MiMeDB: Showing metabocard for N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole (MMDBc0029903)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:46:16 UTC

Update Date

2022-08-31 17:37:32 UTC

Metabolite ID

MMDBc0029903

Metabolite Identification

Common Name

N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole

Description

N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole is also known as alpha-ribazole. It is converted from N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole via dephosphorylation by the enzyme alpha-ribazole phosphatase (EC 3.1.3.73). It can subsequently be used to synthesize Vitamin B12 coenzyme. (KEGG)

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0011112
     RDKit          3D
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
 38 40  0  0  0  0  0  0  0  0999 V2000
    5.0339    0.6903    0.4270 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6096    0.2568    0.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2590   -0.9337    1.0462 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9401   -1.3846    1.0863 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3293   -2.4618    1.5873 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0255   -2.3724    1.3297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2223   -1.2173    0.6484 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5211   -0.8345    0.2285 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7181    0.5312    0.1113 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9591    0.6527   -0.4671 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0579    0.7081    0.6014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8437    1.8046    1.4343 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1710   -0.5122   -1.3806 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2765   -1.2910   -0.9894 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8788   -1.3132   -1.1689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9419   -0.8153   -2.0419 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9744   -0.6087    0.5012 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2723    0.5830   -0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5981    1.0034   -0.1355 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9850    2.2811   -0.7837 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1511    1.7749    0.5096 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5133    0.2617   -0.4947 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5491    0.1645    1.2811 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0110   -1.5520    1.5097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6908   -3.1255    1.6338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2951   -1.2448    0.9097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0676    1.5791   -1.0826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0308   -0.2108    1.2249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0376    0.8051    0.1189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8932    2.0948    1.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3147   -0.2478   -2.4351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0569   -1.7956   -0.1444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0479   -2.3880   -1.2296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1182    0.1674   -2.1436 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4931    1.1819   -0.5705 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8771    2.0951   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    2.6838   -1.4243 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3310    2.9898   -0.0008 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  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 19  2  1  0
 17  4  2  0
 15  8  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  6 25  1  0
  8 26  1  1
 10 27  1  6
 11 28  1  0
 11 29  1  0
 12 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 18 35  1  0
 20 36  1  0
 20 37  1  0
 20 38  1  0
M  END


  Mrv0541 02241201192D          

 20 22  0  0  1  0            999 V2000
   -0.1016    0.2539    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6643    0.6600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1566   -1.5613    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7108    1.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6685    1.4851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3751    0.2412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1212   -1.9548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7362   -0.7827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0931    1.8279    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3878    1.8955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0902    0.6515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1240   -1.5401    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5528   -0.7785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7404    0.0423    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0944    1.4766    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7967    0.2412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1324   -2.3609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5613    0.0423    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8010    1.8998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8475   -2.7672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  1  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  6 11  2  0  0  0  0
 12  7  1  1  0  0  0
  8 13  1  0  0  0  0
  8 14  1  0  0  0  0
 10 15  2  0  0  0  0
 11 16  1  0  0  0  0
 12 17  1  0  0  0  0
 13 18  1  0  0  0  0
 15 19  1  0  0  0  0
 17 20  1  0  0  0  0
  5  9  1  0  0  0  0
 11 15  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029903

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](CO)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H18N2O4/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-13(19)12(18)11(5-17)20-14/h3-4,6,11-14,17-19H,5H2,1-2H3/t11-,12?,13?,14+/m1/s1

> <INCHI_KEY>
HLRUKOJSWOKCPP-RYSNWHEDSA-N

> <FORMULA>
C14H18N2O4

> <MOLECULAR_WEIGHT>
278.3037

> <EXACT_MASS>
278.126657074

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
29.38188642020596

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,5R)-2-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol

> <ALOGPS_LOGP>
0.35

> <JCHEM_LOGP>
0.7263956360000006

> <ALOGPS_LOGS>
-1.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.891804080288225

