NP-MRD: Showing NP-Card for (2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0232147)

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Record Information

Version

2.0

Created at

2022-09-06 13:16:54 UTC

Updated at

2022-09-06 13:16:54 UTC

NP-MRD ID

NP0232147

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

(2S,3R,4S,5S,6R)-2-{[(4aS,5R)-5-hydroxy-7-(hydroxymethyl)-4a-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4aH,5H-cyclopenta[c]pyran-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. (2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol is found in Veronica intercedens. Based on a literature review very few articles have been published on (2S,3R,4S,5S,6R)-2-{[(4aS,5R)-5-hydroxy-7-(hydroxymethyl)-4a-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4aH,5H-cyclopenta[c]pyran-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062215162D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309062215162D          

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 18 19  1  6  0  0  0
  7 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 25 24  1  1  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  1  0  0  0
 28 29  1  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  0  0  0  0
 25 34  1  0  0  0  0
 34 35  1  6  0  0  0
 23 36  2  0  0  0  0
  3 36  1  0  0  0  0
  7 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0232147

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=C3C(CO)=C[C@@H](O)[C@]3(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)C=CO2)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H30O15/c22-4-7-3-10(25)21(36-20-17(31)15(29)13(27)9(6-24)34-20)1-2-32-18(11(7)21)35-19-16(30)14(28)12(26)8(5-23)33-19/h1-3,8-10,12-17,19-20,22-31H,4-6H2/t8-,9-,10-,12-,13-,14+,15+,16-,17-,19+,20+,21-/m1/s1

> <INCHI_KEY>
NNYVBULCQQMSLP-AYLJDYAFSA-N

> <FORMULA>
C21H30O15

> <MOLECULAR_WEIGHT>
522.456

> <EXACT_MASS>
522.158470266

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
47.87011723378906

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(4aS,5R)-5-hydroxy-7-(hydroxymethyl)-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4aH,5H-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
-5.605512045

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.396830895398374

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.889768170509514

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810933261720125

> <JCHEM_POLAR_SURFACE_AREA>
248.44999999999993

> <JCHEM_REFRACTIVITY>
122.8301

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(4aS,5R)-5-hydroxy-7-(hydroxymethyl)-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5H-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  O   UNK     0       0.143  -4.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.650   1.408   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.429   0.999   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.675   1.904   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.082   1.278   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.328   2.183   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.735   1.556   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.981   2.462   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       7.167   3.714   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.413   4.619   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       5.760   4.341   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.599   5.872   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       4.514   3.435   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.107   4.062   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.258  -2.073   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       4.924  -4.383   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       6.258  -5.153   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.258  -6.693   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       7.591  -7.463   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.591  -9.003   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       6.258  -9.773   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       8.925  -6.693   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      10.259  -7.463   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.925  -5.153   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      10.259  -4.383   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       7.591  -4.383   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       7.591  -2.843   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   36                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   20   36                                             
CONECT    8    7    9                                                       
CONECT    9    8   10   18                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    9   19                                                  
CONECT   19   18                                                            
CONECT   20    7   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   36                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   34                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   27   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   25   35                                                  
CONECT   35   34                                                            
CONECT   36   23    3    7                                                  
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₀O₁₅

Average Mass

522.4560 Da

Monoisotopic Mass

522.15847 Da

IUPAC Name

(2S,3R,4S,5S,6R)-2-{[(4aS,5R)-5-hydroxy-7-(hydroxymethyl)-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4aH,5H-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2S,3R,4S,5S,6R)-2-{[(4aS,5R)-5-hydroxy-7-(hydroxymethyl)-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5H-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=C3C(CO)=C[C@@H](O)[C@]3(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)C=CO2)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C21H30O15/c22-4-7-3-10(25)21(36-20-17(31)15(29)13(27)9(6-24)34-20)1-2-32-18(11(7)21)35-19-16(30)14(28)12(26)8(5-23)33-19/h1-3,8-10,12-17,19-20,22-31H,4-6H2/t8-,9-,10-,12-,13-,14+,15+,16-,17-,19+,20+,21-/m1/s1

InChI Key

NNYVBULCQQMSLP-AYLJDYAFSA-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
Veronica intercedens	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

O-glycosyl compound
Pyran
Oxane
Monosaccharide
Secondary alcohol
Ketene acetal or derivatives
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Hydrocarbon derivative
Primary alcohol
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	-5.6	ChemAxon
pKa (Strongest Acidic)	11.89	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	248.45 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	122.83 m³·mol⁻¹	ChemAxon
Polarizability	47.87 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

163023502

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-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0232147)

MOL for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0232147 ((2s,3r,4s,5s,6r)-2-{[(4as,5r)-5-hydroxy-7-(hydroxymethyl)-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5h-cyclopenta[c]pyran-4a-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)