NP-MRD: Showing NP-Card for (2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate (NP0312372)

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Record Information

Version

2.0

Created at

2022-09-11 09:06:34 UTC

Updated at

2022-09-11 09:06:34 UTC

NP-MRD ID

NP0312372

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate

Description

(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity. (2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate is found in Rhodiola sacra. Based on a literature review very few articles have been published on (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
    1.1408   -0.9226    1.4685 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4841   -0.3119    0.4354 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4751    0.0847   -0.4306 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8796   -0.1693   -0.1927 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5636    1.0351   -0.0685 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8847    0.8909    0.2801 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1223    1.4637    1.6845 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7764    2.8084    1.6396 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3568   -0.5370    0.3202 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7427   -0.5262    0.4133 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9208   -1.3224   -0.8921 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9960   -2.6888   -0.5639 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5236   -0.9407   -1.3293 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5569   -0.1003   -2.4344 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8824   -0.0408    0.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2065    0.6434   -0.9933 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5221    0.9142   -1.2673 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4923    0.5032   -0.3816 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8291    0.7936   -0.6872 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1561   -0.1772    0.7768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8458   -0.4547    1.0635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9685   -0.7171    0.7687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5087    1.4429   -0.4492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1997    1.4209    1.9405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5790    0.8895    2.4426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3791    3.2460    0.9930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9397   -1.0071    1.2281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1209   -1.2459   -0.1676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6315   -1.1603   -1.7261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4115   -2.8038    0.2470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9811   -1.8591   -1.5900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3441   -0.5671   -3.2824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4220    0.9596   -1.6805 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8245    1.4505   -2.1744 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5442    0.4836   -0.0219 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9332   -0.4931    1.4625 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6289   -0.9849    1.9736 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  2 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
  4 13  1  0
 13 14  1  0
 13 11  1  0
 11 12  1  0
 11  9  1  0
  9 10  1  0
  9  6  1  0
 21 15  1  0
  8 26  1  0
  7 24  1  0
  7 25  1  0
  6 23  1  6
  4 22  1  1
 16 33  1  0
 17 34  1  0
 19 35  1  0
 20 36  1  0
 21 37  1  0
 13 31  1  6
 14 32  1  0
 11 29  1  6
 12 30  1  0
  9 27  1  1
 10 28  1  0
M  END


  Mrv1652309112211062D          

 21 22  0  0  1  0            999 V2000
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    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   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    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
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
  4 13  1  0  0  0  0
 13 14  1  1  0  0  0
  2 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 15 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0312372

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
XWTGDGASXRARSP-BZNQNGANSA-N

> <FORMULA>
C13H16O8

> <MOLECULAR_WEIGHT>
300.263

> <EXACT_MASS>
300.084517475

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
28.139500425714417

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate

> <JCHEM_LOGP>
-0.7408046909999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.195784824243855

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.469047707670068

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981093823879755

> <JCHEM_POLAR_SURFACE_AREA>
136.68

> <JCHEM_REFRACTIVITY>
67.72630000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate

> <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  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.335  -9.240   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  -6.930   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   13                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    4   14                                                  
CONECT   14   13                                                            
CONECT   15    2   16   21                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   15                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Value	Source
(2R,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoic acid	Generator

Chemical Formula

C₁₃H₁₆O₈

Average Mass

300.2630 Da

Monoisotopic Mass

300.08452 Da

IUPAC Name

(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate

Traditional Name

(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

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

InChI Key

XWTGDGASXRARSP-BZNQNGANSA-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
Rhodiola sacra	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Hexoses

Alternative Parents

Substituents

Hexose monosaccharide
P-hydroxybenzoic acid alkyl ester
P-hydroxybenzoic acid ester
Benzoate ester
Benzoic acid or derivatives
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
Phenol
Oxane
Monocyclic benzene moiety
Benzenoid
Secondary alcohol
Carboxylic acid ester
Polyol
Monocarboxylic acid or derivatives
Oxacycle
Carboxylic acid derivative
Acetal
Organoheterocyclic compound
Primary alcohol
Alcohol
Hydrocarbon derivative
Organic oxide
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	-0.74	ChemAxon
pKa (Strongest Acidic)	8.47	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	136.68 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	67.73 m³·mol⁻¹	ChemAxon
Polarizability	28.14 Å³	ChemAxon
Number of Rings	2	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

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

91247492

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate (NP0312372)

MOL for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)

3D MOL for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)

3D SDF for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)

3D-SDF for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)

PDB for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)

3D PDB for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)

SMILES for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)

INCHI for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)

Structure for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)

3D Structure for NP0312372 ((2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl 4-hydroxybenzoate)