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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:53:41 UTC

Update Date

2021-09-26 22:56:13 UTC

HMDB ID

HMDB0246884

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5'-O-beta-D-Glucosylpyridoxine

Description

2-{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol 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. Based on a literature review very few articles have been published on 2-{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5'-o-beta-d-glucosylpyridoxine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5'-O-beta-D-Glucosylpyridoxine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0246884
     RDKit          3D
5'-O-beta-D-Glucosylpyridoxine
 44 45  0  0  0  0  0  0  0  0999 V2000
   -5.2038    1.9625   -0.5876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0171    1.0659   -0.7857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9120    1.3985   -1.4560 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8715    0.6291   -1.4939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7807   -0.5742   -0.8437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6290   -1.4774   -0.8139 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4838   -0.8351   -1.3632 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5029   -0.8946   -0.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7635   -0.9673   -0.8843 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6730   -0.4524    0.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1075   -0.7749   -0.3230 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9480   -0.4501    0.7505 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5972    1.0754   -0.0028 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9121    1.5861    1.2330 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1633    1.4350   -0.3194 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8163    2.7124    0.1554 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2712    0.4476    0.3878 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6320    0.2955    1.7123 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8936   -0.9602   -0.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8343   -2.1744    0.7577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1619   -1.5701    2.0512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0138   -0.1619   -0.1277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0769   -0.5569    0.5189 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0647    2.9495   -1.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2891    2.0595    0.5087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1347    1.4649   -0.9793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9562    0.9654   -2.0528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8312   -2.3690   -1.4223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4053   -1.7400    0.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2098   -1.6807    0.3407 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4824   -0.8586    1.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3225   -1.7966   -0.6158 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4497   -0.1066   -1.1771 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4973   -0.6638    1.6449 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2653    1.4286   -0.8374 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7136    2.5756    1.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9432    1.3548   -1.3909 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8087    2.6748    0.2914 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2053    0.6830    0.3897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2976   -0.5143    2.1235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9473   -2.7164    0.7431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7677   -2.7839    0.4944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5902   -0.7201    2.1153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6852   -0.9648    0.9754 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  1  0
 20 21  1  0
 19 22  2  0
 22 23  1  0
 22  2  1  0
 17  8  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  4 27  1  0
  6 28  1  0
  6 29  1  0
  8 30  1  0
 10 31  1  0
 11 32  1  0
 11 33  1  0
 12 34  1  0
 13 35  1  0
 14 36  1  0
 15 37  1  0
 16 38  1  0
 17 39  1  0
 18 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
 23 44  1  0
M  END


  Mrv1533004171515212D          

 23 24  0  0  0  0            999 V2000
    1.4289   -1.6500    0.0000 C   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
    2.1434   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  0  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   -2.8875    0.0000 C   0  0  0  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
  1  2  1  0  0  0  0
  2  3  2  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
  8 17  1  0  0  0  0
 17 18  1  0  0  0  0
  5 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 19 22  2  0  0  0  0
  2 22  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246884

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=NC=C(COC2OC(CO)C(O)C(O)C2O)C(CO)=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H21NO8/c1-6-10(18)8(3-16)7(2-15-6)5-22-14-13(21)12(20)11(19)9(4-17)23-14/h2,9,11-14,16-21H,3-5H2,1H3

> <INCHI_KEY>
MDLTWTOQCHCLSZ-UHFFFAOYSA-N

> <FORMULA>
C14H21NO8

> <MOLECULAR_WEIGHT>
331.321

> <EXACT_MASS>
331.12671664

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
32.69950838613424

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-1.90

> <JCHEM_LOGP>
-2.722156943999999

> <ALOGPS_LOGS>
-1.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.210072331862856

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.395478924855869

> <JCHEM_PKA_STRONGEST_BASIC>
5.5820293461560295

> <JCHEM_POLAR_SURFACE_AREA>
152.73

> <JCHEM_REFRACTIVITY>
76.51859999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.55e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0246884
     RDKit          3D
5'-O-beta-D-Glucosylpyridoxine
 44 45  0  0  0  0  0  0  0  0999 V2000
   -5.2038    1.9625   -0.5876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0171    1.0659   -0.7857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9120    1.3985   -1.4560 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8715    0.6291   -1.4939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7807   -0.5742   -0.8437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6290   -1.4774   -0.8139 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4838   -0.8351   -1.3632 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5029   -0.8946   -0.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7635   -0.9673   -0.8843 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6730   -0.4524    0.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1075   -0.7749   -0.3230 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9480   -0.4501    0.7505 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5972    1.0754   -0.0028 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9121    1.5861    1.2330 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1633    1.4350   -0.3194 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8163    2.7124    0.1554 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2712    0.4476    0.3878 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6320    0.2955    1.7123 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8936   -0.9602   -0.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8343   -2.1744    0.7577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1619   -1.5701    2.0512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0138   -0.1619   -0.1277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0769   -0.5569    0.5189 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0647    2.9495   -1.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2891    2.0595    0.5087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1347    1.4649   -0.9793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9562    0.9654   -2.0528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8312   -2.3690   -1.4223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4053   -1.7400    0.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2098   -1.6807    0.3407 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4824   -0.8586    1.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3225   -1.7966   -0.6158 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4497   -0.1066   -1.1771 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4973   -0.6638    1.6449 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2653    1.4286   -0.8374 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7136    2.5756    1.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9432    1.3548   -1.3909 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8087    2.6748    0.2914 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2053    0.6830    0.3897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2976   -0.5143    2.1235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9473   -2.7164    0.7431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7677   -2.7839    0.4944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5902   -0.7201    2.1153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6852   -0.9648    0.9754 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  1  0
 20 21  1  0
 19 22  2  0
 22 23  1  0
 22  2  1  0
 17  8  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  4 27  1  0
  6 28  1  0
  6 29  1  0
  8 30  1  0
 10 31  1  0
 11 32  1  0
 11 33  1  0
 12 34  1  0
 13 35  1  0
 14 36  1  0
 15 37  1  0
 16 38  1  0
 17 39  1  0
 18 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
 23 44  1  0
M  END

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       4.001  -5.390   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.335 -12.320   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668 -14.630   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       8.002 -13.860   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.001 -14.630   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.001 -16.170   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.667 -13.860   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334 -14.630   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   22                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   19                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    8   18                                                  
CONECT   18   17                                                            
CONECT   19    5   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   19    2   23                                                  
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

COMPND    HMDB0246884
HETATM    1  C1  UNL     1      -5.204   1.963  -0.588  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.017   1.066  -0.786  1.00  0.00           C  
HETATM    3  N1  UNL     1      -2.912   1.398  -1.456  1.00  0.00           N  
HETATM    4  C3  UNL     1      -1.871   0.629  -1.494  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.781  -0.574  -0.844  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.629  -1.477  -0.814  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.484  -0.835  -1.363  1.00  0.00           O  
HETATM    8  C6  UNL     1       1.503  -0.895  -0.383  1.00  0.00           C  
HETATM    9  O2  UNL     1       2.763  -0.967  -0.884  1.00  0.00           O  
HETATM   10  C7  UNL     1       3.673  -0.452   0.035  1.00  0.00           C  
HETATM   11  C8  UNL     1       5.108  -0.775  -0.323  1.00  0.00           C  
HETATM   12  O3  UNL     1       5.948  -0.450   0.751  1.00  0.00           O  
HETATM   13  C9  UNL     1       3.597   1.075  -0.003  1.00  0.00           C  
HETATM   14  O4  UNL     1       3.912   1.586   1.233  1.00  0.00           O  
HETATM   15  C10 UNL     1       2.163   1.435  -0.319  1.00  0.00           C  
HETATM   16  O5  UNL     1       1.816   2.712   0.155  1.00  0.00           O  
HETATM   17  C11 UNL     1       1.271   0.448   0.388  1.00  0.00           C  
HETATM   18  O6  UNL     1       1.632   0.296   1.712  1.00  0.00           O  
HETATM   19  C12 UNL     1      -2.894  -0.960  -0.154  1.00  0.00           C  
HETATM   20  C13 UNL     1      -2.834  -2.174   0.758  1.00  0.00           C  
HETATM   21  O7  UNL     1      -3.162  -1.570   2.051  1.00  0.00           O  
HETATM   22  C14 UNL     1      -4.014  -0.162  -0.128  1.00  0.00           C  
HETATM   23  O8  UNL     1      -5.077  -0.557   0.519  1.00  0.00           O  
HETATM   24  H1  UNL     1      -5.065   2.950  -1.060  1.00  0.00           H  
HETATM   25  H2  UNL     1      -5.289   2.060   0.509  1.00  0.00           H  
HETATM   26  H3  UNL     1      -6.135   1.465  -0.979  1.00  0.00           H  
HETATM   27  H4  UNL     1      -0.956   0.965  -2.053  1.00  0.00           H  
HETATM   28  H5  UNL     1      -0.831  -2.369  -1.422  1.00  0.00           H  
HETATM   29  H6  UNL     1      -0.405  -1.740   0.221  1.00  0.00           H  
HETATM   30  H7  UNL     1       1.210  -1.681   0.341  1.00  0.00           H  
HETATM   31  H8  UNL     1       3.482  -0.859   1.005  1.00  0.00           H  
HETATM   32  H9  UNL     1       5.322  -1.797  -0.616  1.00  0.00           H  
HETATM   33  H10 UNL     1       5.450  -0.107  -1.177  1.00  0.00           H  
HETATM   34  H11 UNL     1       5.497  -0.664   1.645  1.00  0.00           H  
HETATM   35  H12 UNL     1       4.265   1.429  -0.837  1.00  0.00           H  
HETATM   36  H13 UNL     1       3.714   2.576   1.213  1.00  0.00           H  
HETATM   37  H14 UNL     1       1.943   1.355  -1.391  1.00  0.00           H  
HETATM   38  H15 UNL     1       0.809   2.675   0.291  1.00  0.00           H  
HETATM   39  H16 UNL     1       0.205   0.683   0.390  1.00  0.00           H  
HETATM   40  H17 UNL     1       1.298  -0.514   2.124  1.00  0.00           H  
HETATM   41  H18 UNL     1      -1.947  -2.716   0.743  1.00  0.00           H  
HETATM   42  H19 UNL     1      -3.768  -2.784   0.494  1.00  0.00           H  
HETATM   43  H20 UNL     1      -2.590  -0.720   2.115  1.00  0.00           H  
HETATM   44  H21 UNL     1      -5.685  -0.965   0.975  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3    3   22
CONECT    3    4
CONECT    4    5    5   27
CONECT    5    6   19
CONECT    6    7   28   29
CONECT    7    8
CONECT    8    9   17   30
CONECT    9   10
CONECT   10   11   13   31
CONECT   11   12   32   33
CONECT   12   34
CONECT   13   14   15   35
CONECT   14   36
CONECT   15   16   17   37
CONECT   16   38
CONECT   17   18   39
CONECT   18   40
CONECT   19   20   22   22
CONECT   20   21   41   42
CONECT   21   43
CONECT   22   23
CONECT   23   44
END

HMDB0246884
     RDKit          3D
5'-O-beta-D-Glucosylpyridoxine
 44 45  0  0  0  0  0  0  0  0999 V2000
   -5.2038    1.9625   -0.5876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0171    1.0659   -0.7857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9120    1.3985   -1.4560 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8715    0.6291   -1.4939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7807   -0.5742   -0.8437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6290   -1.4774   -0.8139 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4838   -0.8351   -1.3632 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5029   -0.8946   -0.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7635   -0.9673   -0.8843 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6730   -0.4524    0.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1075   -0.7749   -0.3230 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9480   -0.4501    0.7505 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5972    1.0754   -0.0028 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9121    1.5861    1.2330 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1633    1.4350   -0.3194 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8163    2.7124    0.1554 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2712    0.4476    0.3878 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6320    0.2955    1.7123 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8936   -0.9602   -0.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8343   -2.1744    0.7577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1619   -1.5701    2.0512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0138   -0.1619   -0.1277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0769   -0.5569    0.5189 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0647    2.9495   -1.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2891    2.0595    0.5087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1347    1.4649   -0.9793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9562    0.9654   -2.0528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8312   -2.3690   -1.4223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4053   -1.7400    0.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2098   -1.6807    0.3407 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4824   -0.8586    1.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3225   -1.7966   -0.6158 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4497   -0.1066   -1.1771 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4973   -0.6638    1.6449 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2653    1.4286   -0.8374 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7136    2.5756    1.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9432    1.3548   -1.3909 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8087    2.6748    0.2914 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2053    0.6830    0.3897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2976   -0.5143    2.1235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9473   -2.7164    0.7431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7677   -2.7839    0.4944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5902   -0.7201    2.1153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6852   -0.9648    0.9754 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  1  0
 20 21  1  0
 19 22  2  0
 22 23  1  0
 22  2  1  0
 17  8  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  4 27  1  0
  6 28  1  0
  6 29  1  0
  8 30  1  0
 10 31  1  0
 11 32  1  0
 11 33  1  0
 12 34  1  0
 13 35  1  0
 14 36  1  0
 15 37  1  0
 16 38  1  0
 17 39  1  0
 18 40  1  0
 20 41  1  0
 20 42  1  0
 21 43  1  0
 23 44  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₄H₂₁NO₈

