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Showing NP-Card for Pyridoxamine (NP0000922)

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Record Information
Version1.0
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
DescriptionPyridoxamine is one form of vitamin B6. Chemically it is based on a pyridine ring structure, with hydroxyl, methyl, aminomethyl, and hydroxymethyl substituents. It differs from pyridoxine by the substituent at the 4-position. The hydroxyl at position 3 and aminomethyl group at position 4 of its ring endow pyridoxamine with a variety of chemical properties, including the scavenging of free radical species and carbonyl species formed in sugar and lipid degradation and chelation of metal ions that catalyze Amadori reactions. Pyridoxamine, also known as PM, 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. Within humans, pyridoxamine participates in a number of enzymatic reactions. In particular, pyridoxamine can be converted into pyridoxal; which is mediated by the enzyme pyridoxine-5'-phosphate oxidase. In addition, pyridoxamine can be converted into pyridoxamine 5'-phosphate; which is catalyzed by the enzyme pyridoxal kinase. Pyridoxamine also inhibits the formation of advanced lipoxidation endproducts during lipid peroxidation reactions by reaction with dicarbonyl intermediates. In humans, pyridoxamine is involved in vitamin B6 metabolism. Outside of the human body, pyridoxamine has been detected, but not quantified in several different foods, such as nutmegs, sparkleberries, fennels, turmerics, and swiss chards. Pyridoxamine inhibits the Maillard reaction and can block the formation of advanced glycation endproducts, which are associated with medical complications of diabetes. Pyridoxamine is hypothesized to trap intermediates in the formation of Amadori products released from glycated proteins, possibly preventing the breakdown of glycated proteins by disrupting the catalysis of this process through disruptive interactions with the metal ions crucial to the redox reaction. One research study found that pyridoxamine specifically reacts with the carbonyl group in Amadori products, but inhibition of post-Amadori reactions (that can lead to advanced glycation endproducts) is due in much greater part to the metal chelation effects of pyridoxamine.
Structure
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MOL3D MOLSDFPDBSMILESInChI

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)

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

Download
3D PDB for NP0000922 (Pyridoxamine)
Download
SMILES for NP0000922 (Pyridoxamine)
CC1=C(O)C(CN)=C(CO)C=N1
Download
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
Spectra
Spectrum TypeDescriptionDepositor IDDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaKNApSAcK Database
Cannabis sativaCannabisDB
      Not Available
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
logP10(-1.2) g/LALOGPS
logP10(-1.6) g/LChemAxon
logS10(-0.76) g/LALOGPS
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  ]