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Showing metabocard for 5,6-Dihydro-1,10-phenanthroline (HMDB0246859)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:52:16 UTC
Update Date2021-09-26 22:56:11 UTC
HMDB IDHMDB0246859
Secondary Accession NumbersNone
Metabolite Identification
Common Name5,6-Dihydro-1,10-phenanthroline
Description5,6-Dihydro-1,10-phenanthroline, also known as 1,10-phenanthroline hydrate or O-phenanthroline, belongs to the class of organic compounds known as phenanthrolines. These are aromatic polycyclic compounds containing the phenanthroline skeleton, which is a derivative of phenanthrene, and consists of two pyridine rings non-linearly joined by a benzene ring. Based on a literature review a significant number of articles have been published on 5,6-Dihydro-1,10-phenanthroline. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5,6-dihydro-1,10-phenanthroline is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5,6-Dihydro-1,10-phenanthroline 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 HMDB0246859 (5,6-Dihydro-1,10-phenanthroline)

  Mrv1652309112101522D          

 14 16  0  0  0  0            999 V2000
    1.5395   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6020    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  5 10  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  3 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0246859 (5,6-Dihydro-1,10-phenanthroline)

HMDB0246859
     RDKit          3D
5,6-Dihydro-1,10-phenanthroline
 24 26  0  0  0  0  0  0  0  0999 V2000
    3.4841    0.5550   -0.2162 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8341    1.7616   -0.0829 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5020    1.8063    0.0826 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7466    0.6879    0.1258 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3461   -0.5427   -0.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7366   -0.5941   -0.1754 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6333   -1.8267    0.0280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8338   -1.7688    0.2118 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4110   -0.4306    0.3415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7874   -0.2997    0.5162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3986    0.9167    0.6449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6370    2.0657    0.6022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3092    1.9455    0.4339 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6957    0.7355    0.3051 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5764    0.5394   -0.3510 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4603    2.6561   -0.1201 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2422   -1.5450   -0.2796 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8272   -2.3128   -0.9746 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1170   -2.5479    0.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3914   -2.3344   -0.5859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0852   -2.3203    1.1662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3921   -1.2043    0.5505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4772    0.9949    0.7808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0872    3.0626    0.7014 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
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  6  1  1  0
 14  9  1  0
 14  4  1  0
  1 15  1  0
  2 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
 10 22  1  0
 11 23  1  0
 12 24  1  0
M  END
Download

3D SDF for HMDB0246859 (5,6-Dihydro-1,10-phenanthroline)

  Mrv1652309112101522D          

 14 16  0  0  0  0            999 V2000
    1.5395   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6020    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  5 10  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  3 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246859

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CC2=C(N=CC=C2)C2=C1C=CC=N2

> <INCHI_IDENTIFIER>
InChI=1S/C12H10N2/c1-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1/h1-4,7-8H,5-6H2

> <INCHI_KEY>
NDWJTDJESZWTGD-UHFFFAOYSA-N

> <FORMULA>
C12H10N2

> <MOLECULAR_WEIGHT>
182.226

> <EXACT_MASS>
182.08439833

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
19.974346504321325

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,6-dihydro-1,10-phenanthroline

> <ALOGPS_LOGP>
2.38

> <JCHEM_LOGP>
2.5199438513333337

> <ALOGPS_LOGS>
-2.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
3.4945652399535723

> <JCHEM_POLAR_SURFACE_AREA>
25.78

> <JCHEM_REFRACTIVITY>
54.4166

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.53e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,6-dihydro-1,10-phenanthroline

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0246859 (5,6-Dihydro-1,10-phenanthroline)

HMDB0246859
     RDKit          3D
5,6-Dihydro-1,10-phenanthroline
 24 26  0  0  0  0  0  0  0  0999 V2000
    3.4841    0.5550   -0.2162 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8341    1.7616   -0.0829 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5020    1.8063    0.0826 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7466    0.6879    0.1258 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3461   -0.5427   -0.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7366   -0.5941   -0.1754 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6333   -1.8267    0.0280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8338   -1.7688    0.2118 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4110   -0.4306    0.3415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7874   -0.2997    0.5162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3986    0.9167    0.6449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6370    2.0657    0.6022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3092    1.9455    0.4339 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6957    0.7355    0.3051 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5764    0.5394   -0.3510 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4603    2.6561   -0.1201 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2422   -1.5450   -0.2796 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8272   -2.3128   -0.9746 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1170   -2.5479    0.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3914   -2.3344   -0.5859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0852   -2.3203    1.1662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3921   -1.2043    0.5505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4772    0.9949    0.7808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0872    3.0626    0.7014 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
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  6  1  1  0
 14  9  1  0
 14  4  1  0
  1 15  1  0
  2 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
 10 22  1  0
 11 23  1  0
 12 24  1  0
M  END
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PDB for HMDB0246859 (5,6-Dihydro-1,10-phenanthroline)

