrv1533004251512452D          

 33 36  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0324348

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2OC=CC3C(OC4OCC(O)C(O)C4O)C=C(CO)C23)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O13/c21-4-7-3-10(31-19-16(27)13(24)9(23)6-30-19)8-1-2-29-18(12(7)8)33-20-17(28)15(26)14(25)11(5-22)32-20/h1-3,8-28H,4-6H2

> <INCHI_KEY>
FLXYYVTUDYLYMR-UHFFFAOYSA-N

> <FORMULA>
C20H30O13

> <MOLECULAR_WEIGHT>
478.447

> <EXACT_MASS>
478.168641026

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
46.81240821851927

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1H,4aH,5H,7aH-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol

> <ALOGPS_LOGP>
-2.37

> <JCHEM_LOGP>
-4.322370606000001

> <ALOGPS_LOGS>
-0.98

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.457118971777184

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.924654894863417

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7415130627837714

> <JCHEM_POLAR_SURFACE_AREA>
207.98999999999998

> <JCHEM_REFRACTIVITY>
105.62760000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.02e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1H,4aH,5H,7aH-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  O   UNK     0      12.789   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      11.455   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.122   4.620   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.788   3.850   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.454   4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.121   3.850   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.454   1.540   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.846  -1.941   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.340  -2.261   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.864  -3.725   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -0.642  -4.046   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.673  -2.901   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -3.179  -3.221   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.197  -1.436   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -2.227  -0.292   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.310  -1.116   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.786   0.348   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.846   3.481   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       3.877   4.625   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.454   6.160   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       6.121   6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       8.788   6.930   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.788   8.470   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      10.122   6.160   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      11.455   6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   32                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   28                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   27                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   27                                                  
CONECT   12   11   13   23                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   21                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   14   22                                                  
CONECT   22   21                                                            
CONECT   23   12   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27   24    7   11                                                  
CONECT   28    5   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30    3   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₃₀O₁₃

Average Mass

478.4470 Da

Monoisotopic Mass

478.16864 Da

IUPAC Name

2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1H,4aH,5H,7aH-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol

Traditional Name

2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1H,4aH,5H,7aH-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2OC=CC3C(OC4OCC(O)C(O)C4O)C=C(CO)C23)C(O)C(O)C1O

InChI Identifier

InChI=1S/C20H30O13/c21-4-7-3-10(31-19-16(27)13(24)9(23)6-30-19)8-1-2-29-18(12(7)8)33-20-17(28)15(26)14(25)11(5-22)32-20/h1-3,8-28H,4-6H2

InChI Key

FLXYYVTUDYLYMR-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
Verbascum phlomoides	LOTUS Database	35616633
Verbascum sinuatum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Iridoid O-glycosides

Alternative Parents

Substituents

Iridoid o-glycoside
Glycosyl compound
Iridoid-skeleton
O-glycosyl compound
Bicyclic monoterpenoid
Monoterpenoid
Monosaccharide
Oxane
Secondary alcohol
Acetal
Organoheterocyclic compound
Oxacycle
Polyol
Organooxygen compound
Primary alcohol
Hydrocarbon derivative
Organic oxygen compound
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	-2.4	ALOGPS
logP	-4.3	ChemAxon
logS	-0.98	ALOGPS
pKa (Strongest Acidic)	11.92	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	207.99 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	105.63 m³·mol⁻¹	ChemAxon
Polarizability	46.81 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-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol (NP0324348)

MOL for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)

3D MOL for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)

3D SDF for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)

3D-SDF for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)

PDB for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)

3D PDB for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)

SMILES for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)

INCHI for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)

Structure for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)

3D Structure for NP0324348 (2-(hydroxymethyl)-6-{[7-(hydroxymethyl)-5-[(3,4,5-trihydroxyoxan-2-yl)oxy]-1h,4ah,5h,7ah-cyclopenta[c]pyran-1-yl]oxy}oxane-3,4,5-triol)