NP-MRD: Showing NP-Card for Sibiricose A2 (NP0082748)

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Record Information

Version

2.0

Created at

2022-04-29 03:50:13 UTC

Updated at

2022-04-29 03:50:13 UTC

NP-MRD ID

NP0082748

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sibiricose A2

Description

[(2R,3S,4S,5R,6R)-6-{[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(3,4,5-trimethoxyphenyl)prop-2-enoate belongs to the class of organic compounds known as coumaric acids and derivatives. These are aromatic compounds containing Aromatic compounds containing a cinnamic acid moiety (or a derivative thereof) hydroxylated at the C2 (ortho-), C3 (meta-), or C4 (para-) carbon atom of the benzene ring. Sibiricose A2 is found in Polygala sibirica . Based on a literature review very few articles have been published on [(2R,3S,4S,5R,6R)-6-{[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(3,4,5-trimethoxyphenyl)prop-2-enoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292205502D          

 39 41  0  0  1  0            999 V2000
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  4 38  1  1  0  0  0
  3 39  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292205502D          

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   -5.3032   -5.1712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9442   -4.7297    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4963   -5.3428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6518    2.0874    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0378    1.7443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  1  0  0  0
  9  8  1  1  0  0  0
  9 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
  9 13  1  0  0  0  0
 13 14  1  1  0  0  0
 12 15  1  6  0  0  0
 11 16  1  1  0  0  0
 16 17  1  0  0  0  0
  9 18  1  6  0  0  0
 18 19  1  0  0  0  0
  5 20  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 26 31  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 29 34  1  0  0  0  0
 34 35  1  0  0  0  0
 28 36  1  0  0  0  0
 36 37  1  0  0  0  0
  4 38  1  1  0  0  0
  3 39  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0082748

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(\C=C\C(=O)OC[C@H]2O[C@H](O[C@]3(CO)O[C@H](CO)[C@@H](O)[C@@H]3O)[C@H](O)[C@@H](O)[C@@H]2O)=CC(OC)=C1OC

> <INCHI_IDENTIFIER>
InChI=1S/C24H34O15/c1-33-12-6-11(7-13(34-2)21(12)35-3)4-5-16(27)36-9-15-17(28)19(30)20(31)23(37-15)39-24(10-26)22(32)18(29)14(8-25)38-24/h4-7,14-15,17-20,22-23,25-26,28-32H,8-10H2,1-3H3/b5-4+/t14-,15-,17-,18-,19+,20-,22+,23-,24+/m1/s1

> <INCHI_KEY>
AOLXCIMAVBSZMY-JKCNAQEDSA-N

> <FORMULA>
C24H34O15

> <MOLECULAR_WEIGHT>
562.521

> <EXACT_MASS>
562.189770395

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
54.78385226711693

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6R)-6-{[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(3,4,5-trimethoxyphenyl)prop-2-enoate

> <ALOGPS_LOGP>
-0.87

> <JCHEM_LOGP>
-1.9679580426666667

> <ALOGPS_LOGS>
-2.19

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.395584027616426

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.84196414751296

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981433338188096

> <JCHEM_POLAR_SURFACE_AREA>
223.28999999999994

> <JCHEM_REFRACTIVITY>
127.73139999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.66e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6R)-6-{[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(3,4,5-trimethoxyphenyl)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  O   UNK     0       0.881   0.327   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.625   0.647   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.101   2.112   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.607   2.432   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.638   1.287   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.162  -0.177   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.656  -0.497   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.180  -1.962   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -2.210  -3.106   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.456  -4.012   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.980  -5.476   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.440  -5.476   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.964  -4.012   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.500  -3.536   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -0.535  -6.722   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -3.885  -6.722   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -3.259  -8.129   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -3.241  -1.962   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -4.747  -2.282   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -5.144   1.608   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -6.175   0.463   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -5.699  -1.001   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -4.192  -1.322   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -6.729  -2.146   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -6.253  -3.611   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -7.284  -4.755   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -6.808  -6.220   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -7.838  -7.364   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -9.345  -7.044   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -9.821  -5.579   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -8.790  -4.435   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0     -11.327  -5.259   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0     -11.803  -3.794   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0     -10.375  -8.188   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -9.899  -9.653   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -7.363  -8.829   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -8.393  -9.973   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -3.083   3.896   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -0.071   3.256   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   39                                                  
CONECT    4    3    5   38                                                  
CONECT    5    4    6   20                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   13   18                                             
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   15                                                  
CONECT   13   12    9   14                                                  
CONECT   14   13                                                            
CONECT   15   12                                                            
CONECT   16   11   17                                                       
CONECT   17   16                                                            
CONECT   18    9   19                                                       
CONECT   19   18                                                            
CONECT   20    5   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   31                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   36                                                  
CONECT   29   28   30   34                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30   26                                                       
CONECT   32   30   33                                                       
CONECT   33   32                                                            
CONECT   34   29   35                                                       
CONECT   35   34                                                            
CONECT   36   28   37                                                       
CONECT   37   36                                                            
CONECT   38    4                                                            
CONECT   39    3                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   82    0
END