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       2.874  -1.897   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.414  -1.897   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.104   2.104   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       5.184   2.104   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       6.724   2.104   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    4   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    3                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END
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3D PDB for HMDB0246859 (5,6-Dihydro-1,10-phenanthroline)

COMPND    HMDB0246859
HETATM    1  C1  UNL     1       3.484   0.555  -0.216  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.834   1.762  -0.083  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.502   1.806   0.083  1.00  0.00           N  
HETATM    4  C3  UNL     1       0.747   0.688   0.126  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.346  -0.543  -0.002  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.737  -0.594  -0.175  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.633  -1.827   0.028  1.00  0.00           C  
HETATM    8  C7  UNL     1      -0.834  -1.769   0.212  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.411  -0.431   0.341  1.00  0.00           C  
HETATM   10  C9  UNL     1      -2.787  -0.300   0.516  1.00  0.00           C  
HETATM   11  C10 UNL     1      -3.399   0.917   0.645  1.00  0.00           C  
HETATM   12  C11 UNL     1      -2.637   2.066   0.602  1.00  0.00           C  
HETATM   13  N2  UNL     1      -1.309   1.946   0.434  1.00  0.00           N  
HETATM   14  C12 UNL     1      -0.696   0.736   0.305  1.00  0.00           C  
HETATM   15  H1  UNL     1       4.576   0.539  -0.351  1.00  0.00           H  
HETATM   16  H2  UNL     1       3.460   2.656  -0.120  1.00  0.00           H  
HETATM   17  H3  UNL     1       3.242  -1.545  -0.280  1.00  0.00           H  
HETATM   18  H4  UNL     1       0.827  -2.313  -0.975  1.00  0.00           H  
HETATM   19  H5  UNL     1       1.117  -2.548   0.752  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.391  -2.334  -0.586  1.00  0.00           H  
HETATM   21  H7  UNL     1      -1.085  -2.320   1.166  1.00  0.00           H  
HETATM   22  H8  UNL     1      -3.392  -1.204   0.550  1.00  0.00           H  
HETATM   23  H9  UNL     1      -4.477   0.995   0.781  1.00  0.00           H  
HETATM   24  H10 UNL     1      -3.087   3.063   0.701  1.00  0.00           H  
CONECT    1    2    2    6   15
CONECT    2    3   16
CONECT    3    4    4
CONECT    4    5   14
CONECT    5    6    6    7
CONECT    6   17
CONECT    7    8   18   19
CONECT    8    9   20   21
CONECT    9   10   10   14
CONECT   10   11   22
CONECT   11   12   12   23
CONECT   12   13   24
CONECT   13   14   14
END
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SMILES for HMDB0246859 (5,6-Dihydro-1,10-phenanthroline)

C1CC2=C(N=CC=C2)C2=C1C=CC=N2
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INCHI for HMDB0246859 (5,6-Dihydro-1,10-phenanthroline)

InChI=1S/C12H10N2/c1-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1/h1-4,7-8H,5-6H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,10-Phenanthroline hydrateHMDB
1,10-Phenanthroline monohydrochorideHMDB
O-PhenanthrolineHMDB
1,10-PhenanthrolineHMDB
1,10-Phenanthroline hydrochorideHMDB
1,10-Phenanthroline monoperchlorateHMDB
Copper phenanthrolineHMDB
(OP)2Cu(I)HMDB
1,10-Phenanthroline, zinc saltHMDB
O-PHEHMDB
Chemical FormulaC12H10N2
Average Molecular Weight182.226
Monoisotopic Molecular Weight182.08439833
IUPAC Name5,6-dihydro-1,10-phenanthroline
Traditional Name5,6-dihydro-1,10-phenanthroline
CAS Registry NumberNot Available
SMILES
C1CC2=C(N=CC=C2)C2=C1C=CC=N2
InChI Identifier
InChI=1S/C12H10N2/c1-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1/h1-4,7-8H,5-6H2
InChI KeyNDWJTDJESZWTGD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phenanthrolines. These are aromatic polycyclic compounds containing the phenanthroline skeleton, which is a derivative of phenanthrene, and consists of two pyridine rings non-linearly joined by a benzene ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPhenanthrolines
Sub ClassNot Available
Direct ParentPhenanthrolines
Alternative Parents
Substituents
  • 1,10-phenanthroline
  • 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 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 ID10280674
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound13528147
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 ]