Showing metabocard for 5,6-Dimethylbenzimidazole (MMDBc0049910)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:46:01 UTC
Update Date2023-12-14 16:53:09 UTC
Metabolite IDMMDBc0049910
Metabolite Identification
Common Name5,6-Dimethylbenzimidazole
DescriptionDimethylbenzimidazole is an intermediate in Riboflavin metabolism. Dimethylbenzimidazole is the second to last step for the synthesis of alpha-Ribazole. It is converted from Riboflavin then it is converted to N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole via the enzyme nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb45940bb0>


  Mrv1652304272018482D          

 11 12  0  0  0  0            999 V2000
   -2.7112    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7112   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7018    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9967    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9967   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169    0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169   -0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  6  2  0  0  0  0
  3  8  1  0  0  0  0
  4  7  2  0  0  0  0
  4  9  1  0  0  0  0
  5 10  2  0  0  0  0
  5 11  1  0  0  0  0
  6  7  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007fdb45940bb0>

HMDB0003701
     RDKit          3D
Dimethylbenzimidazole
 21 22  0  0  0  0  0  0  0  0999 V2000
   -2.3836    1.2311    0.0574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0007    0.6708    0.0174 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1165    1.4928   -0.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3972    0.9867   -0.0439 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6204    1.5397   -0.0728 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5716    0.5879   -0.1037 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9059   -0.5817   -0.0933 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5774   -0.3803   -0.0570 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4593   -1.1999   -0.0325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8267   -0.7015    0.0045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0114   -1.6172    0.0301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9338    1.0669   -0.8713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2989    2.3229    0.2971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9629    0.7230    0.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0213    2.5631    0.0031 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6588    0.7290   -0.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3258   -1.5573   -0.1103 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6308   -2.2734   -0.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3780   -1.6544    1.0962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6385   -2.6489   -0.1812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8079   -1.2993   -0.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10  2  1  0
  8  4  2  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  6 16  1  0
  7 17  1  0
  9 18  1  0
 11 19  1  0
 11 20  1  0
 11 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fdb45940bb0>


  Mrv1652304272018482D          

 11 12  0  0  0  0            999 V2000
   -2.7112    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7112   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7018    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9967    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9967   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169    0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169   -0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  6  2  0  0  0  0
  3  8  1  0  0  0  0
  4  7  2  0  0  0  0
  4  9  1  0  0  0  0
  5 10  2  0  0  0  0
  5 11  1  0  0  0  0
  6  7  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049910

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=CC2=C(C=C1C)N=CN2

> <INCHI_IDENTIFIER>
InChI=1S/C9H10N2/c1-6-3-8-9(4-7(6)2)11-5-10-8/h3-5H,1-2H3,(H,10,11)

> <INCHI_KEY>
LJUQGASMPRMWIW-UHFFFAOYSA-N

> <FORMULA>
C9H10N2

> <MOLECULAR_WEIGHT>
146.1891

> <EXACT_MASS>
146.08439833

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
16.4703364092055

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,6-dimethyl-1H-1,3-benzodiazole

> <ALOGPS_LOGP>
1.88

> <JCHEM_LOGP>
2.2863467776666666

> <ALOGPS_LOGS>
-1.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.725186577116627

> <JCHEM_PKA_STRONGEST_BASIC>
6.425313062256422

> <JCHEM_POLAR_SURFACE_AREA>
28.68

> <JCHEM_REFRACTIVITY>
45.0509

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.08e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,6-dimethylbenzimidazole

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for #<Metabolite:0x00007fdb45940bb0>

HMDB0003701
     RDKit          3D
Dimethylbenzimidazole
 21 22  0  0  0  0  0  0  0  0999 V2000
   -2.3836    1.2311    0.0574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0007    0.6708    0.0174 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1165    1.4928   -0.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3972    0.9867   -0.0439 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6204    1.5397   -0.0728 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5716    0.5879   -0.1037 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9059   -0.5817   -0.0933 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5774   -0.3803   -0.0570 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4593   -1.1999   -0.0325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8267   -0.7015    0.0045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0114   -1.6172    0.0301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9338    1.0669   -0.8713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2989    2.3229    0.2971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9629    0.7230    0.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0213    2.5631    0.0031 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6588    0.7290   -0.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3258   -1.5573   -0.1103 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6308   -2.2734   -0.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3780   -1.6544    1.0962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6385   -2.6489   -0.1812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8079   -1.2993   -0.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10  2  1  0
  8  4  2  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  6 16  1  0
  7 17  1  0
  9 18  1  0
 11 19  1  0
 11 20  1  0
 11 21  1  0
M  END
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PDB for #<Metabolite:0x00007fdb45940bb0>

