Showing metabocard for Pyridoxal (MMDBc0000200)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:39:31 UTC
Update Date2024-10-06 18:37:20 UTC
Metabolite IDMMDBc0000200
Metabolite Identification
Common NamePyridoxal
DescriptionThe 4-carboxyaldehyde 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. Pyridoxal has been identified in the human placenta (PMID: 32033212 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f4705c2b7c8>


  Mrv1652309042000242D          

 12 12  0  0  0  0            999 V2000
    0.7145    2.0625    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    0.8250    0.0000 N   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 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 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
   -1.4289    0.0000    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  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
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
  5 11  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f4705c2b7c8>

HMDB0001545
     RDKit          3D
Pyridoxal
 21 21  0  0  0  0  0  0  0  0999 V2000
   -3.0457    1.1173   -0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5924    0.8083   -0.3262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6474    1.6878   -0.6640 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6675    1.4148   -0.5792 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1385    0.2032   -0.1358 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5804   -0.1198   -0.0347 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3808    0.9193   -0.4291 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1819   -0.7434    0.2270 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6798   -2.0263    0.6969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0736   -2.9412    1.0456 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1626   -0.4489    0.1345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1452   -1.3258    0.4718 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6074    0.3062   -0.9266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4699    1.3633    0.5719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1327    2.0110   -1.0809 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4212    2.1507   -0.8614 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7550   -1.0566   -0.6179 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8248   -0.3892    1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6119    1.5109    0.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7678   -2.2013    0.7484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1325   -2.2405    0.8108 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  2  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
 12 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f4705c2b7c8>


  Mrv1652309042000242D          

 12 12  0  0  0  0            999 V2000
    0.7145    2.0625    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    0.8250    0.0000 N   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 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 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
   -1.4289    0.0000    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  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
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
  5 11  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000200

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3

> <INCHI_KEY>
RADKZDMFGJYCBB-UHFFFAOYSA-N

> <FORMULA>
C8H9NO3

> <MOLECULAR_WEIGHT>
167.162

> <EXACT_MASS>
167.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
16.280640988280627

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde

> <ALOGPS_LOGP>
0.02

> <JCHEM_LOGP>
0.17853081366666687

> <ALOGPS_LOGS>
-1.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.658014655901226

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.971193899104745

> <JCHEM_PKA_STRONGEST_BASIC>
4.110818751313327

> <JCHEM_POLAR_SURFACE_AREA>
70.42

> <JCHEM_REFRACTIVITY>
43.8734

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.17e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridoxal

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f4705c2b7c8>

HMDB0001545
     RDKit          3D
Pyridoxal
 21 21  0  0  0  0  0  0  0  0999 V2000
   -3.0457    1.1173   -0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5924    0.8083   -0.3262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6474    1.6878   -0.6640 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6675    1.4148   -0.5792 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1385    0.2032   -0.1358 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5804   -0.1198   -0.0347 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3808    0.9193   -0.4291 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1819   -0.7434    0.2270 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6798   -2.0263    0.6969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0736   -2.9412    1.0456 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1626   -0.4489    0.1345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1452   -1.3258    0.4718 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6074    0.3062   -0.9266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4699    1.3633    0.5719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1327    2.0110   -1.0809 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4212    2.1507   -0.8614 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7550   -1.0566   -0.6179 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8248   -0.3892    1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6119    1.5109    0.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7678   -2.2013    0.7484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1325   -2.2405    0.8108 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  2  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
 12 21  1  0
M  END
Download

PDB for #<Metabolite:0x00007f4705c2b7c8>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    6   10                                                       
CONECT   10    9                                                            
CONECT   11    5   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:0x00007f4705c2b7c8>

COMPND    HMDB0001545
HETATM    1  C1  UNL     1      -3.046   1.117  -0.423  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.592   0.808  -0.326  1.00  0.00           C  
HETATM    3  N1  UNL     1      -0.647   1.688  -0.664  1.00  0.00           N  
HETATM    4  C3  UNL     1       0.668   1.415  -0.579  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.138   0.203  -0.136  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.580  -0.120  -0.035  1.00  0.00           C  
HETATM    7  O1  UNL     1       3.381   0.919  -0.429  1.00  0.00           O  
HETATM    8  C6  UNL     1       0.182  -0.743   0.227  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.680  -2.026   0.697  1.00  0.00           C  
HETATM   10  O2  UNL     1      -0.074  -2.941   1.046  1.00  0.00           O  
HETATM   11  C8  UNL     1      -1.163  -0.449   0.135  1.00  0.00           C  
HETATM   12  O3  UNL     1      -2.145  -1.326   0.472  1.00  0.00           O  
HETATM   13  H1  UNL     1      -3.607   0.306  -0.927  1.00  0.00           H  
HETATM   14  H2  UNL     1      -3.470   1.363   0.572  1.00  0.00           H  
HETATM   15  H3  UNL     1      -3.133   2.011  -1.081  1.00  0.00           H  
HETATM   16  H4  UNL     1       1.421   2.151  -0.861  1.00  0.00           H  
HETATM   17  H5  UNL     1       2.755  -1.057  -0.618  1.00  0.00           H  
HETATM   18  H6  UNL     1       2.825  -0.389   1.026  1.00  0.00           H  
HETATM   19  H7  UNL     1       3.612   1.511   0.345  1.00  0.00           H  
HETATM   20  H8  UNL     1       1.768  -2.201   0.748  1.00  0.00           H  
HETATM   21  H9  UNL     1      -2.133  -2.240   0.811  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   10   20
CONECT   11   12
CONECT   12   21
END
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SMILES for #<Metabolite:0x00007f4705c2b7c8>

CC1=NC=C(CO)C(C=O)=C1O
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INCHI for #<Metabolite:0x00007f4705c2b7c8>

InChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3
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Synonyms
ValueSource
3-HYDROXY-5-(hydroxymethyl)-2-methylisonicotinaldehydeChEBI
PyridoxaldehydeChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehydeHMDB
Molecular FormulaC8H9NO3
Average Mass167.162
Monoisotopic Mass167.058243159
IUPAC Name3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde
Traditional Namepyridoxal
CAS Registry Number66-72-8
SMILES
CC1=NC=C(CO)C(C=O)=C1O
InChI Identifier
InChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3
InChI KeyRADKZDMFGJYCBB-UHFFFAOYSA-N