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.455603310049778

> <JCHEM_PKA_STRONGEST_BASIC>
5.99802750713596

> <JCHEM_POLAR_SURFACE_AREA>
87.74000000000001

> <JCHEM_REFRACTIVITY>
71.6472

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.03e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,5R)-2-(5,6-dimethyl-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0011112
     RDKit          3D
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
 38 40  0  0  0  0  0  0  0  0999 V2000
    5.0339    0.6903    0.4270 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6096    0.2568    0.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2590   -0.9337    1.0462 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9401   -1.3846    1.0863 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3293   -2.4618    1.5873 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0255   -2.3724    1.3297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2223   -1.2173    0.6484 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5211   -0.8345    0.2285 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7181    0.5312    0.1113 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9591    0.6527   -0.4671 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0579    0.7081    0.6014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8437    1.8046    1.4343 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1710   -0.5122   -1.3806 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2765   -1.2910   -0.9894 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8788   -1.3132   -1.1689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9419   -0.8153   -2.0419 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9744   -0.6087    0.5012 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2723    0.5830   -0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5981    1.0034   -0.1355 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9850    2.2811   -0.7837 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1511    1.7749    0.5096 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5133    0.2617   -0.4947 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5491    0.1645    1.2811 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0110   -1.5520    1.5097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6908   -3.1255    1.6338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2951   -1.2448    0.9097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0676    1.5791   -1.0826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0308   -0.2108    1.2249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0376    0.8051    0.1189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8932    2.0948    1.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3147   -0.2478   -2.4351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0569   -1.7956   -0.1444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0479   -2.3880   -1.2296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1182    0.1674   -2.1436 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4931    1.1819   -0.5705 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8771    2.0951   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    2.6838   -1.4243 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3310    2.9898   -0.0008 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  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 19  2  1  0
 17  4  2  0
 15  8  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  6 25  1  0
  8 26  1  1
 10 27  1  6
 11 28  1  0
 11 29  1  0
 12 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 18 35  1  0
 20 36  1  0
 20 37  1  0
 20 38  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  N   UNK     0      -0.190   0.474   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.240   1.232   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.292  -2.914   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.327   1.911   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.248   2.772   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.567   0.450   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.093  -3.649   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.374  -1.461   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -0.174   3.412   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       2.591   3.538   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.902   1.216   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.965  -2.875   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.899  -1.453   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.382   0.079   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.910   2.756   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.221   0.450   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.980  -4.407   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.914   0.079   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.229   3.546   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -5.315  -5.165   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10    9                                                  
CONECT    6    2   11                                                       
CONECT    7    3   12                                                       
CONECT    8    3   13   14                                                  
CONECT    9    4    5                                                       
CONECT   10    5   15                                                       
CONECT   11    6   16   15                                                  
CONECT   12    7   17   13                                                  
CONECT   13    8   18   12                                                  
CONECT   14    8                                                            
CONECT   15   10   19   11                                                  
CONECT   16   11                                                            
CONECT   17   12   20                                                       
CONECT   18   13                                                            
CONECT   19   15                                                            
CONECT   20   17                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

COMPND    HMDB0011112
HETATM    1  C1  UNL     1       5.034   0.690   0.427  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.610   0.257   0.441  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.259  -0.934   1.046  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.940  -1.385   1.086  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.329  -2.462   1.587  1.00  0.00           N  
HETATM    6  C5  UNL     1       0.025  -2.372   1.330  1.00  0.00           C  
HETATM    7  N2  UNL     1      -0.222  -1.217   0.648  1.00  0.00           N  
HETATM    8  C6  UNL     1      -1.521  -0.834   0.228  1.00  0.00           C  
HETATM    9  O1  UNL     1      -1.718   0.531   0.111  1.00  0.00           O  
HETATM   10  C7  UNL     1      -2.959   0.653  -0.467  1.00  0.00           C  
HETATM   11  C8  UNL     1      -4.058   0.708   0.601  1.00  0.00           C  
HETATM   12  O2  UNL     1      -3.844   1.805   1.434  1.00  0.00           O  
HETATM   13  C9  UNL     1      -3.171  -0.512  -1.381  1.00  0.00           C  
HETATM   14  O3  UNL     1      -4.277  -1.291  -0.989  1.00  0.00           O  
HETATM   15  C10 UNL     1      -1.879  -1.313  -1.169  1.00  0.00           C  
HETATM   16  O4  UNL     1      -0.942  -0.815  -2.042  1.00  0.00           O  
HETATM   17  C11 UNL     1       0.974  -0.609   0.501  1.00  0.00           C  
HETATM   18  C12 UNL     1       1.272   0.583  -0.113  1.00  0.00           C  
HETATM   19  C13 UNL     1       2.598   1.003  -0.136  1.00  0.00           C  
HETATM   20  C14 UNL     1       2.985   2.281  -0.784  1.00  0.00           C  
HETATM   21  H1  UNL     1       5.151   1.775   0.510  1.00  0.00           H  
HETATM   22  H2  UNL     1       5.513   0.262  -0.495  1.00  0.00           H  
HETATM   23  H3  UNL     1       5.549   0.164   1.281  1.00  0.00           H  
HETATM   24  H4  UNL     1       4.011  -1.552   1.510  1.00  0.00           H  
HETATM   25  H5  UNL     1      -0.691  -3.125   1.634  1.00  0.00           H  
HETATM   26  H6  UNL     1      -2.295  -1.245   0.910  1.00  0.00           H  
HETATM   27  H7  UNL     1      -3.068   1.579  -1.083  1.00  0.00           H  
HETATM   28  H8  UNL     1      -4.031  -0.211   1.225  1.00  0.00           H  
HETATM   29  H9  UNL     1      -5.038   0.805   0.119  1.00  0.00           H  
HETATM   30  H10 UNL     1      -2.893   2.095   1.418  1.00  0.00           H  
HETATM   31  H11 UNL     1      -3.315  -0.248  -2.435  1.00  0.00           H  
HETATM   32  H12 UNL     1      -4.057  -1.796  -0.144  1.00  0.00           H  
HETATM   33  H13 UNL     1      -2.048  -2.388  -1.230  1.00  0.00           H  
HETATM   34  H14 UNL     1      -1.118   0.167  -2.144  1.00  0.00           H  
HETATM   35  H15 UNL     1       0.493   1.182  -0.570  1.00  0.00           H  
HETATM   36  H16 UNL     1       3.877   2.095  -1.441  1.00  0.00           H  
HETATM   37  H17 UNL     1       2.190   2.684  -1.424  1.00  0.00           H  
HETATM   38  H18 UNL     1       3.331   2.990  -0.001  1.00  0.00           H  
CONECT    1    2   21   22   23
CONECT    2    3    3   19
CONECT    3    4   24
CONECT    4    5   17   17
CONECT    5    6    6
CONECT    6    7   25
CONECT    7    8   17
CONECT    8    9   15   26
CONECT    9   10
CONECT   10   11   13   27
CONECT   11   12   28   29
CONECT   12   30
CONECT   13   14   15   31
CONECT   14   32
CONECT   15   16   33
CONECT   16   34
CONECT   17   18
CONECT   18   19   19   35
CONECT   19   20
CONECT   20   36   37   38
END

HMDB0011112
     RDKit          3D
N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
 38 40  0  0  0  0  0  0  0  0999 V2000
    5.0339    0.6903    0.4270 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6096    0.2568    0.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2590   -0.9337    1.0462 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9401   -1.3846    1.0863 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3293   -2.4618    1.5873 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0255   -2.3724    1.3297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2223   -1.2173    0.6484 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5211   -0.8345    0.2285 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7181    0.5312    0.1113 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9591    0.6527   -0.4671 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0579    0.7081    0.6014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8437    1.8046    1.4343 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1710   -0.5122   -1.3806 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2765   -1.2910   -0.9894 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8788   -1.3132   -1.1689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9419   -0.8153   -2.0419 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9744   -0.6087    0.5012 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2723    0.5830   -0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5981    1.0034   -0.1355 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9850    2.2811   -0.7837 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1511    1.7749    0.5096 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5133    0.2617   -0.4947 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5491    0.1645    1.2811 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0110   -1.5520    1.5097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6908   -3.1255    1.6338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2951   -1.2448    0.9097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0676    1.5791   -1.0826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0308   -0.2108    1.2249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0376    0.8051    0.1189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8932    2.0948    1.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3147   -0.2478   -2.4351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0569   -1.7956   -0.1444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0479   -2.3880   -1.2296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1182    0.1674   -2.1436 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4931    1.1819   -0.5705 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8771    2.0951   -1.4412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    2.6838   -1.4243 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3310    2.9898   -0.0008 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  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 19  2  1  0
 17  4  2  0
 15  8  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  6 25  1  0
  8 26  1  1
 10 27  1  6
 11 28  1  0
 11 29  1  0
 12 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 18 35  1  0
 20 36  1  0
 20 37  1  0
 20 38  1  0
M  END

