MiMeDB: Showing metabocard for N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole (MMDBc0029733)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:39:27 UTC

Update Date

2024-10-15 17:24:24 UTC

Metabolite ID

MMDBc0029733

Metabolite Identification

Common Name

N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole

Description

N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole (or alpha-ribazole-5'-Phosphate) is an intermediate in Riboflavin metabolism. In particular, alpha-Ribazole 5'-phosphate is converted from Dimethylbenzimidazole via the enzyme nicotinate-nucleotide-dimethylbenzimidazole

Structure

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

HMDB0003882
     RDKit          3D
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole
 43 45  0  0  0  0  0  0  0  0999 V2000
   -6.0390    0.5559   -0.3707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5546    0.5970   -0.3847 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8716    1.7869   -0.2468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4938    1.8770   -0.2533 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6169    2.9013   -0.1383 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3911    2.3533   -0.2215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4573    1.0350   -0.3831 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6226    0.0606   -0.5169 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8023    0.6388   -0.8776 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6604    0.6692    0.1840 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7897   -0.3424    0.0821 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5730   -0.1399   -1.0453 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7809   -1.3262   -1.0321 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.8393   -2.0267    0.3171 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5461   -2.4331   -2.2773 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2642   -0.5045   -1.2464 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8812    0.3113    1.4327 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3133    1.4126    2.0407 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8201   -0.6023    0.8361 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3567   -0.5371    1.5996 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7616    0.7172   -0.4055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4247   -0.5027   -0.5474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8045   -0.5523   -0.5359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4494   -1.8786   -0.6911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4499   -0.3150    0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3917    1.4775    0.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3645    0.6176   -1.4457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4599    2.6857   -0.1285 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5728    2.8811   -0.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3236   -0.6973   -1.2565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0744    1.6979    0.2736 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3750   -1.3577    0.0984 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3947   -0.2234    1.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2707   -3.2891   -1.8730 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2746    0.1892   -0.5284 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5129   -0.2209    2.1658 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9193    2.1895    1.8716 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1494   -1.6419    0.7594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1804    0.0479    2.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8199   -1.3935   -0.6649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8164   -2.0165   -1.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7293   -2.6920   -0.4649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3276   -2.0094   -0.0215 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
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
  7 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 23  2  1  0
 21  4  2  0
 19  8  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  6 29  1  0
  8 30  1  6
 10 31  1  1
 11 32  1  0
 11 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  1
 18 37  1  0
 19 38  1  6
 20 39  1  0
 22 40  1  0
 24 41  1  0
 24 42  1  0
 24 43  1  0
M  END


  Mrv0541 02231219482D          

 24 26  0  0  1  0            999 V2000
   13.4713  -10.2244    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.7510   -9.8058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7398  -11.3031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.1880   -9.8058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7510   -8.9798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0344  -10.2281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0685  -10.8240    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.4833  -12.0875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.1880   -8.9798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.0344   -8.5687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3215   -9.8058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4122  -11.3031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.6611  -12.0875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.9660  -12.7476    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3215   -8.9798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6955  -10.2131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6314  -11.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1744  -12.7476    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6558   -8.5687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8733  -11.5840    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0473  -11.5764    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.2289  -11.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0510  -10.7580    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0435  -12.3986    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  1  1  6  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  0  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
  7 12  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  1  6  0  0  0
 10 15  2  0  0  0  0
 11 16  1  0  0  0  0
 12 17  1  1  0  0  0
 13 18  1  6  0  0  0
 15 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 21 24  2  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>
MMDBc0029733

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C14H19N2O7P/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-13(18)12(17)11(23-14)5-22-24(19,20)21/h3-4,6,11-14,17-18H,5H2,1-2H3,(H2,19,20,21)/t11-,12-,13-,14+/m1/s1

> <INCHI_KEY>
ZMRGXEJKZPRBPJ-SYQHCUMBSA-N

> <FORMULA>
C14H19N2O7P

> <MOLECULAR_WEIGHT>
358.2836

> <EXACT_MASS>
358.092987484

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
34.12708648100771

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5S)-5-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-0.32

