Showing metabocard for Pyridoxamine (MMDBc0000195)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:39:20 UTC
Update Date2022-08-31 00:00:33 UTC
Metabolite IDMMDBc0000195
Metabolite Identification
Common NamePyridoxamine
DescriptionThe 4-aminomethyl form of vitamin B6. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate. -- Pubchem; Pyridoxamine is one of the compounds that can be called vitamin B6, along with Pyridoxal and Pyridoxine. -- Wikipedia .
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f5abc187360>


  Mrv1652309042000232D          

 12 12  0  0  0  0            999 V2000
   -0.1168    0.4157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5978    0.0034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8383    0.0034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1134    1.2369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5978   -0.8280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3055    0.4157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8383   -0.8280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5461    0.4157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5978    1.6457    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1168   -1.2471    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0202    0.0034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5495   -1.2369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  2  0  0  0  0
  3  8  1  0  0  0  0
  4  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
  7 10  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f5abc187360>

HMDB0001431
     RDKit          3D
Pyridoxamine
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.3902   -0.4471    0.5629 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9068   -0.5770    0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3108   -1.7623    0.3268 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0094   -1.9135    0.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7911   -0.8191   -0.1510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2081   -1.0495   -0.4445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5772   -2.3712   -0.1540 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2307    0.4202   -0.1980 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0403    1.5859   -0.5517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1459    1.8568    0.3596 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1489    0.5482    0.0270 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7549    1.7783   -0.0260 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5718   -0.0577    1.5588 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8255    0.1902   -0.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8441   -1.4618    0.4032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4388   -2.9045    0.1203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9099   -0.2658   -0.2992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1879   -1.1637   -1.6281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4532   -2.4548    0.8682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3305    2.5010   -0.2789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2060    1.7729   -1.6176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9881    2.5585    1.0923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9691    2.1209   -0.2413 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7143    1.9151    0.0608 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
 10 23  1  0
 12 24  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f5abc187360>


  Mrv1652309042000232D          

 12 12  0  0  0  0            999 V2000
   -0.1168    0.4157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5978    0.0034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8383    0.0034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1134    1.2369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5978   -0.8280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3055    0.4157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8383   -0.8280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5461    0.4157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5978    1.6457    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1168   -1.2471    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0202    0.0034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5495   -1.2369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  2  0  0  0  0
  3  8  1  0  0  0  0
  4  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
  7 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000195

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3

> <INCHI_KEY>
NHZMQXZHNVQTQA-UHFFFAOYSA-N

> <FORMULA>
C8H12N2O2

> <MOLECULAR_WEIGHT>
168.1931

> <EXACT_MASS>
168.089877638

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
17.524325285309423

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.23

> <JCHEM_LOGP>
-1.6069905405485954

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.85255410474139

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.809408884689676

> <JCHEM_PKA_STRONGEST_BASIC>
9.612992220108088

> <JCHEM_POLAR_SURFACE_AREA>
79.37

> <JCHEM_REFRACTIVITY>
45.76279999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.90e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridoxamine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f5abc187360>

HMDB0001431
     RDKit          3D
Pyridoxamine
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.3902   -0.4471    0.5629 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9068   -0.5770    0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3108   -1.7623    0.3268 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0094   -1.9135    0.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7911   -0.8191   -0.1510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2081   -1.0495   -0.4445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5772   -2.3712   -0.1540 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2307    0.4202   -0.1980 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0403    1.5859   -0.5517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1459    1.8568    0.3596 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1489    0.5482    0.0270 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7549    1.7783   -0.0260 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5718   -0.0577    1.5588 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8255    0.1902   -0.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8441   -1.4618    0.4032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4388   -2.9045    0.1203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9099   -0.2658   -0.2992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1879   -1.1637   -1.6281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4532   -2.4548    0.8682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3305    2.5010   -0.2789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2060    1.7729   -1.6176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9881    2.5585    1.0923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9691    2.1209   -0.2413 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7143    1.9151    0.0608 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
 10 23  1  0
 12 24  1  0
M  END
Download

PDB for #<Metabolite:0x00007f5abc187360>

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      -0.218   0.776   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.116   0.006   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.565   0.006   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.212   2.309   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.116  -1.546   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.437   0.776   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.565  -1.546   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.886   0.776   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       1.116   3.072   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      -0.218  -2.328   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       3.771   0.006   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.892  -2.309   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10                                                       
CONECT    6    2   11                                                       
CONECT    7    3   12   10                                                  
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5    7                                                       
CONECT   11    6                                                            
CONECT   12    7                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for #<Metabolite:0x00007f5abc187360>

COMPND    HMDB0001431
HETATM    1  C1  UNL     1       3.390  -0.447   0.563  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.907  -0.577   0.295  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.311  -1.762   0.327  1.00  0.00           N  
HETATM    4  C3  UNL     1       0.009  -1.913   0.114  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.791  -0.819  -0.151  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.208  -1.050  -0.444  1.00  0.00           C  
HETATM    7  O1  UNL     1      -2.577  -2.371  -0.154  1.00  0.00           O  
HETATM    8  C6  UNL     1      -0.231   0.420  -0.198  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.040   1.586  -0.552  1.00  0.00           C  
HETATM   10  N2  UNL     1      -2.146   1.857   0.360  1.00  0.00           N  
HETATM   11  C8  UNL     1       1.149   0.548   0.027  1.00  0.00           C  
HETATM   12  O2  UNL     1       1.755   1.778  -0.026  1.00  0.00           O  
HETATM   13  H1  UNL     1       3.572  -0.058   1.559  1.00  0.00           H  
HETATM   14  H2  UNL     1       3.825   0.190  -0.199  1.00  0.00           H  
HETATM   15  H3  UNL     1       3.844  -1.462   0.403  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.439  -2.905   0.120  1.00  0.00           H  
HETATM   17  H5  UNL     1      -2.910  -0.266  -0.299  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.188  -1.164  -1.628  1.00  0.00           H  
HETATM   19  H7  UNL     1      -2.453  -2.455   0.868  1.00  0.00           H  
HETATM   20  H8  UNL     1      -0.330   2.501  -0.279  1.00  0.00           H  
HETATM   21  H9  UNL     1      -1.206   1.773  -1.618  1.00  0.00           H  
HETATM   22  H10 UNL     1      -1.988   2.559   1.092  1.00  0.00           H  
HETATM   23  H11 UNL     1      -2.969   2.121  -0.241  1.00  0.00           H  
HETATM   24  H12 UNL     1       2.714   1.915   0.061  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   23
CONECT   11   12
CONECT   12   24
END
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SMILES for #<Metabolite:0x00007f5abc187360>

CC1=C(O)C(CN)=C(CO)C=N1
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INCHI for #<Metabolite:0x00007f5abc187360>

InChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3
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Synonyms
ValueSource
4-(AMINOMETHYL)-5-(hydroxymethyl)-2-methylpyridin-3-olChEBI
PMChEBI
2-Methyl-4-aminomethyl-5-hydroxymethyl-3-pyridinolHMDB
4-(Aminomethyl)-5-(hydroxymethyl)-2-methyl-3-pyridinolHMDB
4-(Aminomethyl)-5-hydroxy-6-methyl-3-pyridinemethanolHMDB
PyridoxylamineHMDB
Molecular FormulaC8H12N2O2
Average Mass168.1931
Monoisotopic Mass168.089877638
IUPAC Name4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol
Traditional Namepyridoxamine
CAS Registry Number85-87-0
SMILES
CC1=C(O)C(CN)=C(CO)C=N1
InChI Identifier
InChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3
InChI KeyNHZMQXZHNVQTQA-UHFFFAOYSA-N