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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-08-13 06:36:08 UTC

Update Date

2021-09-14 14:58:36 UTC

HMDB ID

HMDB0003882

Secondary Accession Numbers

HMDB03882

Metabolite Identification

Common Name

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

Description

N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole, also known as alpha-ribazole-5'-p or 5,6-dimethyl-1-alpha-D-ribofuranosylbenzimidazole 5'-phosphate, 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. N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole exists in all living organisms, ranging from bacteria to humans. N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make N1-(5-phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole a potential biomarker for the consumption of these foods. N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on N1-(5-Phospho-a-D-ribosyl)-5,6-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
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  6  7  1  0
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 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
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  6 29  1  0
  8 30  1  6
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 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>
HMDB0003882

> <DATABASE_NAME>
hmdb

> <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

View in JSmol View NMR Assignments View Stereo Labels

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

Chemical Formula

C₁₄H₁₉N₂O₇P

Average Molecular Weight

358.2836

Monoisotopic Molecular Weight

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 )

Ontology

Not Available

Endogenous (HMDB: HMDB0003882)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Adenosylcobalamin Salvage from Cobinamide (PathBank: SMP0122099)

Role

Industrial application

Pharmaceutical industry

Pharmaceutical (HMDB: HMDB0003882)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	-0.524	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	180.21	31661259
DarkChem	[M-H]-	177.895	31661259
DeepCCS	[M+H]+	170.019	30932474
DeepCCS	[M-H]-	167.623	30932474
DeepCCS	[M-2H]-	201.827	30932474
DeepCCS	[M+Na]+	177.836	30932474
AllCCS	[M+H]+	182.2	32859911
AllCCS	[M+H-H2O]+	179.4	32859911
AllCCS	[M+NH4]+	184.8	32859911
AllCCS	[M+Na]+	185.5	32859911
AllCCS	[M-H]-	177.3	32859911
AllCCS	[M+Na-2H]-	177.3	32859911
AllCCS	[M+HCOO]-	177.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	3.95 minutes	32390414
Predicted by Siyang on May 30, 2022	10.1182 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	6.3 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	385.6 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	789.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	222.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	72.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	164.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	57.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	346.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	281.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	755.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	622.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	249.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	667.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	146.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	216.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	713.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	402.5 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	389.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole	CC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O	4099.0	Standard polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole	CC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O	2177.0	Standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole	CC1=CC2=C(C=C1C)N(C=N2)[C@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O	3298.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,1TMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O)[C@@H](O[Si](C)(C)C)[C@H]1O)C=N2	3033.7	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,1TMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]1O[Si](C)(C)C)C=N2	3013.0	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,1TMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O)[C@H]1O)C=N2	3124.3	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,2TMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)C=N2	2976.8	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,2TMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O)C=N2	3072.3	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,2TMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C)C=N2	3057.9	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,2TMS,isomer #4	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]1O)C=N2	3098.3	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)C=N2	3052.5	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)C=N2	3008.8	Standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)C=N2	3672.8	Standard polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O)C=N2	3080.2	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O)C=N2	3006.0	Standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O)C=N2	3460.6	Standard polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C)C=N2	3065.6	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C)C=N2	3022.2	Standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C)C=N2	3495.8	Standard polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,4TMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)C=N2	3081.7	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,4TMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)C=N2	2994.3	Standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,4TMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)C=N2	3303.5	Standard polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,1TBDMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O)C=N2	3310.0	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,1TBDMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3290.1	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,1TBDMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]1O)C=N2	3364.0	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,2TBDMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3487.6	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,2TBDMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O)C=N2	3558.2	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,2TBDMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3541.6	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,2TBDMS,isomer #4	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]1O)C=N2	3564.4	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TBDMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3709.7	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TBDMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3606.5	Standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TBDMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3854.4	Standard polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TBDMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O)C=N2	3734.2	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TBDMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O)C=N2	3558.6	Standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TBDMS,isomer #2	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O)C=N2	3713.8	Standard polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TBDMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3715.7	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TBDMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3570.7	Standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,3TBDMS,isomer #3	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3748.5	Standard polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,4TBDMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3880.9	Semi standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,4TBDMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3677.8	Standard non polar	33892256
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole,4TBDMS,isomer #1	CC1=CC2=C(C=C1C)N([C@H]1O[C@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C)C=N2	3637.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9612000000-fb21cfa813df9fff3f0d	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole GC-MS (2 TMS) - 70eV, Positive	splash10-01vk-5943100000-cb128df76b1b27f96534	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 10V, Positive-QTOF	splash10-0002-0924000000-ca83b2cabb6f848fb606	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 20V, Positive-QTOF	splash10-0002-1910000000-f1a785d3193f0d8ff5bc	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 40V, Positive-QTOF	splash10-0002-0900000000-047b40eca213cd9b3d4d	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 10V, Negative-QTOF	splash10-0a6s-7709000000-c0797f58260c9a1a6a6c	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 20V, Negative-QTOF	splash10-002b-8900000000-1229d2ae6136dbe43637	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 40V, Negative-QTOF	splash10-004i-9200000000-e3828a9e7ec68e9998b4	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 10V, Negative-QTOF	splash10-0a4i-3009000000-6535ffb46debd0ae1f34	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 20V, Negative-QTOF	splash10-004i-9001000000-578749d5ff31e4fab5ea	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 40V, Negative-QTOF	splash10-004i-9100000000-d4ee221347b2259634d2	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 10V, Positive-QTOF	splash10-0a4j-0719000000-2538d2d5f670e5ddcec9	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 20V, Positive-QTOF	splash10-0002-0923000000-40c17e787a25cabb848e	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole 40V, Positive-QTOF	splash10-0002-4900000000-6c85eaa5dbac4013d383	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

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

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. 14 kDa phosphohistidine phosphatase

General function:: Involved in phosphohistidine phosphatase activity
Specific function:: Exhibits phosphohistidine phosphatase activity.
Gene Name:: PHPT1
Uniprot ID:: Q9NRX4
Molecular weight:: Not Available

Showing metabocard for N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole (HMDB0003882)

MOL for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

3D MOL for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

3D SDF for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

3D-SDF for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

PDB for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

3D PDB for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

SMILES for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

INCHI for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

Structure for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

3D Structure for HMDB0003882 (N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes