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Showing metabocard for Pyridopyrimidine (HMDB0256973)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:36:45 UTC
Update Date2022-11-23 22:29:18 UTC
HMDB IDHMDB0256973
Secondary Accession NumbersNone
Metabolite Identification
Common NamePyridopyrimidine
Descriptionpyrido[3,2-d]pyrimidine belongs to the class of organic compounds known as pyridopyrimidines. Pyridopyrimidines are compounds containing a pyridopyrimidine, which consists of a pyridine fused to a pyrimidine. Pyridine is 6-membered ring consisting of five carbon atoms and a nitrogen atom. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Based on a literature review a significant number of articles have been published on pyrido[3,2-d]pyrimidine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pyridopyrimidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pyridopyrimidine 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 HMDB0256973 (Pyridopyrimidine)


  Mrv1652309112119372D          

 10 11  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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    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  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
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  1 10  1  0  0  0  0
M  END
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3D MOL for HMDB0256973 (Pyridopyrimidine)

HMDB0256973
     RDKit          3D
PYRIDOPYRIMIDINE
 15 16  0  0  0  0  0  0  0  0999 V2000
   -2.2318   -0.1414   -0.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9675    1.2128   -0.1670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6719    1.5679   -0.1109 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3434    0.7107   -0.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6687    1.1018    0.0421 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6793    0.2011    0.1408 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4093   -1.1160    0.1872 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1355   -1.5204    0.1347 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1001   -0.6480    0.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2073   -1.0759   -0.0174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2600   -0.4650   -0.1611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7456    1.9686   -0.2459 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9131    2.1497    0.0068 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2500   -1.7926    0.2660 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4152   -2.1534    0.0213 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  9  1  0
  9 10  2  0
 10  1  1  0
  9  4  1  0
  1 11  1  0
  2 12  1  0
  5 13  1  0
  7 14  1  0
 10 15  1  0
M  END
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3D SDF for HMDB0256973 (Pyridopyrimidine)


  Mrv1652309112119372D          

 10 11  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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    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  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
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  1 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256973

> <DATABASE_NAME>
hmdb

> <SMILES>
C1=CC2=NC=NC=C2N=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H5N3/c1-2-6-7(9-3-1)4-8-5-10-6/h1-5H

> <INCHI_KEY>
BWESROVQGZSBRX-UHFFFAOYSA-N

> <FORMULA>
C7H5N3

> <MOLECULAR_WEIGHT>
131.138

> <EXACT_MASS>
131.048347173

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
12.630142309741297

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyrido[3,2-d]pyrimidine

> <ALOGPS_LOGP>
0.12

> <JCHEM_LOGP>
0.5932404370000001

> <ALOGPS_LOGS>
-0.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
2.71962184643854

> <JCHEM_POLAR_SURFACE_AREA>
38.67

> <JCHEM_REFRACTIVITY>
36.2716

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.38e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrido[3,2-d]pyrimidine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256973 (Pyridopyrimidine)

HMDB0256973
     RDKit          3D
PYRIDOPYRIMIDINE
 15 16  0  0  0  0  0  0  0  0999 V2000
   -2.2318   -0.1414   -0.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9675    1.2128   -0.1670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6719    1.5679   -0.1109 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3434    0.7107   -0.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6687    1.1018    0.0421 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6793    0.2011    0.1408 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4093   -1.1160    0.1872 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1355   -1.5204    0.1347 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1001   -0.6480    0.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2073   -1.0759   -0.0174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2600   -0.4650   -0.1611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7456    1.9686   -0.2459 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9131    2.1497    0.0068 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2500   -1.7926    0.2660 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4152   -2.1534    0.0213 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  9  1  0
  9 10  2  0
 10  1  1  0
  9  4  1  0
  1 11  1  0
  2 12  1  0
  5 13  1  0
  7 14  1  0
 10 15  1  0
M  END
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PDB for HMDB0256973 (Pyridopyrimidine)

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       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       5.335   0.000   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       6.668  -2.310   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.667  -3.080   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
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    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9    1                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for HMDB0256973 (Pyridopyrimidine)

