Showing metabocard for Pyridoxine (MMDBc0000081)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:29:41 UTC
Update Date2022-08-30 23:30:35 UTC
Metabolite IDMMDBc0000081
Metabolite Identification
Common NamePyridoxine
DescriptionThe 4-methanol form of vitamin B6 which is converted to pyridoxal phosphate which is a coenzyme for synthesis of amino acids, neurotransmitters (serotonin, norepinephrine), sphingolipids, aminolevulinic acid. Although pyridoxine and Vitamin B6 are still frequently used as synonyms, especially by medical researchers, this practice is erroneous and sometimes misleading (EE Snell; Ann NY Acad Sci, vol 585 pg 1, 1990). Pyridoxine is one of the compounds that can be called vitamin B6. Pyridoxine assists in the balancing of sodium and potassium as well as promoting red blood cell production. It is linked to cancer immunity and helps fight the formation of homocysteine. It has been suggested that Pyridoxine might help children with learning difficulties, and may also prevent dandruff, eczema, and psoriasis. In addition, pyridoxine can help balance hormonal changes in women and aid in immune system. Lack of pyridoxine may cause anemia, nerve damage, seizures, skin problems, and sores in the mouth. -- Wikipedia Deficiency, though rare because of widespread distribution in foods, leads to the development of peripheral neuritis in adults and affects the central nervous system in children (DOSE - 3rd edition). Pyridoxine in the urine is a biomarker for the consumption of soy products.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055d24ae20078>


  Mrv1652309032023582D          

 12 12  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   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   -0.8250    0.0000 N   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    0.4125    0.0000 C   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
    1.4289    0.8250    0.0000 C   0  0  0  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
   -1.4289   -0.8250    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
    0.0000    1.6500    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
  2  1  1  0  0  0  0
  7  2  1  0  0  0  0
  1  3  2  0  0  0  0
  4  2  2  0  0  0  0
 11  4  1  0  0  0  0
  5  4  1  0  0  0  0
 10  5  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  2  0  0  0  0
  9  6  1  0  0  0  0
  8  7  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x000055d24ae20078>

HMDB0000239
     RDKit          3D
Pyridoxine
 23 23  0  0  0  0  0  0  0  0999 V2000
   -3.1576   -0.8297    0.0962 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6704   -0.7838    0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9205   -1.8891   -0.2037 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4339   -1.8043   -0.2830 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1046   -0.6120   -0.1602 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5635   -0.5726   -0.2529 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0555   -1.8585   -0.4672 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3593    0.5300    0.0509 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0584    1.8144    0.1847 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1039    2.8125    0.3895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0171    0.4236    0.1286 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7752    1.5557    0.3391 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5419   -1.8048   -0.2922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5256   -0.6892    1.1210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6236   -0.0498   -0.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0198   -2.7194   -0.4513 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0606   -0.1946    0.6614 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8410    0.0345   -1.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9364   -2.3470    0.3809 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6292    2.1007   -0.7197 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7196    1.8410    1.0874 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1263    3.5093   -0.2923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7801    1.5331    0.4037 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
  5  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  2  0
 11 12  1  0
 11  2  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  4 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
 12 23  1  0
M  END
Download

3D SDF for #<Metabolite:0x000055d24ae20078>


  Mrv1652309032023582D          

 12 12  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   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   -0.8250    0.0000 N   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    0.4125    0.0000 C   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
    1.4289    0.8250    0.0000 C   0  0  0  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
   -1.4289   -0.8250    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
    0.0000    1.6500    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
  2  1  1  0  0  0  0
  7  2  1  0  0  0  0
  1  3  2  0  0  0  0
  4  2  2  0  0  0  0
 11  4  1  0  0  0  0
  5  4  1  0  0  0  0
 10  5  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  2  0  0  0  0
  9  6  1  0  0  0  0
  8  7  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000081

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=C(O)C(CO)=C(CO)C=N1

> <INCHI_IDENTIFIER>
InChI=1S/C8H11NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,10-12H,3-4H2,1H3

> <INCHI_KEY>
LXNHXLLTXMVWPM-UHFFFAOYSA-N

> <FORMULA>
C8H11NO3

> <MOLECULAR_WEIGHT>
169.1778

> <EXACT_MASS>
169.073893223

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.112304740817216

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol

> <ALOGPS_LOGP>
-0.57

> <JCHEM_LOGP>
-0.9513212983333332

> <ALOGPS_LOGS>
-1.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.533140285427315

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.397430003835803

> <JCHEM_PKA_STRONGEST_BASIC>
5.584997111043129

> <JCHEM_POLAR_SURFACE_AREA>
73.58000000000001

> <JCHEM_REFRACTIVITY>
44.1053

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.61e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridoxine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x000055d24ae20078>

HMDB0000239
     RDKit          3D
Pyridoxine
 23 23  0  0  0  0  0  0  0  0999 V2000
   -3.1576   -0.8297    0.0962 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6704   -0.7838    0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9205   -1.8891   -0.2037 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4339   -1.8043   -0.2830 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1046   -0.6120   -0.1602 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5635   -0.5726   -0.2529 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0555   -1.8585   -0.4672 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3593    0.5300    0.0509 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0584    1.8144    0.1847 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1039    2.8125    0.3895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0171    0.4236    0.1286 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7752    1.5557    0.3391 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5419   -1.8048   -0.2922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5256   -0.6892    1.1210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6236   -0.0498   -0.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0198   -2.7194   -0.4513 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0606   -0.1946    0.6614 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8410    0.0345   -1.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9364   -2.3470    0.3809 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6292    2.1007   -0.7197 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7196    1.8410    1.0874 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1263    3.5093   -0.2923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7801    1.5331    0.4037 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
  5  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  2  0
 11 12  1  0
 11  2  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  4 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
 12 23  1  0
M  END
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PDB for #<Metabolite:0x000055d24ae20078>

