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Showing metabocard for N-pyrimidin-5-ylformamide (HMDB0255241)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 14:49:56 UTC
Update Date2021-09-26 23:09:52 UTC
HMDB IDHMDB0255241
Secondary Accession NumbersNone
Metabolite Identification
Common NameN-pyrimidin-5-ylformamide
Description5-formamidopyrimidine belongs to the class of organic compounds known as n-arylamides. These are organic compounds that contain a carboxamide group that is N-linked to a aryl group. They have the generic structure RC(=O)N(R')H, R = organyl group and R'= aryl group. Based on a literature review a significant number of articles have been published on 5-formamidopyrimidine. This compound has been identified in human blood as reported by (PMID: 31557052 ). N-pyrimidin-5-ylformamide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically N-pyrimidin-5-ylformamide 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 HMDB0255241 (N-pyrimidin-5-ylformamide)


  Mrv1652309112116502D          

  9  9  0  0  0  0            999 V2000
   -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 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 N   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
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   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
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
Download

3D MOL for HMDB0255241 (N-pyrimidin-5-ylformamide)

HMDB0255241
     RDKit          3D
N-pyrimidin-5-ylformamide
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.1695   -1.8547    0.5830 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4472   -0.7491    0.0838 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5127    0.2421   -0.2494 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1185    0.1884   -0.0919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5599   -0.8820    0.4309 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9242   -0.8385    0.5440 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6404    0.2278    0.1575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0093    1.2953   -0.3595 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6776    1.2715   -0.4779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5314   -0.6086   -0.0808 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9102    1.1403   -0.6715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0312   -1.7729    0.7605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7152    0.2151    0.2667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1318    2.1252   -0.8953 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  2 10  1  0
  3 11  1  0
  5 12  1  0
  7 13  1  0
  9 14  1  0
M  END
Download

3D SDF for HMDB0255241 (N-pyrimidin-5-ylformamide)


  Mrv1652309112116502D          

  9  9  0  0  0  0            999 V2000
   -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 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 N   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
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   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
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255241

> <DATABASE_NAME>
hmdb

> <SMILES>
O=CNC1=CN=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H5N3O/c9-4-8-5-1-6-3-7-2-5/h1-4H,(H,8,9)

> <INCHI_KEY>
NKKLCOFTJVNYAQ-UHFFFAOYSA-N

> <FORMULA>
C5H5N3O

> <MOLECULAR_WEIGHT>
123.115

> <EXACT_MASS>
123.043261793

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
11.120977200086841

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-(pyrimidin-5-yl)formamide

> <ALOGPS_LOGP>
-0.75

> <JCHEM_LOGP>
-0.7612528846666665

> <ALOGPS_LOGS>
-1.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.265204122620386

> <JCHEM_PKA_STRONGEST_BASIC>
0.8371326132890864

> <JCHEM_POLAR_SURFACE_AREA>
54.88

> <JCHEM_REFRACTIVITY>
33.0948

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.03e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
formamidopyrimidine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0255241 (N-pyrimidin-5-ylformamide)

HMDB0255241
     RDKit          3D
N-pyrimidin-5-ylformamide
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.1695   -1.8547    0.5830 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4472   -0.7491    0.0838 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5127    0.2421   -0.2494 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1185    0.1884   -0.0919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5599   -0.8820    0.4309 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9242   -0.8385    0.5440 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6404    0.2278    0.1575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0093    1.2953   -0.3595 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6776    1.2715   -0.4779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5314   -0.6086   -0.0808 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9102    1.1403   -0.6715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0312   -1.7729    0.7605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7152    0.2151    0.2667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1318    2.1252   -0.8953 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  2 10  1  0
  3 11  1  0
  5 12  1  0
  7 13  1  0
  9 14  1  0
M  END
Download

PDB for HMDB0255241 (N-pyrimidin-5-ylformamide)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -0.000   1.540   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  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000  -0.000   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    2    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0255241 (N-pyrimidin-5-ylformamide)