> <JCHEM_LOGP>
-1.513658450999334

> <ALOGPS_LOGS>
-2.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.44340389593101

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2246976829386815

> <JCHEM_PKA_STRONGEST_BASIC>
5.805156458191586

> <JCHEM_POLAR_SURFACE_AREA>
134.27

> <JCHEM_REFRACTIVITY>
82.5201

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.53e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-ribazole-5'-P

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0003882
     RDKit          3D
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole
 43 45  0  0  0  0  0  0  0  0999 V2000
   -6.0390    0.5559   -0.3707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5546    0.5970   -0.3847 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8716    1.7869   -0.2468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4938    1.8770   -0.2533 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6169    2.9013   -0.1383 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3911    2.3533   -0.2215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4573    1.0350   -0.3831 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6226    0.0606   -0.5169 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8023    0.6388   -0.8776 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6604    0.6692    0.1840 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7897   -0.3424    0.0821 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5730   -0.1399   -1.0453 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7809   -1.3262   -1.0321 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.8393   -2.0267    0.3171 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5461   -2.4331   -2.2773 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2642   -0.5045   -1.2464 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8812    0.3113    1.4327 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3133    1.4126    2.0407 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8201   -0.6023    0.8361 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3567   -0.5371    1.5996 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7616    0.7172   -0.4055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4247   -0.5027   -0.5474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8045   -0.5523   -0.5359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4494   -1.8786   -0.6911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4499   -0.3150    0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3917    1.4775    0.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3645    0.6176   -1.4457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4599    2.6857   -0.1285 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5728    2.8811   -0.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3236   -0.6973   -1.2565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0744    1.6979    0.2736 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3750   -1.3577    0.0984 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3947   -0.2234    1.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2707   -3.2891   -1.8730 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2746    0.1892   -0.5284 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5129   -0.2209    2.1658 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9193    2.1895    1.8716 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1494   -1.6419    0.7594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1804    0.0479    2.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8199   -1.3935   -0.6649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8164   -2.0165   -1.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7293   -2.6920   -0.4649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3276   -2.0094   -0.0215 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
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
  7 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 23  2  1  0
 21  4  2  0
 19  8  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  6 29  1  0
  8 30  1  6
 10 31  1  1
 11 32  1  0
 11 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  1
 18 37  1  0
 19 38  1  6
 20 39  1  0
 22 40  1  0
 24 41  1  0
 24 42  1  0
 24 43  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  N   UNK     0      25.146 -19.086   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      23.802 -18.304   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      23.781 -21.099   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      26.484 -18.304   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      23.802 -16.762   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      22.464 -19.092   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      22.528 -20.205   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      23.302 -22.563   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      26.484 -16.762   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      22.464 -15.995   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      21.133 -18.304   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      21.303 -21.099   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.767 -22.563   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      24.203 -23.796   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      21.133 -16.762   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      19.965 -19.064   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      19.845 -20.613   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      20.859 -23.796   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      19.891 -15.995   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      18.430 -21.623   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0      16.888 -21.609   0.000  0.00  0.00           P+0
HETATM   22  O   UNK     0      15.361 -21.609   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      16.895 -20.082   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      16.881 -23.144   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   21                                                       
CONECT   21   20   22   23   24                                             
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   21                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