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.000  -1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.001   0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000   3.080   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    7    4                                                  
CONECT    3    1    6                                                       
CONECT    4    2   11    5                                                  
CONECT    5    4   10    6                                                  
CONECT    6    3    5    9                                                  
CONECT    7    2    8                                                       
CONECT    8    7                                                            
CONECT    9    6                                                            
CONECT   10    5                                                            
CONECT   11    4   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for #<Metabolite:0x000055d24ae20078>

COMPND    HMDB0000239
HETATM    1  C1  UNL     1      -3.158  -0.830   0.096  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.670  -0.784   0.003  1.00  0.00           C  
HETATM    3  N1  UNL     1      -0.921  -1.889  -0.204  1.00  0.00           N  
HETATM    4  C3  UNL     1       0.434  -1.804  -0.283  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.105  -0.612  -0.160  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.564  -0.573  -0.253  1.00  0.00           C  
HETATM    7  O1  UNL     1       3.056  -1.859  -0.467  1.00  0.00           O  
HETATM    8  C6  UNL     1       0.359   0.530   0.051  1.00  0.00           C  
HETATM    9  C7  UNL     1       1.058   1.814   0.185  1.00  0.00           C  
HETATM   10  O2  UNL     1       0.104   2.812   0.390  1.00  0.00           O  
HETATM   11  C8  UNL     1      -1.017   0.424   0.129  1.00  0.00           C  
HETATM   12  O3  UNL     1      -1.775   1.556   0.339  1.00  0.00           O  
HETATM   13  H1  UNL     1      -3.542  -1.805  -0.292  1.00  0.00           H  
HETATM   14  H2  UNL     1      -3.526  -0.689   1.121  1.00  0.00           H  
HETATM   15  H3  UNL     1      -3.624  -0.050  -0.567  1.00  0.00           H  
HETATM   16  H4  UNL     1       1.020  -2.719  -0.451  1.00  0.00           H  
HETATM   17  H5  UNL     1       3.061  -0.195   0.661  1.00  0.00           H  
HETATM   18  H6  UNL     1       2.841   0.035  -1.156  1.00  0.00           H  
HETATM   19  H7  UNL     1       2.936  -2.347   0.381  1.00  0.00           H  
HETATM   20  H8  UNL     1       1.629   2.101  -0.720  1.00  0.00           H  
HETATM   21  H9  UNL     1       1.720   1.841   1.087  1.00  0.00           H  
HETATM   22  H10 UNL     1       0.126   3.509  -0.292  1.00  0.00           H  
HETATM   23  H11 UNL     1      -2.780   1.533   0.404  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3    3   11
CONECT    3    4
CONECT    4    5    5   16
CONECT    5    6    8
CONECT    6    7   17   18
CONECT    7   19
CONECT    8    9   11   11
CONECT    9   10   20   21
CONECT   10   22
CONECT   11   12
CONECT   12   23
END
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SMILES for #<Metabolite:0x000055d24ae20078>

CC1=C(O)C(CO)=C(CO)C=N1
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INCHI for #<Metabolite:0x000055d24ae20078>

InChI=1S/C8H11NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,10-12H,3-4H2,1H3
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Synonyms
ValueSource
2-Methyl-3-hydroxy-4,5-dihydroxymethylpyridineChEBI
3-Hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridineChEBI
3-Hydroxy-4,5-dimethylol-alpha-picolineChEBI
5-Hydroxy-6-methyl-3,4-pyridinedimethanolChEBI
PyridoxolChEBI
Vitamin b6ChEBI
3-Hydroxy-4,5-dimethylol-a-picolineGenerator
3-Hydroxy-4,5-dimethylol-α-picolineGenerator
2-Methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridineHMDB
2-Methyl-3-hydroxy-4,5-di(hydroxymethyl)pyridineHMDB
2-Methyl-4,5-bis(hydroxymethyl)-3-hydroxypyridineHMDB
3-Hydroxy-2-picoline-4,5-dimethanolHMDB
AdermineHMDB
GravidoxHMDB
HydoxinHMDB
PiridossinaHMDB
PiridoxinaHMDB
PyridoxinHMDB
PyridoxinumHMDB
PyridoxolumHMDB
Pyridoxol hydrochlorideHMDB
RodexHMDB
Pyridoxine hydrochlorideHMDB
Molecular FormulaC8H11NO3
Average Mass169.1778
Monoisotopic Mass169.073893223
IUPAC Name4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol
Traditional Namepyridoxine
CAS Registry Number65-23-6
SMILES
CC1=C(O)C(CO)=C(CO)C=N1
InChI Identifier
InChI=1S/C8H11NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,10-12H,3-4H2,1H3
InChI KeyLXNHXLLTXMVWPM-UHFFFAOYSA-N