COMPND    HMDB0255241
HETATM    1  O1  UNL     1       2.170  -1.855   0.583  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.447  -0.749   0.084  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.513   0.242  -0.249  1.00  0.00           N  
HETATM    4  C2  UNL     1       0.118   0.188  -0.092  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.560  -0.882   0.431  1.00  0.00           C  
HETATM    6  N2  UNL     1      -1.924  -0.839   0.544  1.00  0.00           N  
HETATM    7  C4  UNL     1      -2.640   0.228   0.157  1.00  0.00           C  
HETATM    8  N3  UNL     1      -2.009   1.295  -0.360  1.00  0.00           N  
HETATM    9  C5  UNL     1      -0.678   1.272  -0.478  1.00  0.00           C  
HETATM   10  H1  UNL     1       3.531  -0.609  -0.081  1.00  0.00           H  
HETATM   11  H2  UNL     1       1.910   1.140  -0.671  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.031  -1.773   0.761  1.00  0.00           H  
HETATM   13  H4  UNL     1      -3.715   0.215   0.267  1.00  0.00           H  
HETATM   14  H5  UNL     1      -0.132   2.125  -0.895  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4   11
CONECT    4    5    5    9
CONECT    5    6   12
CONECT    6    7    7
CONECT    7    8   13
CONECT    8    9    9
CONECT    9   14
END
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SMILES for HMDB0255241 (N-pyrimidin-5-ylformamide)

O=CNC1=CN=CN=C1
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INCHI for HMDB0255241 (N-pyrimidin-5-ylformamide)

InChI=1S/C5H5N3O/c9-4-8-5-1-6-3-7-2-5/h1-4H,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
FormamidopyrimidineChEBI
Chemical FormulaC5H5N3O
Average Molecular Weight123.115
Monoisotopic Molecular Weight123.043261793
IUPAC NameN-(pyrimidin-5-yl)formamide
Traditional Nameformamidopyrimidine
CAS Registry NumberNot Available
SMILES
O=CNC1=CN=CN=C1
InChI Identifier
InChI=1S/C5H5N3O/c9-4-8-5-1-6-3-7-2-5/h1-4H,(H,8,9)
InChI KeyNKKLCOFTJVNYAQ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as n-arylamides. These are organic compounds that contain a carboxamide group that is N-linked to a aryl group. They have the generic structure RC(=O)N(R')H, R = organyl group and R'= aryl group.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassN-arylamides
Direct ParentN-arylamides
Alternative Parents
Substituents
  • N-arylamide
  • Pyrimidine
  • Heteroaromatic compound
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP-0.75ALOGPS
logP-0.76ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)12.27ChemAxon
pKa (Strongest Basic)0.84ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area54.88 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity33.09 m³·mol⁻¹ChemAxon
Polarizability11.12 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+123.9230932474
DeepCCS[M-H]-121.07230932474
DeepCCS[M-2H]-157.76330932474
DeepCCS[M+Na]+132.51430932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
N-pyrimidin-5-ylformamideO=CNC1=CN=CN=C12086.1Standard polar33892256
N-pyrimidin-5-ylformamideO=CNC1=CN=CN=C11318.2Standard non polar33892256
N-pyrimidin-5-ylformamideO=CNC1=CN=CN=C11468.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
N-pyrimidin-5-ylformamide,1TMS,isomer #1C[Si](C)(C)N(C=O)C1=CN=CN=C11397.6Semi standard non polar33892256
N-pyrimidin-5-ylformamide,1TMS,isomer #1C[Si](C)(C)N(C=O)C1=CN=CN=C11514.1Standard non polar33892256
N-pyrimidin-5-ylformamide,1TMS,isomer #1C[Si](C)(C)N(C=O)C1=CN=CN=C12019.2Standard polar33892256
N-pyrimidin-5-ylformamide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C=O)C1=CN=CN=C11588.9Semi standard non polar33892256
N-pyrimidin-5-ylformamide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C=O)C1=CN=CN=C11689.4Standard non polar33892256
N-pyrimidin-5-ylformamide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C=O)C1=CN=CN=C12197.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - N-pyrimidin-5-ylformamide GC-MS (Non-derivatized) - 70eV, Positivesplash10-00dj-9500000000-392c6ead80ea633c792c2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-pyrimidin-5-ylformamide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart 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 ID466188
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID35877
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
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 ]