Synonyms

Value	Source
N1-(a-D-Ribosyl)-5,6-dimethyl-benzimidazole	Generator
N1-(Α-D-ribosyl)-5,6-dimethyl-benzimidazole	Generator
(2S,5R)-2-(5,6 Dimethylbenzimidazol-1-yl)-5 (hydroxymethyl)oxolane-3,4-diol	HMDB
5,6-Dimethyl-1-a-D-ribofuranosyl-1H-benzimidazole	HMDB
5,6-Dimethyl-1-alpha-delta-ribofuranosyl-1H-benzimidazole	HMDB
a-Ribazole	HMDB
alpha-Ribazole	HMDB
N1-(alpha-D-Ribosyl)-5,6-dimethylbenzimidazole	HMDB
N1-(alpha-delta-Ribosyl)-5,6-dimethylbenzimidazole	HMDB

Molecular Formula

C₁₄H₁₈N₂O₄

Average Mass

278.3037

Monoisotopic Mass

278.126657074

IUPAC Name

(2S,5R)-2-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

(2S,5R)-2-(5,6-dimethyl-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol

CAS Registry Number

Not Available

SMILES

CC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](CO)C(O)C1O

InChI Identifier

InChI=1S/C14H18N2O4/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-13(19)12(18)11(5-17)20-14/h3-4,6,11-14,17-19H,5H2,1-2H3/t11-,12?,13?,14+/m1/s1

InChI Key

HLRUKOJSWOKCPP-RYSNWHEDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzimidazole ribonucleosides and ribonucleotides. These are nucleosides with a structure that consists of an imidazole moiety of benzimidazole is N-linked to a ribose (or deoxyribose). Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Benzimidazole ribonucleosides and ribonucleotides

Sub Class

Not Available

Direct Parent

Benzimidazole ribonucleosides and ribonucleotides

Alternative Parents

Substituents

1-ribofuranosylbenzimidazole
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Benzimidazole
Monosaccharide
N-substituted imidazole
Benzenoid
Azole
Heteroaromatic compound
Imidazole
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	4.03 g/L	ALOGPS
logP	0.35	ALOGPS
logP	0.73	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	12.46	ChemAxon
pKa (Strongest Basic)	6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	87.74 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	71.65 m³·mol⁻¹	ChemAxon
Polarizability	29.38 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0c01-9330000000-689525590087845886d0	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-05dr-6967600000-599f6974301e18e156c8	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-002b-0960000000-caf2068534b445ebedc9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-1910000000-d37ce3a70cce736343f0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-1900000000-df05b1aea7df1fbcf30a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004j-0690000000-77b436d3918c437841c7	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-0900000000-2a72e9c715cb7e187a0c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0002-1900000000-d0b6a5aa908f50a2969b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0900000000-ec86bad39756964675dc	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-0900000000-c514f16784cfa467b6ec	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000t-0900000000-f8563f3a5ea022479f4a	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0910000000-481df73ff3b8689b9528	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-0900000000-8f3a4e497c02cd33d097	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0002-2900000000-d54bc813eef1d7fc515a	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0196656	14 kDa phosphohistidine phosphatase	Enzyme	Q9NRX4	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0011112

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB027894

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440780

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T: Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem. 2007 Nov 1;370(1):17-25. doi: 10.1016/j.ab.2007.07.022. Epub 2007 Aug 1. [PubMed:17765195 ]
Winder CL, Dunn WB, Schuler S, Broadhurst D, Jarvis R, Stephens GM, Goodacre R: Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Anal Chem. 2008 Apr 15;80(8):2939-48. doi: 10.1021/ac7023409. Epub 2008 Mar 11. [PubMed:18331064 ]
Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14. doi: 10.1093/nar/gkr988. Epub 2011 Nov 10. [PubMed:22080510 ]

Showing metabocard for N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole (MMDBc0029903)

MOL for #<Metabolite:0x00007fece156cef0>

3D MOL for #<Metabolite:0x00007fece156cef0>

3D SDF for #<Metabolite:0x00007fece156cef0>

3D-SDF for #<Metabolite:0x00007fece156cef0>

PDB for #<Metabolite:0x00007fece156cef0>

3D PDB for #<Metabolite:0x00007fece156cef0>

SMILES for #<Metabolite:0x00007fece156cef0>

INCHI for #<Metabolite:0x00007fece156cef0>

Structure for #<Metabolite:0x00007fece156cef0>

3D Structure for #<Metabolite:0x00007fece156cef0>