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Showing metabocard for N-(2-Pyrimidinyl)formamide (HMDB0252442)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 10:19:48 UTC
Update Date2021-09-26 23:05:01 UTC
HMDB IDHMDB0252442
Secondary Accession NumbersNone
Metabolite Identification
Common NameN-(2-Pyrimidinyl)formamide
DescriptionN-(2-Pyrimidinyl)formamide 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 very few articles have been published on N-(2-Pyrimidinyl)formamide. This compound has been identified in human blood as reported by (PMID: 31557052 ). N-(2-pyrimidinyl)formamide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically N-(2-Pyrimidinyl)formamide 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 HMDB0252442 (N-(2-Pyrimidinyl)formamide)

  Mrv1652309112112202D          

  9  9  0  0  0  0            999 V2000
    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 N   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    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
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
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3D MOL for HMDB0252442 (N-(2-Pyrimidinyl)formamide)

HMDB0252442
     RDKit          3D
N-(2-Pyrimidinyl)formamide
 14 14  0  0  0  0  0  0  0  0999 V2000
    3.7761    0.5801   -1.1231 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6695    0.1894   -0.6728 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4697    0.9191   -0.8179 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2699    0.3896   -0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2651   -0.7870    0.3757 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8442   -1.3163    0.9027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0343   -0.6052    0.7658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0550    0.6029    0.1068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8974    1.0557   -0.3885 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6591   -0.7518   -0.1538 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4423    1.8359   -1.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7960   -2.2676    1.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9499   -1.0026    1.1791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9749    1.1578   -0.0019 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
  6 12  1  0
  7 13  1  0
  8 14  1  0
M  END
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3D SDF for HMDB0252442 (N-(2-Pyrimidinyl)formamide)

  Mrv1652309112112202D          

  9  9  0  0  0  0            999 V2000
    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 N   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    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
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0252442

> <DATABASE_NAME>
hmdb

> <SMILES>
O=CNC1=NC=CC=N1

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

> <INCHI_KEY>
ANCSTOBSCOWSPF-UHFFFAOYSA-N

> <FORMULA>
C5H5N3O

> <MOLECULAR_WEIGHT>
123.115

> <EXACT_MASS>
123.043261793

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
11.297241633017059

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-(pyrimidin-2-yl)formamide

> <ALOGPS_LOGP>
-0.15

> <JCHEM_LOGP>
-0.08246686266666667

> <ALOGPS_LOGS>
-1.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.195806907904217

> <JCHEM_PKA_STRONGEST_BASIC>
0.8339900037716499

> <JCHEM_POLAR_SURFACE_AREA>
54.88

> <JCHEM_REFRACTIVITY>
33.0408

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.87e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-(pyrimidin-2-yl)formamide

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0252442 (N-(2-Pyrimidinyl)formamide)

HMDB0252442
     RDKit          3D
N-(2-Pyrimidinyl)formamide
 14 14  0  0  0  0  0  0  0  0999 V2000
    3.7761    0.5801   -1.1231 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6695    0.1894   -0.6728 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4697    0.9191   -0.8179 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2699    0.3896   -0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2651   -0.7870    0.3757 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8442   -1.3163    0.9027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0343   -0.6052    0.7658 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0550    0.6029    0.1068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8974    1.0557   -0.3885 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6591   -0.7518   -0.1538 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4423    1.8359   -1.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7960   -2.2676    1.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9499   -1.0026    1.1791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9749    1.1578   -0.0019 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
  6 12  1  0
  7 13  1  0
  8 14  1  0
M  END
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PDB for HMDB0252442 (N-(2-Pyrimidinyl)formamide)

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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+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                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    4    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 HMDB0252442 (N-(2-Pyrimidinyl)formamide)

COMPND    HMDB0252442
HETATM    1  O1  UNL     1       3.776   0.580  -1.123  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.670   0.189  -0.673  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.470   0.919  -0.818  1.00  0.00           N  
HETATM    4  C2  UNL     1       0.270   0.390  -0.271  1.00  0.00           C  
HETATM    5  N2  UNL     1       0.265  -0.787   0.376  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.844  -1.316   0.903  1.00  0.00           C  
HETATM    7  C4  UNL     1      -2.034  -0.605   0.766  1.00  0.00           C  
HETATM    8  C5  UNL     1      -2.055   0.603   0.107  1.00  0.00           C  
HETATM    9  N3  UNL     1      -0.897   1.056  -0.388  1.00  0.00           N  
HETATM   10  H1  UNL     1       2.659  -0.752  -0.154  1.00  0.00           H  
HETATM   11  H2  UNL     1       1.442   1.836  -1.315  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.796  -2.268   1.415  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.950  -1.003   1.179  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.975   1.158  -0.002  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
CONECT    6    7    7   12
CONECT    7    8   13
CONECT    8    9    9   14
END
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SMILES for HMDB0252442 (N-(2-Pyrimidinyl)formamide)

O=CNC1=NC=CC=N1
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INCHI for HMDB0252442 (N-(2-Pyrimidinyl)formamide)

InChI=1S/C5H5N3O/c9-4-8-5-6-2-1-3-7-5/h1-4H,(H,6,7,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H5N3O
Average Molecular Weight123.115
Monoisotopic Molecular Weight123.043261793
IUPAC NameN-(pyrimidin-2-yl)formamide
Traditional NameN-(pyrimidin-2-yl)formamide
CAS Registry NumberNot Available
SMILES
O=CNC1=NC=CC=N1
InChI Identifier
InChI=1S/C5H5N3O/c9-4-8-5-6-2-1-3-7-5/h1-4H,(H,6,7,8,9)
InChI KeyANCSTOBSCOWSPF-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 DescriptorsNot Available
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
Predicted Chromatographic Properties
Spectra
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 ID224096
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound255580
PDB IDNot Available
ChEBI IDNot Available
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 ]