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Showing metabocard for 3-Pyridinecarboxaldehyde (HMDB0245978)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:01:21 UTC
Update Date2021-09-26 22:54:45 UTC
HMDB IDHMDB0245978
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Pyridinecarboxaldehyde
Descriptionpyridine-3-carbaldehyde, also known as nicotinaldehyde, belongs to the class of organic compounds known as pyridine carboxaldehydes. These are aromatic compounds containing a pyridine ring which bears a carboxaldehyde group. Based on a literature review very few articles have been published on pyridine-3-carbaldehyde. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-pyridinecarboxaldehyde is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-Pyridinecarboxaldehyde is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0245978 (3-Pyridinecarboxaldehyde)


  Mrv1652306141617282D          

  8  8  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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 C   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 N   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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
M  END
Download

3D MOL for HMDB0245978 (3-Pyridinecarboxaldehyde)

HMDB0245978
     RDKit          3D
3-Pyridinecarboxaldehyde
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.9547   -0.6661   -0.1997 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1503    0.2942   -0.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7264   -0.0012   -0.0407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1782    1.0599    0.0646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5079    0.7351    0.1223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9184   -0.5870    0.0771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0363   -1.5957   -0.0243 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2764   -1.2936   -0.0821 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5326    1.2937   -0.0751 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1928    2.0873    0.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2571    1.5268    0.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9739   -0.7695    0.1268 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0387   -2.0839   -0.1655 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  2  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
  8 13  1  0
M  END
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3D SDF for HMDB0245978 (3-Pyridinecarboxaldehyde)


  Mrv1652306141617282D          

  8  8  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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 C   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 N   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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245978

> <DATABASE_NAME>
hmdb

> <SMILES>
O=CC1=CC=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H5NO/c8-5-6-2-1-3-7-4-6/h1-5H

> <INCHI_KEY>
QJZUKDFHGGYHMC-UHFFFAOYSA-N

> <FORMULA>
C6H5NO

> <MOLECULAR_WEIGHT>
107.112

> <EXACT_MASS>
107.037113785

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
10.356175445162634

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridine-3-carbaldehyde

> <ALOGPS_LOGP>
0.20

> <JCHEM_LOGP>
0.46807573366666677

> <ALOGPS_LOGS>
0.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
3.8754774501691434

> <JCHEM_POLAR_SURFACE_AREA>
29.96

> <JCHEM_REFRACTIVITY>
30.485099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.87e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-pyridinecarboxaldehyde

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0245978 (3-Pyridinecarboxaldehyde)

HMDB0245978
     RDKit          3D
3-Pyridinecarboxaldehyde
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.9547   -0.6661   -0.1997 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1503    0.2942   -0.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7264   -0.0012   -0.0407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1782    1.0599    0.0646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5079    0.7351    0.1223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9184   -0.5870    0.0771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0363   -1.5957   -0.0243 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2764   -1.2936   -0.0821 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5326    1.2937   -0.0751 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1928    2.0873    0.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2571    1.5268    0.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9739   -0.7695    0.1268 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0387   -2.0839   -0.1655 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  2  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
  8 13  1  0
M  END
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PDB for HMDB0245978 (3-Pyridinecarboxaldehyde)

HEADER    PROTEIN                                 14-JUN-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-JUN-16         0                                  
HETATM    1  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0245978 (3-Pyridinecarboxaldehyde)

COMPND    HMDB0245978
HETATM    1  O1  UNL     1       2.955  -0.666  -0.200  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.150   0.294  -0.105  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.726  -0.001  -0.041  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.178   1.060   0.065  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.508   0.735   0.122  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.918  -0.587   0.077  1.00  0.00           C  
HETATM    7  N1  UNL     1      -1.036  -1.596  -0.024  1.00  0.00           N  
HETATM    8  C6  UNL     1       0.276  -1.294  -0.082  1.00  0.00           C  
HETATM    9  H1  UNL     1       2.533   1.294  -0.075  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.193   2.087   0.097  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.257   1.527   0.205  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.974  -0.769   0.127  1.00  0.00           H  
HETATM   13  H5  UNL     1       1.039  -2.084  -0.166  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4    4    8
CONECT    4    5   10
CONECT    5    6    6   11
CONECT    6    7   12
CONECT    7    8    8
CONECT    8   13
END
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SMILES for HMDB0245978 (3-Pyridinecarboxaldehyde)

O=CC1=CC=CN=C1
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INCHI for HMDB0245978 (3-Pyridinecarboxaldehyde)

InChI=1S/C6H5NO/c8-5-6-2-1-3-7-4-6/h1-5H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-PyridinecarboxaldehydeChEBI
NicotinaldehydeChEBI
Pyridine-3-aldehydeChEBI
3-PyridinaldehydeMeSH
Chemical FormulaC6H5NO
Average Molecular Weight107.112
Monoisotopic Molecular Weight107.037113785
IUPAC Namepyridine-3-carbaldehyde
Traditional Name3-pyridinecarboxaldehyde
CAS Registry NumberNot Available
SMILES
O=CC1=CC=CN=C1
InChI Identifier
InChI=1S/C6H5NO/c8-5-6-2-1-3-7-4-6/h1-5H
InChI KeyQJZUKDFHGGYHMC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridine carboxaldehydes. These are aromatic compounds containing a pyridine ring which bears a carboxaldehyde group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridine carboxaldehydes
Direct ParentPyridine carboxaldehydes
Alternative Parents
Substituents
  • 3-pyridine carboxaldehyde
  • Aryl-aldehyde
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aldehyde
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.2ALOGPS
logP0.47ChemAxon
logS0.24ALOGPS
pKa (Strongest Basic)3.88ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area29.96 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.49 m³·mol⁻¹ChemAxon
Polarizability10.36 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+121.80830932474
DeepCCS[M-H]-119.1430932474
DeepCCS[M-2H]-155.57230932474
DeepCCS[M+Na]+130.36830932474
AllCCS[M+H]+121.732859911
AllCCS[M+H-H2O]+116.732859911
AllCCS[M+NH4]+126.432859911
AllCCS[M+Na]+127.732859911
AllCCS[M-H]-119.432859911
AllCCS[M+Na-2H]-121.832859911
AllCCS[M+HCOO]-124.632859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202210.4619 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.23 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1105.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid372.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid116.6 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid259.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid65.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid297.8 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid451.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)192.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid772.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid48.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1073.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid249.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid320.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate640.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA377.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water196.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-PyridinecarboxaldehydeO=CC1=CC=CN=C11738.9Standard polar33892256
3-PyridinecarboxaldehydeO=CC1=CC=CN=C1975.9Standard non polar33892256
3-PyridinecarboxaldehydeO=CC1=CC=CN=C1983.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Pyridinecarboxaldehyde GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-9700000000-b085e88b013d342430c82021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Pyridinecarboxaldehyde GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Pyridinecarboxaldehyde 10V, Positive-QTOFsplash10-0a4i-2900000000-b658d3731dcc6d44fea72021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Pyridinecarboxaldehyde 20V, Positive-QTOFsplash10-0a7i-9500000000-5216bbf08d493947c1192021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Pyridinecarboxaldehyde 40V, Positive-QTOFsplash10-0ufr-9000000000-20a5139ba9aca39c145f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Pyridinecarboxaldehyde 10V, Negative-QTOFsplash10-0a4i-0900000000-22be3dc9468f125f63ef2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Pyridinecarboxaldehyde 20V, Negative-QTOFsplash10-004i-9000000000-c2850ce6846335b0374d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Pyridinecarboxaldehyde 40V, Negative-QTOFsplash10-016r-9000000000-9a22eff06e3e78eccc272021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID9943
KEGG Compound IDC07327
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID28345
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1193091
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]