COMPND    HMDB0256973
HETATM    1  C1  UNL     1      -2.232  -0.141  -0.119  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.967   1.213  -0.167  1.00  0.00           C  
HETATM    3  N1  UNL     1      -0.672   1.568  -0.111  1.00  0.00           N  
HETATM    4  C3  UNL     1       0.343   0.711  -0.014  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.669   1.102   0.042  1.00  0.00           C  
HETATM    6  N2  UNL     1       2.679   0.201   0.141  1.00  0.00           N  
HETATM    7  C5  UNL     1       2.409  -1.116   0.187  1.00  0.00           C  
HETATM    8  N3  UNL     1       1.135  -1.520   0.135  1.00  0.00           N  
HETATM    9  C6  UNL     1       0.100  -0.648   0.036  1.00  0.00           C  
HETATM   10  C7  UNL     1      -1.207  -1.076  -0.017  1.00  0.00           C  
HETATM   11  H1  UNL     1      -3.260  -0.465  -0.161  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.746   1.969  -0.246  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.913   2.150   0.007  1.00  0.00           H  
HETATM   14  H4  UNL     1       3.250  -1.793   0.266  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.415  -2.153   0.021  1.00  0.00           H  
CONECT    1    2    2   10   11
CONECT    2    3   12
CONECT    3    4    4
CONECT    4    5    9
CONECT    5    6    6   13
CONECT    6    7
CONECT    7    8    8   14
CONECT    8    9
CONECT    9   10   10
CONECT   10   15
END
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SMILES for HMDB0256973 (Pyridopyrimidine)

C1=CC2=NC=NC=C2N=C1
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INCHI for HMDB0256973 (Pyridopyrimidine)

InChI=1S/C7H5N3/c1-2-6-7(9-3-1)4-8-5-10-6/h1-5H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Pyrido(3,2-D)pyrimidineMeSH
Chemical FormulaC7H5N3
Average Molecular Weight131.138
Monoisotopic Molecular Weight131.048347173
IUPAC Namepyrido[3,2-d]pyrimidine
Traditional Namepyrido[3,2-d]pyrimidine
CAS Registry NumberNot Available
SMILES
C1=CC2=NC=NC=C2N=C1
InChI Identifier
InChI=1S/C7H5N3/c1-2-6-7(9-3-1)4-8-5-10-6/h1-5H
InChI KeyBWESROVQGZSBRX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridopyrimidines. Pyridopyrimidines are compounds containing a pyridopyrimidine, which consists of a pyridine fused to a pyrimidine. Pyridine is 6-membered ring consisting of five carbon atoms and a nitrogen atom. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridopyrimidines
Sub ClassNot Available
Direct ParentPyridopyrimidines
Alternative Parents
Substituents
  • Pyridopyrimidine
  • Pyrimidine
  • Pyridine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
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
logP0.12ALOGPS
logP0.59ChemAxon
logS-0.74ALOGPS
pKa (Strongest Basic)2.72ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area38.67 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity36.27 m³·mol⁻¹ChemAxon
Polarizability12.63 ųChemAxon
Number of Rings2ChemAxon
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]+125.86830932474
DeepCCS[M-H]-122.61330932474
DeepCCS[M-2H]-159.64830932474
DeepCCS[M+Na]+134.91130932474
AllCCS[M+H]+125.532859911
AllCCS[M+H-H2O]+120.532859911
AllCCS[M+NH4]+130.232859911
AllCCS[M+Na]+131.532859911
AllCCS[M-H]-123.532859911
AllCCS[M+Na-2H]-124.632859911
AllCCS[M+HCOO]-125.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PYRIDOPYRIMIDINEC1=CC2=NC=NC=C2N=C11976.7Standard polar33892256
PYRIDOPYRIMIDINEC1=CC2=NC=NC=C2N=C11294.6Standard non polar33892256
PYRIDOPYRIMIDINEC1=CC2=NC=NC=C2N=C11316.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pyridopyrimidine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f89-1900000000-2701bb0fbbf22f08b04c2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyridopyrimidine 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)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart 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 ID10384850
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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 ]