NP-MRD: Showing NP-Card for (2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol (NP0317947)

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Record Information

Version

2.0

Created at

2022-09-11 18:08:29 UTC

Updated at

2022-09-11 18:08:29 UTC

NP-MRD ID

NP0317947

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol

Description

4-(Methoxymethyl)-5-(beta-D-glucopyranosyloxy)-6-methylpyridine-3-methanol belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group. (2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol is found in Albizia julibrissin. Based on a literature review very few articles have been published on 4-(Methoxymethyl)-5-(beta-D-glucopyranosyloxy)-6-methylpyridine-3-methanol.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309112220082D          

 24 25  0  0  1  0            999 V2000
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.0000    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
   -0.7145   -1.2375    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
   -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 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
   -0.7145   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  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    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  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  2  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
  4 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0317947

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COCC1=C(CO)C=NC(C)=C1O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H23NO8/c1-7-14(9(6-22-2)8(4-17)3-16-7)24-15-13(21)12(20)11(19)10(5-18)23-15/h3,10-13,15,17-21H,4-6H2,1-2H3/t10-,11-,12+,13-,15+/m1/s1

> <INCHI_KEY>
OZAMFSFIKVSAHM-VVSAWPALSA-N

> <FORMULA>
C15H23NO8

> <MOLECULAR_WEIGHT>
345.348

> <EXACT_MASS>
345.142366705

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
34.064308422981185

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol

> <JCHEM_LOGP>
-2.576262887999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.179909248117003

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.19818352598483

> <JCHEM_PKA_STRONGEST_BASIC>
5.035546895093064

> <JCHEM_POLAR_SURFACE_AREA>
141.73000000000002

> <JCHEM_REFRACTIVITY>
81.00090000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol

> <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  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -5.335  -3.080   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -1.334  -5.390   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    4   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   23                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   14   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

View in JSmol

Synonyms

Value	Source
4-(Methoxymethyl)-5-(b-D-glucopyranosyloxy)-6-methylpyridine-3-methanol	Generator
4-(Methoxymethyl)-5-(β-D-glucopyranosyloxy)-6-methylpyridine-3-methanol	Generator

Chemical Formula

C₁₅H₂₃NO₈

Average Mass

345.3480 Da

Monoisotopic Mass

345.14237 Da

IUPAC Name

(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol

Traditional Name

(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

COCC1=C(CO)C=NC(C)=C1O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C15H23NO8/c1-7-14(9(6-22-2)8(4-17)3-16-7)24-15-13(21)12(20)11(19)10(5-18)23-15/h3,10-13,15,17-21H,4-6H2,1-2H3/t10-,11-,12+,13-,15+/m1/s1

InChI Key

OZAMFSFIKVSAHM-VVSAWPALSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Albizia julibrissin	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridoxines

Direct Parent

Pyridoxines

Alternative Parents

Substituents

Pyridoxine
Glycosyl compound
O-glycosyl compound
Methylpyridine
Monosaccharide
Oxane
Heteroaromatic compound
Secondary alcohol
Azacycle
Oxacycle
Acetal
Dialkyl ether
Polyol
Ether
Aromatic alcohol
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Primary alcohol
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
logP	-2.6	ChemAxon
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	5.04	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	141.73 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	81 m³·mol⁻¹	ChemAxon
Polarizability	34.06 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

14260867

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol (NP0317947)

MOL for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)

3D MOL for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)

3D SDF for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)

3D-SDF for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)

PDB for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)

3D PDB for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)

SMILES for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)

INCHI for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)

Structure for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)

3D Structure for NP0317947 ((2r,3s,4s,5r,6s)-2-(hydroxymethyl)-6-{[5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-yl]oxy}oxane-3,4,5-triol)