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      -5.061   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.061  -1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.393   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.393  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.310   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.727   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.727  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.060   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.060  -0.770   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.405   1.246   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.405  -1.246   0.000  0.00  0.00           N+0
CONECT    1    6                                                            
CONECT    2    7                                                            
CONECT    3    6    8                                                       
CONECT    4    7    9                                                       
CONECT    5   10   11                                                       
CONECT    6    1    3    7                                                  
CONECT    7    2    4    6                                                  
CONECT    8    3    9   10                                                  
CONECT    9    4    8   11                                                  
CONECT   10    5    8                                                       
CONECT   11    5    9                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for #<Metabolite:0x00007fdb45940bb0>

COMPND    HMDB0003701
HETATM    1  C1  UNL     1      -2.384   1.231   0.057  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.001   0.671   0.017  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.116   1.493  -0.007  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.397   0.987  -0.044  1.00  0.00           C  
HETATM    5  N1  UNL     1       2.620   1.540  -0.073  1.00  0.00           N  
HETATM    6  C5  UNL     1       3.572   0.588  -0.104  1.00  0.00           C  
HETATM    7  N2  UNL     1       2.906  -0.582  -0.093  1.00  0.00           N  
HETATM    8  C6  UNL     1       1.577  -0.380  -0.057  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.459  -1.200  -0.033  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.827  -0.701   0.004  1.00  0.00           C  
HETATM   11  C9  UNL     1      -2.011  -1.617   0.030  1.00  0.00           C  
HETATM   12  H1  UNL     1      -2.934   1.067  -0.871  1.00  0.00           H  
HETATM   13  H2  UNL     1      -2.299   2.323   0.297  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.963   0.723   0.881  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.021   2.563   0.003  1.00  0.00           H  
HETATM   16  H5  UNL     1       4.659   0.729  -0.132  1.00  0.00           H  
HETATM   17  H6  UNL     1       3.326  -1.557  -0.110  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.631  -2.273  -0.044  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.378  -1.654   1.096  1.00  0.00           H  
HETATM   20  H9  UNL     1      -1.639  -2.649  -0.181  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.808  -1.299  -0.639  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    3   10
CONECT    3    4   15
CONECT    4    5    8    8
CONECT    5    6    6
CONECT    6    7   16
CONECT    7    8   17
CONECT    8    9
CONECT    9   10   10   18
CONECT   10   11
CONECT   11   19   20   21
END
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SMILES for #<Metabolite:0x00007fdb45940bb0>

CC1=CC2=C(C=C1C)N=CN2
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INCHI for #<Metabolite:0x00007fdb45940bb0>

InChI=1S/C9H10N2/c1-6-3-8-9(4-7(6)2)11-5-10-8/h3-5H,1-2H3,(H,10,11)
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Synonyms
ValueSource
DimedazolChEBI
DimedazoleChEBI
DimesolChEBI
DimezolChEBI
5,6-DimethylbenzimidazoleKegg
5,6-Dimethyl-1H-benzimidazoleHMDB
DimezolDimedazolHMDB
5,6-Dimethylbenzimidazole hydrochlorideMeSH, HMDB
Molecular FormulaC9H10N2
Average Mass146.1891
Monoisotopic Mass146.08439833
IUPAC Name5,6-dimethyl-1H-1,3-benzodiazole
Traditional Name5,6-dimethylbenzimidazole
CAS Registry NumberNot Available
SMILES
CC1=CC2=C(C=C1C)N=CN2
InChI Identifier
InChI=1S/C9H10N2/c1-6-3-8-9(4-7(6)2)11-5-10-8/h3-5H,1-2H3,(H,10,11)
InChI KeyLJUQGASMPRMWIW-UHFFFAOYSA-N