COMPND    HMDB0003882
HETATM    1  C1  UNL     1      -6.039   0.556  -0.371  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.555   0.597  -0.385  1.00  0.00           C  
HETATM    3  C3  UNL     1      -3.872   1.787  -0.247  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.494   1.877  -0.253  1.00  0.00           C  
HETATM    5  N1  UNL     1      -1.617   2.901  -0.138  1.00  0.00           N  
HETATM    6  C5  UNL     1      -0.391   2.353  -0.221  1.00  0.00           C  
HETATM    7  N2  UNL     1      -0.457   1.035  -0.383  1.00  0.00           N  
HETATM    8  C6  UNL     1       0.623   0.061  -0.517  1.00  0.00           C  
HETATM    9  O1  UNL     1       1.802   0.639  -0.878  1.00  0.00           O  
HETATM   10  C7  UNL     1       2.660   0.669   0.184  1.00  0.00           C  
HETATM   11  C8  UNL     1       3.790  -0.342   0.082  1.00  0.00           C  
HETATM   12  O2  UNL     1       4.573  -0.140  -1.045  1.00  0.00           O  
HETATM   13  P1  UNL     1       5.781  -1.326  -1.032  1.00  0.00           P  
HETATM   14  O3  UNL     1       5.839  -2.027   0.317  1.00  0.00           O  
HETATM   15  O4  UNL     1       5.546  -2.433  -2.277  1.00  0.00           O  
HETATM   16  O5  UNL     1       7.264  -0.505  -1.246  1.00  0.00           O  
HETATM   17  C9  UNL     1       1.881   0.311   1.433  1.00  0.00           C  
HETATM   18  O6  UNL     1       1.313   1.413   2.041  1.00  0.00           O  
HETATM   19  C10 UNL     1       0.820  -0.602   0.836  1.00  0.00           C  
HETATM   20  O7  UNL     1      -0.357  -0.537   1.600  1.00  0.00           O  
HETATM   21  C11 UNL     1      -1.762   0.717  -0.406  1.00  0.00           C  
HETATM   22  C12 UNL     1      -2.425  -0.503  -0.547  1.00  0.00           C  
HETATM   23  C13 UNL     1      -3.804  -0.552  -0.536  1.00  0.00           C  
HETATM   24  C14 UNL     1      -4.449  -1.879  -0.691  1.00  0.00           C  
HETATM   25  H1  UNL     1      -6.450  -0.315   0.152  1.00  0.00           H  
HETATM   26  H2  UNL     1      -6.392   1.477   0.138  1.00  0.00           H  
HETATM   27  H3  UNL     1      -6.364   0.618  -1.446  1.00  0.00           H  
HETATM   28  H4  UNL     1      -4.460   2.686  -0.128  1.00  0.00           H  
HETATM   29  H5  UNL     1       0.573   2.881  -0.169  1.00  0.00           H  
HETATM   30  H6  UNL     1       0.324  -0.697  -1.256  1.00  0.00           H  
HETATM   31  H7  UNL     1       3.074   1.698   0.274  1.00  0.00           H  
HETATM   32  H8  UNL     1       3.375  -1.358   0.098  1.00  0.00           H  
HETATM   33  H9  UNL     1       4.395  -0.223   1.007  1.00  0.00           H  
HETATM   34  H10 UNL     1       5.271  -3.289  -1.873  1.00  0.00           H  
HETATM   35  H11 UNL     1       7.275   0.189  -0.528  1.00  0.00           H  
HETATM   36  H12 UNL     1       2.513  -0.221   2.166  1.00  0.00           H  
HETATM   37  H13 UNL     1       1.919   2.190   1.872  1.00  0.00           H  
HETATM   38  H14 UNL     1       1.149  -1.642   0.759  1.00  0.00           H  
HETATM   39  H15 UNL     1      -0.180   0.048   2.383  1.00  0.00           H  
HETATM   40  H16 UNL     1      -1.820  -1.394  -0.665  1.00  0.00           H  
HETATM   41  H17 UNL     1      -4.816  -2.017  -1.724  1.00  0.00           H  
HETATM   42  H18 UNL     1      -3.729  -2.692  -0.465  1.00  0.00           H  
HETATM   43  H19 UNL     1      -5.328  -2.009  -0.022  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3    3   23
CONECT    3    4   28
CONECT    4    5   21   21
CONECT    5    6    6
CONECT    6    7   29
CONECT    7    8   21
CONECT    8    9   19   30
CONECT    9   10
CONECT   10   11   17   31
CONECT   11   12   32   33
CONECT   12   13
CONECT   13   14   14   15   16
CONECT   15   34
CONECT   16   35
CONECT   17   18   19   36
CONECT   18   37
CONECT   19   20   38
CONECT   20   39
CONECT   21   22
CONECT   22   23   23   40
CONECT   23   24
CONECT   24   41   42   43
END