Average Molecular Weight

331.321

Monoisotopic Molecular Weight

331.12671664

IUPAC Name

2-{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

CC1=NC=C(COC2OC(CO)C(O)C(O)C2O)C(CO)=C1O

InChI Identifier

InChI=1S/C14H21NO8/c1-6-10(18)8(3-16)7(2-15-6)5-22-14-13(21)12(20)11(19)9(4-17)23-14/h2,9,11-14,16-21H,3-5H2,1H3

InChI Key

MDLTWTOQCHCLSZ-UHFFFAOYSA-N

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

Hexose monosaccharide
Pyridoxine
Glycosyl compound
O-glycosyl compound
Hydroxypyridine
Methylpyridine
Monosaccharide
Oxane
Heteroaromatic compound
Secondary alcohol
Acetal
Oxacycle
Azacycle
Polyol
Organooxygen compound
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Organic nitrogen compound
Organopnictogen compound
Primary alcohol
Organic oxygen compound
Aromatic alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a small molecule (CPD-455 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.9	ALOGPS
logP	-2.7	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	9.4	ChemAxon
pKa (Strongest Basic)	5.58	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	152.73 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	76.52 m³·mol⁻¹	ChemAxon
Polarizability	32.7 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	173.903	30932474
DeepCCS	[M-H]-	171.545	30932474
DeepCCS	[M-2H]-	204.884	30932474
DeepCCS	[M+Na]+	180.111	30932474
AllCCS	[M+H]+	176.7	32859911
AllCCS	[M+H-H2O]+	173.6	32859911
AllCCS	[M+NH4]+	179.5	32859911
AllCCS	[M+Na]+	180.3	32859911
AllCCS	[M-H]-	175.3	32859911
AllCCS	[M+Na-2H]-	175.3	32859911
AllCCS	[M+HCOO]-	175.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	10.1828 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	7.35 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	427.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	221.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	57.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	164.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	50.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	272.7 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	277.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	735.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	580.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	52.0 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	862.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	190.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	203.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	490.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	534.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	492.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5'-O-beta-D-Glucosylpyridoxine	CC1=NC=C(COC2OC(CO)C(O)C(O)C2O)C(CO)=C1O	3308.2	Standard polar	33892256
5'-O-beta-D-Glucosylpyridoxine	CC1=NC=C(COC2OC(CO)C(O)C(O)C2O)C(CO)=C1O	3086.9	Standard non polar	33892256
5'-O-beta-D-Glucosylpyridoxine	CC1=NC=C(COC2OC(CO)C(O)C(O)C2O)C(CO)=C1O	3014.6	Semi standard non polar	33892256

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

2568609

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3321053

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 5'-O-beta-D-Glucosylpyridoxine (HMDB0246884)

MOL for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

3D MOL for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

3D SDF for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

3D-SDF for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

PDB for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

3D PDB for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

SMILES for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

INCHI for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

Structure for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

3D Structure for HMDB0246884 (5'-O-beta-D-Glucosylpyridoxine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized