NP-MRD: Showing NP-Card for 4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid (NP0324873)

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Record Information

Version

2.0

Created at

2022-09-12 05:12:26 UTC

Updated at

2022-09-12 05:12:26 UTC

NP-MRD ID

NP0324873

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid

Description

4-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. Based on a literature review very few articles have been published on 4-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
    5.1673   -1.7380    2.7994 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2450   -1.3139    1.6260 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4580   -1.2455    0.9903 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0406   -0.8918    0.9349 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8244   -0.9604    1.5724 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6614   -0.5550    0.9108 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7716   -0.0943   -0.3732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6876    0.3224   -1.0946 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6441    0.3727   -0.7348 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2118    1.6449   -0.9042 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4131    1.7509   -0.2583 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1912    1.9864    1.2350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4433    2.0948    1.8817 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3936    0.6563   -0.5042 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.2667    0.9967   -1.5522 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8174   -0.6844   -0.7949 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4808   -1.3231    0.3980 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5116   -0.5585   -1.5878 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8202    0.0012   -2.8052 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9989   -0.0208   -1.0279 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1225   -0.4230   -0.3603 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7716   -0.4459    0.4890 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7148   -1.3216    2.5877 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7231   -0.6189    1.4323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7754    0.0088    0.2974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8924    2.6980   -0.6552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6466    2.9385    1.3177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6719    1.1407    1.7173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4790    1.5494    2.7008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0268    0.5513    0.4217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7520    1.4989   -2.2387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5119   -1.3079   -1.3598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3156   -1.5750    0.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0416   -1.5401   -1.6766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0208    0.0763   -3.3544 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0532    0.3514   -2.0524 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0877   -0.3741   -0.8513 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  2  0
  6  5  1  0
  5  4  2  0
  4 21  1  0
 21 20  2  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  9 18  1  0
 18 19  1  0
 18 16  1  0
 16 17  1  0
 16 14  1  0
 14 15  1  0
 14 11  1  0
 20  7  1  0
 13 29  1  0
 12 27  1  0
 12 28  1  0
 11 26  1  6
  9 25  1  1
  6 24  1  0
  5 23  1  0
 21 37  1  0
 20 36  1  0
  3 22  1  0
 18 34  1  6
 19 35  1  0
 16 32  1  6
 17 33  1  0
 14 30  1  1
 15 31  1  0
M  END


  Mrv1652309122207122D          

 21 22  0  0  1  0            999 V2000
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  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  6  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
  9 18  1  0  0  0  0
 18 19  1  1  0  0  0
  7 20  1  0  0  0  0
 20 21  2  0  0  0  0
  4 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0324873

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H](OC2=CC=C(C=C2)C(O)=O)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C13H16O8/c14-5-8-9(15)10(16)11(17)13(21-8)20-7-3-1-6(2-4-7)12(18)19/h1-4,8-11,13-17H,5H2,(H,18,19)/t8-,9-,10+,11-,13+/m1/s1

> <INCHI_KEY>
XSSDYIMYZONMBL-HMUNZLOLSA-N

> <FORMULA>
C13H16O8

> <MOLECULAR_WEIGHT>
300.263

> <EXACT_MASS>
300.084517475

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
28.003742742732772

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid

> <JCHEM_LOGP>
-0.9408046909999994

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.20014178463899

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.319042228061938

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092343686506

> <JCHEM_POLAR_SURFACE_AREA>
136.68

> <JCHEM_REFRACTIVITY>
67.4395

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.667 -12.320   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   21                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   20                                                  
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    4                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Value	Source
4-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoate	Generator

Chemical Formula

C₁₃H₁₆O₈

Average Mass

300.2630 Da

Monoisotopic Mass

300.08452 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H](OC2=CC=C(C=C2)C(O)=O)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C13H16O8/c14-5-8-9(15)10(16)11(17)13(21-8)20-7-3-1-6(2-4-7)12(18)19/h1-4,8-11,13-17H,5H2,(H,18,19)/t8-,9-,10+,11-,13+/m1/s1

InChI Key

XSSDYIMYZONMBL-HMUNZLOLSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
Hexose monosaccharide
O-glycosyl compound
Benzoic acid or derivatives
Benzoic acid
Phenoxy compound
Benzoyl
Phenol ether
Sugar acid
Monocyclic benzene moiety
Monosaccharide
Benzenoid
Oxane
Secondary alcohol
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Carboxylic acid
Carboxylic acid derivative
Oxacycle
Acetal
Polyol
Alcohol
Hydrocarbon derivative
Organic oxide
Primary alcohol
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

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

57514829

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid (NP0324873)

MOL for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)

3D MOL for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)

3D SDF for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)

3D-SDF for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)

PDB for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)

3D PDB for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)

SMILES for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)

INCHI for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)

Structure for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)

3D Structure for NP0324873 (4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzoic acid)