HMDB0003882
     RDKit          3D
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole
 43 45  0  0  0  0  0  0  0  0999 V2000
   -6.0390    0.5559   -0.3707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5546    0.5970   -0.3847 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8716    1.7869   -0.2468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4938    1.8770   -0.2533 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6169    2.9013   -0.1383 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3911    2.3533   -0.2215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4573    1.0350   -0.3831 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6226    0.0606   -0.5169 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8023    0.6388   -0.8776 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6604    0.6692    0.1840 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7897   -0.3424    0.0821 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5730   -0.1399   -1.0453 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7809   -1.3262   -1.0321 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.8393   -2.0267    0.3171 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5461   -2.4331   -2.2773 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2642   -0.5045   -1.2464 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8812    0.3113    1.4327 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3133    1.4126    2.0407 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8201   -0.6023    0.8361 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3567   -0.5371    1.5996 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7616    0.7172   -0.4055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4247   -0.5027   -0.5474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8045   -0.5523   -0.5359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4494   -1.8786   -0.6911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4499   -0.3150    0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3917    1.4775    0.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3645    0.6176   -1.4457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4599    2.6857   -0.1285 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5728    2.8811   -0.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3236   -0.6973   -1.2565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0744    1.6979    0.2736 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3750   -1.3577    0.0984 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3947   -0.2234    1.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2707   -3.2891   -1.8730 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2746    0.1892   -0.5284 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5129   -0.2209    2.1658 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9193    2.1895    1.8716 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1494   -1.6419    0.7594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1804    0.0479    2.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8199   -1.3935   -0.6649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8164   -2.0165   -1.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7293   -2.6920   -0.4649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3276   -2.0094   -0.0215 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
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
  7 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 23  2  1  0
 21  4  2  0
 19  8  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  6 29  1  0
  8 30  1  6
 10 31  1  1
 11 32  1  0
 11 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  1
 18 37  1  0
 19 38  1  6
 20 39  1  0
 22 40  1  0
 24 41  1  0
 24 42  1  0
 24 43  1  0
M  END

Synonyms

Value	Source
5,6-Dimethyl-1-alpha-D-ribofuranosylbenzimidazole 5'-phosphate	ChEBI
alpha-Ribazole-5'-p	ChEBI
ALPHA-RIBAZOLE-5'-phosphATE	ChEBI
N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole	ChEBI
N(1)-(5-Phosphoribosyl)-5,6-dimethylbenzimidazole	ChEBI
PHOSPHORIC ACID mono-[5-(5,6-dimethyl-benzoimidazol-1-yl)-3,4-dihydroxy-tetrahydro-furan-2ylmethyl] ester	ChEBI
alpha-Ribazole 5'-phosphate	Kegg
5,6-Dimethyl-1-a-D-ribofuranosylbenzimidazole 5'-phosphate	Generator
5,6-Dimethyl-1-a-D-ribofuranosylbenzimidazole 5'-phosphoric acid	Generator
5,6-Dimethyl-1-alpha-D-ribofuranosylbenzimidazole 5'-phosphoric acid	Generator
5,6-Dimethyl-1-α-D-ribofuranosylbenzimidazole 5'-phosphate	Generator
5,6-Dimethyl-1-α-D-ribofuranosylbenzimidazole 5'-phosphoric acid	Generator
a-Ribazole-5'-p	Generator
Α-ribazole-5'-p	Generator
a-RIBAZOLE-5'-phosphate	Generator
a-RIBAZOLE-5'-phosphoric acid	Generator
alpha-RIBAZOLE-5'-phosphoric acid	Generator
Α-ribazole-5'-phosphate	Generator
Α-ribazole-5'-phosphoric acid	Generator
N1-(5-Phospho-α-D-ribosyl)-5,6-dimethylbenzimidazole	Generator
PHOSPHate mono-[5-(5,6-dimethyl-benzoimidazol-1-yl)-3,4-dihydroxy-tetrahydro-furan-2ylmethyl] ester	Generator
a-Ribazole 5'-phosphate	Generator
a-Ribazole 5'-phosphoric acid	Generator
alpha-Ribazole 5'-phosphoric acid	Generator
Α-ribazole 5'-phosphate	Generator
Α-ribazole 5'-phosphoric acid	Generator
alpha-Ribazole-5'-PO4	HMDB
N1-(5-phospho-alpha-delta-Ribosyl)-5,6-dimethylbenzimidazole	HMDB

