Showing metabocard for 4-deoxypyridoxine (MMDBc0034224)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 05:21:23 UTC
Update Date2022-08-31 22:45:26 UTC
Metabolite IDMMDBc0034224
Metabolite Identification
Common Name4-deoxypyridoxine
Description4-deoxypyridoxine belongs to the class of organic compounds known as methylpyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group. 4-deoxypyridoxine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on 4-deoxypyridoxine.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f121c018f30>


  Mrv0541 06081214512D          

 11 11  0  0  0  0            999 V2000
    0.7145    2.0625    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    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
    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 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    1.2375    0.0000 C   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
  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  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 11  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f121c018f30>

HMDB0246408
     RDKit          3D
4-Deoxypyridoxine
 22 22  0  0  0  0  0  0  0  0999 V2000
    3.1368   -0.7778    0.2225 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6529   -0.6860    0.1778 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8464   -1.7576    0.3106 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4982   -1.6273    0.2634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1066   -0.4040    0.0790 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5850   -0.3292    0.0368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1958   -1.5454    0.1940 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3133    0.7105   -0.0600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9365    2.0425   -0.2600 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0517    0.5413   -0.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8327    1.6755   -0.1491 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4511   -1.7863    0.5624 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4910   -0.5789   -0.8314 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5347   -0.0122    0.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1433   -2.5082    0.3730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8640    0.1222   -0.9384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9348    0.3628    0.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0754   -2.1676   -0.5529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1225    2.8084   -0.3302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4188    2.0286   -1.2630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6433    2.2819    0.5559 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8402    1.6069   -0.1178 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
  8 10  2  0
 10 11  1  0
 10  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  4 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  9 19  1  0
  9 20  1  0
  9 21  1  0
 11 22  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f121c018f30>


  Mrv0541 06081214512D          

 11 11  0  0  0  0            999 V2000
    0.7145    2.0625    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    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
    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 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    1.2375    0.0000 C   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
  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  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0034224

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=NC=C(CO)C(C)=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H11NO2/c1-5-7(4-10)3-9-6(2)8(5)11/h3,10-11H,4H2,1-2H3

> <INCHI_KEY>
KKOWAYISKWGDBG-UHFFFAOYSA-N

> <FORMULA>
C8H11NO2

> <MOLECULAR_WEIGHT>
153.1784

> <EXACT_MASS>
153.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
16.240002204893177

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.38

> <JCHEM_LOGP>
0.32944985833333346

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.936173266273713

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.408001830564865

> <JCHEM_PKA_STRONGEST_BASIC>
6.673690219362241

> <JCHEM_POLAR_SURFACE_AREA>
53.35000000000001

> <JCHEM_REFRACTIVITY>
42.3306

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.63e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-deoxypyridoxine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f121c018f30>

HMDB0246408
     RDKit          3D
4-Deoxypyridoxine
 22 22  0  0  0  0  0  0  0  0999 V2000
    3.1368   -0.7778    0.2225 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6529   -0.6860    0.1778 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8464   -1.7576    0.3106 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4982   -1.6273    0.2634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1066   -0.4040    0.0790 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5850   -0.3292    0.0368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1958   -1.5454    0.1940 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3133    0.7105   -0.0600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9365    2.0425   -0.2600 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0517    0.5413   -0.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8327    1.6755   -0.1491 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4511   -1.7863    0.5624 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4910   -0.5789   -0.8314 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5347   -0.0122    0.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1433   -2.5082    0.3730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8640    0.1222   -0.9384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9348    0.3628    0.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0754   -2.1676   -0.5529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1225    2.8084   -0.3302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4188    2.0286   -1.2630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6433    2.2819    0.5559 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8402    1.6069   -0.1178 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
  8 10  2  0
 10 11  1  0
 10  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  4 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  9 19  1  0
  9 20  1  0
  9 21  1  0
 11 22  1  0
M  END
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PDB for #<Metabolite:0x00007f121c018f30>

HEADER    PROTEIN                                 08-JUN-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-JUN-12         0                                  
HETATM    1  O   UNK     0       1.334   3.850   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  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   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  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    4   10                                                       
CONECT   10    9                                                            
CONECT   11    3                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for #<Metabolite:0x00007f121c018f30>

COMPND    HMDB0246408
HETATM    1  C1  UNL     1       3.137  -0.778   0.222  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.653  -0.686   0.178  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.846  -1.758   0.311  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.498  -1.627   0.263  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.107  -0.404   0.079  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.585  -0.329   0.037  1.00  0.00           C  
HETATM    7  O1  UNL     1      -3.196  -1.545   0.194  1.00  0.00           O  
HETATM    8  C6  UNL     1      -0.313   0.710  -0.060  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.937   2.042  -0.260  1.00  0.00           C  
HETATM   10  C8  UNL     1       1.052   0.541  -0.007  1.00  0.00           C  
HETATM   11  O2  UNL     1       1.833   1.675  -0.149  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.451  -1.786   0.562  1.00  0.00           H  
HETATM   13  H2  UNL     1       3.491  -0.579  -0.831  1.00  0.00           H  
HETATM   14  H3  UNL     1       3.535  -0.012   0.918  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.143  -2.508   0.373  1.00  0.00           H  
HETATM   16  H5  UNL     1      -2.864   0.122  -0.938  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.935   0.363   0.817  1.00  0.00           H  
HETATM   18  H7  UNL     1      -3.075  -2.168  -0.553  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.123   2.808  -0.330  1.00  0.00           H  
HETATM   20  H9  UNL     1      -1.419   2.029  -1.263  1.00  0.00           H  
HETATM   21  H10 UNL     1      -1.643   2.282   0.556  1.00  0.00           H  
HETATM   22  H11 UNL     1       2.840   1.607  -0.118  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    3   10
CONECT    3    4
CONECT    4    5    5   15
CONECT    5    6    8
CONECT    6    7   16   17
CONECT    7   18
CONECT    8    9   10   10
CONECT    9   19   20   21
CONECT   10   11
CONECT   11   22
END
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SMILES for #<Metabolite:0x00007f121c018f30>

CC1=NC=C(CO)C(C)=C1O
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INCHI for #<Metabolite:0x00007f121c018f30>

InChI=1S/C8H11NO2/c1-5-7(4-10)3-9-6(2)8(5)11/h3,10-11H,4H2,1-2H3
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Synonyms
ValueSource
4-DeoxypyridoxalChEBI
4-DeoxypyridoxolChEBI
4-Deoxypyridoxine hydrochlorideMeSH
4'-DeoxypyridoxineMeSH
Molecular FormulaC8H11NO2
Average Mass153.1784
Monoisotopic Mass153.078978601
IUPAC Name5-(hydroxymethyl)-2,4-dimethylpyridin-3-ol
Traditional Name4-deoxypyridoxine
CAS Registry Number61-67-6
SMILES
CC1=NC=C(CO)C(C)=C1O
InChI Identifier
InChI=1S/C8H11NO2/c1-5-7(4-10)3-9-6(2)8(5)11/h3,10-11H,4H2,1-2H3
InChI KeyKKOWAYISKWGDBG-UHFFFAOYSA-N