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Showing metabocard for 1,8-Naphthyridine (HMDB0244251)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:25:26 UTC
Update Date2021-09-26 22:51:53 UTC
HMDB IDHMDB0244251
Secondary Accession NumbersNone
Metabolite Identification
Common Name1,8-Naphthyridine
Description1,8-Naphthyridine, also known as 1,8-diazanaphthalene or 1,8-pyridopyridine, belongs to the class of organic compounds known as naphthyridines. Naphthyridines are compounds containing a naphthyridine moiety, a naphthalene in which a carbon atom has been replaced by a nitrogen in each of the two rings. The naphthyridine skeleton can also be described as an assembly two fused pyridine rings, which do not share their nitrogen atom. Based on a literature review a significant number of articles have been published on 1,8-Naphthyridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1,8-naphthyridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1,8-Naphthyridine 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 HMDB0244251 (1,8-Naphthyridine)

  Mrv1652304272018262D          

 10 11  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  5  1  0  0  0  0
  2  4  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  4  7  2  0  0  0  0
  5  9  2  0  0  0  0
  6 10  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  END
Download

3D MOL for HMDB0244251 (1,8-Naphthyridine)

HMDB0244251
     RDKit          3D
1,8-Naphthyridine
 16 17  0  0  0  0  0  0  0  0999 V2000
    2.3975    0.1928    0.3310 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3602   -0.0034   -1.0341 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1667   -0.1639   -1.6528 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0185   -0.1371   -0.9727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1563   -0.3010   -1.6235 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3265   -0.2772   -0.9550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4082   -0.0880    0.4115 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1960    0.0794    1.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0056    0.0560    0.3918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2165    0.2224    1.0443 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3117    0.3233    0.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3057   -0.0202   -1.5570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2741   -0.4106   -1.4882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3607   -0.0720    0.9311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2231    0.2285    2.1309 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1624    0.3711    2.1142 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
  6 13  1  0
  7 14  1  0
  8 15  1  0
 10 16  1  0
M  END
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3D SDF for HMDB0244251 (1,8-Naphthyridine)

  Mrv1652304272018262D          

 10 11  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7144    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  5  1  0  0  0  0
  2  4  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  4  7  2  0  0  0  0
  5  9  2  0  0  0  0
  6 10  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244251

> <DATABASE_NAME>
hmdb

> <SMILES>
C1=CC2=CC=CN=C2N=C1

> <INCHI_IDENTIFIER>
InChI=1S/C8H6N2/c1-3-7-4-2-6-10-8(7)9-5-1/h1-6H

> <INCHI_KEY>
FLBAYUMRQUHISI-UHFFFAOYSA-N

> <FORMULA>
C8H6N2

> <MOLECULAR_WEIGHT>
130.15

> <EXACT_MASS>
130.053098201

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
13.300514293032629

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,8-naphthyridine

> <ALOGPS_LOGP>
1.25

> <JCHEM_LOGP>
1.238232598666667

> <ALOGPS_LOGS>
-1.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
0.9169774685641662

> <JCHEM_POLAR_SURFACE_AREA>
25.78

> <JCHEM_REFRACTIVITY>
39.395199999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.75e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,8-naphthyridine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0244251 (1,8-Naphthyridine)

HMDB0244251
     RDKit          3D
1,8-Naphthyridine
 16 17  0  0  0  0  0  0  0  0999 V2000
    2.3975    0.1928    0.3310 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3602   -0.0034   -1.0341 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1667   -0.1639   -1.6528 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0185   -0.1371   -0.9727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1563   -0.3010   -1.6235 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3265   -0.2772   -0.9550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4082   -0.0880    0.4115 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1960    0.0794    1.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0056    0.0560    0.3918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2165    0.2224    1.0443 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3117    0.3233    0.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3057   -0.0202   -1.5570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2741   -0.4106   -1.4882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3607   -0.0720    0.9311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2231    0.2285    2.1309 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1624    0.3711    2.1142 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
  6 13  1  0
  7 14  1  0
  8 15  1  0
 10 16  1  0
M  END
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PDB for HMDB0244251 (1,8-Naphthyridine)

HEADER    PROTEIN                                 27-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-20         0                                  
HETATM    1  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.540  -2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.770   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.540   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -0.770   1.334   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      -3.080   0.000   0.000  0.00  0.00           N+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    7                                                       
CONECT    5    1    9                                                       
CONECT    6    2   10                                                       
CONECT    7    3    4    8                                                  
CONECT    8    7    9   10                                                  
CONECT    9    5    8                                                       
CONECT   10    6    8                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for HMDB0244251 (1,8-Naphthyridine)

COMPND    HMDB0244251
HETATM    1  C1  UNL     1       2.398   0.193   0.331  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.360  -0.003  -1.034  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.167  -0.164  -1.653  1.00  0.00           N  
HETATM    4  C3  UNL     1       0.019  -0.137  -0.973  1.00  0.00           C  
HETATM    5  N2  UNL     1      -1.156  -0.301  -1.624  1.00  0.00           N  
HETATM    6  C4  UNL     1      -2.327  -0.277  -0.955  1.00  0.00           C  
HETATM    7  C5  UNL     1      -2.408  -0.088   0.412  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.196   0.079   1.071  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.006   0.056   0.392  1.00  0.00           C  
HETATM   10  C8  UNL     1       1.217   0.222   1.044  1.00  0.00           C  
HETATM   11  H1  UNL     1       3.312   0.323   0.858  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.306  -0.020  -1.557  1.00  0.00           H  
HETATM   13  H3  UNL     1      -3.274  -0.411  -1.488  1.00  0.00           H  
HETATM   14  H4  UNL     1      -3.361  -0.072   0.931  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.223   0.228   2.131  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.162   0.371   2.114  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
CONECT    6    7   13
CONECT    7    8    8   14
CONECT    8    9   15
CONECT    9   10   10
CONECT   10   16
END
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SMILES for HMDB0244251 (1,8-Naphthyridine)

C1=CC2=CC=CN=C2N=C1
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INCHI for HMDB0244251 (1,8-Naphthyridine)

InChI=1S/C8H6N2/c1-3-7-4-2-6-10-8(7)9-5-1/h1-6H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,8-DiazanaphthaleneChEBI
1,8-PyridopyridineChEBI
NapyChEBI
Chemical FormulaC8H6N2
Average Molecular Weight130.15
Monoisotopic Molecular Weight130.053098201
IUPAC Name1,8-naphthyridine
Traditional Name1,8-naphthyridine
CAS Registry NumberNot Available
SMILES
C1=CC2=CC=CN=C2N=C1
InChI Identifier
InChI=1S/C8H6N2/c1-3-7-4-2-6-10-8(7)9-5-1/h1-6H
InChI KeyFLBAYUMRQUHISI-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as naphthyridines. Naphthyridines are compounds containing a naphthyridine moiety, a naphthalene in which a carbon atom has been replaced by a nitrogen in each of the two rings. The naphthyridine skeleton can also be described as an assembly two fused pyridine rings, which do not share their nitrogen atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazanaphthalenes
Sub ClassNaphthyridines
Direct ParentNaphthyridines
Alternative Parents
Substituents
  • Naphthyridine
  • Pyridine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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
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 ID119846
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link1,8-Naphthyridine
METLIN IDNot Available
PubChem Compound136069
PDB IDNot Available
ChEBI ID36628
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 ]