Molecular Formula

C₁₄H₁₉N₂O₇P

Average Mass

358.2836

Monoisotopic Mass

358.092987484

IUPAC Name

{[(2R,3S,4R,5S)-5-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

α-ribazole-5'-P

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C14H19N2O7P/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-13(18)12(17)11(23-14)5-22-24(19,20)21/h3-4,6,11-14,17-18H,5H2,1-2H3,(H2,19,20,21)/t11-,12-,13-,14+/m1/s1

InChI Key

ZMRGXEJKZPRBPJ-SYQHCUMBSA-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
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Benzimidazole
Monoalkyl phosphate
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Benzenoid
Azole
Tetrahydrofuran
Imidazole
Heteroaromatic compound
1,2-diol
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Azacycle
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

ribose monophosphate (CHEBI:16837 )
1-ribosylbenzimidazole (CHEBI:16837 )
dimethylbenzimidazole (CHEBI:16837 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.53 g/L	ALOGPS
logP	-0.32	ALOGPS
logP	-1.5	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	5.81	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	134.27 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	82.52 m³·mol⁻¹	ChemAxon
Polarizability	34.13 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018828	Nicotinamide ribotide	Nicotinic acid	Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase	Transfer of a ribosyl group	PathBank	31602464
MMDBr0018829	N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole	Adenosylcobalamin 5'-phosphate	Adenosylcobinamide-GDP ribazoletransferase	Transfer of ribazole	PathBank	31602464

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/Eubacteria	Proteobacteria	172	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Sheep	Unknown
Bacteria/Eubacteria	Firmicutes	42	Human feces; Human ; Catfish
Bacteria/Eubacteria	Bacteroidetes	6	Human ; Human feces
Bacteria/Eubacteria	Chloroflexi	8
Bacteria/Eubacteria	Chlorobi	8
Bacteria/Eubacteria	Actinobacteria	27	Human ; Cattle
Bacteria/Eubacteria	Deinococcus-thermus	2
Bacteria	Proteobacteria	3	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Sheep	Unknown
Bacteria/Eubacteria	Fusobacteria	1	Human ; Human feces
Bacteria/Eubacteria	Spirochaetes	7	Human
Bacteria/Eubacteria	Thermotogae	4
Archaea/Archaea	Euryarchaeota	21
Bacteria/Eubacteria	Cyanobacteria	8
Archaea/Archaea	Crenarchaeota	11
Archaea	Crenarchaeota	1
Bacteria	nah	1
Bacteria/Eubacteria	Nitrospirae	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

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

External Links

HMDB ID

HMDB0003882

DrugBank ID

DB02030

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023243

KNApSAcK ID

Not Available

Chemspider ID

392720

KEGG Compound ID

C04778

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

444941

PDB ID

Not Available

ChEBI ID

16837

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole (MMDBc0029733)

MOL for #<Metabolite:0x00007f923c90f828>

3D MOL for #<Metabolite:0x00007f923c90f828>

3D SDF for #<Metabolite:0x00007f923c90f828>

3D-SDF for #<Metabolite:0x00007f923c90f828>

PDB for #<Metabolite:0x00007f923c90f828>

3D PDB for #<Metabolite:0x00007f923c90f828>

SMILES for #<Metabolite:0x00007f923c90f828>

INCHI for #<Metabolite:0x00007f923c90f828>

Structure for #<Metabolite:0x00007f923c90f828>

3D Structure for #<Metabolite:0x00007f923c90f828>