Showing NP-Card for Pyridoxamine (NP0000922)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 23:58:35 UTC
NP-MRD IDNP0000922
Secondary Accession NumbersNone
Natural Product Identification
Common NamePyridoxamine
Description
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000922 (Pyridoxamine)

  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 NP0000922 (Pyridoxamine)

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 NP0000922 (Pyridoxamine)

  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>
NP0000922

> <DATABASE_NAME>
NP-MRD

> <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 NP0000922 (Pyridoxamine)

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 NP0000922 (Pyridoxamine)

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 NP0000922 (Pyridoxamine)

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 NP0000922 (Pyridoxamine)

CC1=C(O)C(CN)=C(CO)C=N1
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INCHI for NP0000922 (Pyridoxamine)

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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View in JSmol
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
Chemical FormulaC8H12N2O2
Average Mass168.1931 Da
Monoisotopic Mass168.08988 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridoxamine 5'-phosphates. These are heterocyclic aromatic compounds containing a pyridoxamine that carries a phosphate group at the 5'-position.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridoxamines
Direct ParentPyridoxamine 5'-phosphates
Alternative Parents
Substituents
  • Pyridoxamine 5'-phosphate
  • Aralkylamine
  • Hydroxypyridine
  • Methylpyridine
  • Heteroaromatic compound
  • Azacycle
  • Amine
  • Hydrocarbon derivative
  • Alcohol
  • Aromatic alcohol
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point887.70 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility815 mg/mLNot Available
LogP10.155 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility29 g/LALOGPS
logP-1.2ALOGPS
logP-1.6ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)7.81ChemAxon
pKa (Strongest Basic)9.61ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area79.37 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity45.76 m³·mol⁻¹ChemAxon
Polarizability17.52 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001431
DrugBank IDDB11673
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021819
KNApSAcK IDC00007504
Chemspider ID1023
KEGG Compound IDC00534
BioCyc IDPYRIDOXAMINE
BiGG ID35277
Wikipedia LinkPyridoxamine
METLIN ID238
PubChem Compound1052
PDB IDNot Available
ChEBI ID16410
Good Scents IDrw1480661
References
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Esteve-Romero J, Capella-Peiro ME, Monferrer-Pons L, Gil-Agusti M: Micellar liquid chromatography in clinical chemistry: application to the monitorization of B6 vitamins. Clin Chim Acta. 2004 Oct;348(1-2):69-77. [PubMed:15369738 ]
  3. Berzas Nevado JJ, Murillo Pulgarin JA, Gomez Laguna MA: Determination of pyridoxamine in urine by matrix isopotential synchronous fluorescence spectrometry. Analyst. 1995 Jan;120(1):171-4. [PubMed:7710125 ]
  4. Sharma SK, Dakshinamurti K: Determination of vitamin B6 vitamers and pyridoxic acid in biological samples. J Chromatogr. 1992 Jul 1;578(1):45-51. [PubMed:1400785 ]
  5. Rokitzki L, Sagredos AN, Reuss F, Buchner M, Keul J: Acute changes in vitamin B6 status in endurance athletes before and after a marathon. Int J Sport Nutr. 1994 Jun;4(2):154-65. [PubMed:8054960 ]