Showing NP-Card for Pyridoxal (NP0000298)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-06-29 00:47:07 UTC
NP-MRD IDNP0000298
Secondary Accession NumbersNone
Natural Product Identification
Common NamePyridoxal
DescriptionPyridoxal is a pyridinecarbaldehyde that is pyridine-4-carbaldehyde bearing methyl, hydroxy and hydroxymethyl substituents at positions 2, 3 and 5 respectively. Pyridoxal, also known as pyridoxaldehyde, belongs to the class of organic compounds known as pyridoxals and derivatives. Pyridoxals and derivatives are compounds containing a pyridoxal moiety, which consists of a pyridine ring substituted at positions 2, 3, 4, and 5 by a methyl group, a hydroxyl group, a carbaldehyde group, and a hydroxymethyl group, respectively. Pyridoxal is one form of vitamin B6. Pyridoxal exists in all living species, ranging from bacteria to humans. In humans, pyridoxal is involved in glycine and serine metabolism. Pyridoxal has been detected, but not quantified in several different foods, such as sourdoughs, lichee, arctic blackberries, watercress, and cottonseeds. Some medically relevant bacteria, such as those in the genera Granulicatella and Abiotrophia, require pyridoxal for growth. This nutritional requirement can lead to the culture phenomenon of satellite growth. In in vitro culture, these pyridoxal-dependent bacteria may only grow in areas surrounding colonies of bacteria from other genera ("satellitism") that are capable of producing pyridoxal. Pridoxal has a role as a cofactor, a human metabolite, a Saccharomyces cerevisiae metabolite, an Escherichia coli metabolite and a mouse metabolite.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000298 (Pyridoxal)

  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 NP0000298 (Pyridoxal)

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 NP0000298 (Pyridoxal)

  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>
NP0000298

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0000298 (Pyridoxal)

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 NP0000298 (Pyridoxal)

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 NP0000298 (Pyridoxal)

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 NP0000298 (Pyridoxal)

CC1=NC=C(CO)C(C=O)=C1O
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INCHI for NP0000298 (Pyridoxal)

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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View in JSmol
Synonyms
ValueSource
3-HYDROXY-5-(hydroxymethyl)-2-methylisonicotinaldehydeChEBI
PyridoxaldehydeChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehydeHMDB
Chemical FormulaC8H9NO3
Average Mass167.1620 Da
Monoisotopic Mass167.05824 Da
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
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 pyridoxals and derivatives. Pyridoxals and derivatives are compounds containing a pyridoxal moiety, which consists of a pyridine ring substituted at positions 2,3,4, and 5 by a methyl group, a hydroxyl group, a carbaldehyde group, and a hydroxymethyl group, respectively.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridine carboxaldehydes
Direct ParentPyridoxals and derivatives
Alternative Parents
Substituents
  • Pyridoxal
  • Aryl-aldehyde
  • Hydroxypyridine
  • Methylpyridine
  • Vinylogous acid
  • Heteroaromatic compound
  • Azacycle
  • Hydrocarbon derivative
  • Aldehyde
  • Alcohol
  • Organic oxygen compound
  • Aromatic alcohol
  • Organic nitrogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point165 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility500 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility11.7 g/LALOGPS
logP0.02ALOGPS
logP0.18ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)7.97ChemAxon
pKa (Strongest Basic)4.11ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area70.42 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity43.87 m³·mol⁻¹ChemAxon
Polarizability16.28 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001545
DrugBank IDDB00147
Phenol Explorer Compound IDNot Available
FoodDB IDFDB011169
KNApSAcK IDC00007509
Chemspider ID1021
KEGG Compound IDC00250
BioCyc IDPYRIDOXAL
BiGG ID34393
Wikipedia LinkPyridoxal
METLIN ID6312
PubChem Compound1050
PDB IDNot Available
ChEBI ID17310
Good Scents IDNot Available
References
General References