View in JSmol

Synonyms

Value	Source
[(2R,3S,4S,5R,6R)-6-{[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(3,4,5-trimethoxyphenyl)prop-2-enoic acid	Generator

Chemical Formula

C₂₄H₃₄O₁₅

Average Mass

562.5210 Da

Monoisotopic Mass

562.18977 Da

IUPAC Name

[(2R,3S,4S,5R,6R)-6-{[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(3,4,5-trimethoxyphenyl)prop-2-enoate

Traditional Name

[(2R,3S,4S,5R,6R)-6-{[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(3,4,5-trimethoxyphenyl)prop-2-enoate

CAS Registry Number

Not Available

SMILES

COC1=CC(\C=C\C(=O)OC[C@H]2O[C@H](O[C@]3(CO)O[C@H](CO)[C@@H](O)[C@@H]3O)[C@H](O)[C@@H](O)[C@@H]2O)=CC(OC)=C1OC

InChI Identifier

InChI=1S/C24H34O15/c1-33-12-6-11(7-13(34-2)21(12)35-3)4-5-16(27)36-9-15-17(28)19(30)20(31)23(37-15)39-24(10-26)22(32)18(29)14(8-25)38-24/h4-7,14-15,17-20,22-23,25-26,28-32H,8-10H2,1-3H3/b5-4+/t14-,15-,17-,18-,19+,20-,22+,23-,24+/m1/s1

InChI Key

AOLXCIMAVBSZMY-JKCNAQEDSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Polygala sibirica	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumaric acids and derivatives. These are aromatic compounds containing Aromatic compounds containing a cinnamic acid moiety (or a derivative thereof) hydroxylated at the C2 (ortho-), C3 (meta-), or C4 (para-) carbon atom of the benzene ring.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Cinnamic acids and derivatives

Sub Class

Hydroxycinnamic acids and derivatives

Direct Parent

Coumaric acids and derivatives

Alternative Parents

Substituents

Cinnamic acid ester
Coumaric acid or derivatives
O-glycosyl compound
Glycosyl compound
Disaccharide
C-glycosyl compound
Phenol ether
Phenoxy compound
Styrene
Anisole
Methoxybenzene
Fatty acid ester
Ketal
Alkyl aryl ether
Benzenoid
Monocyclic benzene moiety
Fatty acyl
Oxane
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Oxolane
Carboxylic acid ester
Secondary alcohol
Polyol
Oxacycle
Carboxylic acid derivative
Organoheterocyclic compound
Acetal
Ether
Monocarboxylic acid or derivatives
Carbonyl group
Organooxygen compound
Primary alcohol
Organic oxide
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	-0.87	ALOGPS
logP	-2	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	11.84	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	223.29 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	127.73 m³·mol⁻¹	ChemAxon
Polarizability	54.78 Å³	ChemAxon
Number of Rings	3	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

8920815

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10745487

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Sibiricose A2 (NP0082748)

MOL for NP0082748 (Sibiricose A2)

3D MOL for NP0082748 (Sibiricose A2)

3D SDF for NP0082748 (Sibiricose A2)

3D-SDF for NP0082748 (Sibiricose A2)

PDB for NP0082748 (Sibiricose A2)

3D PDB for NP0082748 (Sibiricose A2)

SMILES for NP0082748 (Sibiricose A2)

INCHI for NP0082748 (Sibiricose A2)

Structure for NP0082748 (Sibiricose A2)

3D Structure for NP0082748 (Sibiricose A2)