MiMeDB: Showing metabocard for 5-amino-6-(D-ribitylamino)uracil (MMDBc0031730)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:46:48 UTC

Update Date

2024-04-30 19:51:47 UTC

Metabolite ID

MMDBc0031730

Metabolite Identification

Common Name

5-amino-6-(D-ribitylamino)uracil

Description

5-amino-6-(D-ribitylamino)uracil is involved in the Cofactor riboflavin biosynthesis pathway. It is a substrate of Riboflavin biosynthesis protein RibD that catalyses the following reactions:‚Üµ 2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil => 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(2)O + 1 phosphate and 6,7-dimethyl-8-(1-D-ribityl)lumazine => 5-amino-6-(D-ribitylamino)uracil + riboflavin

Structure

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

HMDB0011106
     RDKit          3D
5-Amino-6-ribitylamino uracil
 35 35  0  0  0  0  0  0  0  0999 V2000
    2.5793    0.5100   -1.8835 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8547   -0.4078   -0.8419 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0491   -0.4542    0.2697 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.4214    0.3589 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0372    0.4595    1.4786 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0270    1.4883    1.2865 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8824    1.4846    2.3933 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8348    1.3443    0.0379 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7112    2.4545    0.0109 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6935    0.1207   -0.0189 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0054   -1.0714   -0.0049 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4775    0.1722   -1.3244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3735   -0.8824   -1.4273 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3823   -1.3558    1.2121 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4481   -2.1726    1.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6832   -2.9809    2.0053 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2507   -2.1399   -0.0084 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9447   -1.2403   -0.9829 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7033   -1.2271   -1.9833 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4270    1.5072   -1.6208 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5152    0.2734   -2.8962 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7634    1.0880   -0.4172 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5487    0.6898    2.4341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4178   -0.5352    1.6133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5543    2.5049    1.2388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3092    1.3212    3.1920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2212    1.4365   -0.8737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0242    2.5940    0.9499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4082    0.1644    0.8158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3507   -1.6578    0.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7985    0.1175   -2.2000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0652    1.1238   -1.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8633   -0.9482   -0.5746 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8060   -1.4313    2.0717 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0768   -2.7716   -0.1142 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  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  2  0
 18  2  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  6
  7 26  1  0
  8 27  1  6
  9 28  1  0
 10 29  1  1
 11 30  1  0
 12 31  1  0
 12 32  1  0
 13 33  1  0
 14 34  1  0
 17 35  1  0
M  END

 
  Mrv1652309042000342D          

 19 19  0  0  1  0            999 V2000
   18.6570  -18.3475    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.6570  -19.1725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3714  -19.5850    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.0859  -19.1725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.0859  -18.3475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3714  -17.9350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3714  -17.1101    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.9425  -19.5850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.8114  -17.9285    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.8152  -19.5850    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.5297  -19.1725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2441  -19.5850    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   22.9586  -19.1725    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   23.6731  -19.5850    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   24.3875  -19.1725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.1020  -19.5850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.2441  -20.4100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.6731  -20.4098    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.9586  -18.3475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  8  2  0  0  0  0
  5  9  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 12 17  1  1  0  0  0
 14 18  1  1  0  0  0
 13 19  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031730

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=C(NC[C@H](O)[C@H](O)[C@H](O)CO)NC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N4O6/c10-5-7(12-9(19)13-8(5)18)11-1-3(15)6(17)4(16)2-14/h3-4,6,14-17H,1-2,10H2,(H3,11,12,13,18,19)/t3-,4+,6-/m0/s1

> <INCHI_KEY>
XKQZIXVJVUPORE-RPDRRWSUSA-N

> <FORMULA>
C9H16N4O6

> <MOLECULAR_WEIGHT>
276.2465

> <EXACT_MASS>
276.106984264

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
25.817806028191033

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-amino-6-{[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]amino}-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-2.44

> <JCHEM_LOGP>
-4.389022046999999

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.634784897543604

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.47601881113622

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7435879201365787

> <JCHEM_POLAR_SURFACE_AREA>
177.17

> <JCHEM_REFRACTIVITY>
71.48459999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.43e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-arpd

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0011106
     RDKit          3D
5-Amino-6-ribitylamino uracil
 35 35  0  0  0  0  0  0  0  0999 V2000
    2.5793    0.5100   -1.8835 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8547   -0.4078   -0.8419 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0491   -0.4542    0.2697 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.4214    0.3589 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0372    0.4595    1.4786 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0270    1.4883    1.2865 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8824    1.4846    2.3933 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8348    1.3443    0.0379 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7112    2.4545    0.0109 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6935    0.1207   -0.0189 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0054   -1.0714   -0.0049 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4775    0.1722   -1.3244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3735   -0.8824   -1.4273 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3823   -1.3558    1.2121 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4481   -2.1726    1.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6832   -2.9809    2.0053 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2507   -2.1399   -0.0084 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9447   -1.2403   -0.9829 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7033   -1.2271   -1.9833 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4270    1.5072   -1.6208 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5152    0.2734   -2.8962 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7634    1.0880   -0.4172 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5487    0.6898    2.4341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4178   -0.5352    1.6133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5543    2.5049    1.2388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3092    1.3212    3.1920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2212    1.4365   -0.8737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0242    2.5940    0.9499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4082    0.1644    0.8158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3507   -1.6578    0.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7985    0.1175   -2.2000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0652    1.1238   -1.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8633   -0.9482   -0.5746 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8060   -1.4313    2.0717 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0768   -2.7716   -0.1142 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  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  2  0
 18  2  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  6
  7 26  1  0
  8 27  1  6
  9 28  1  0
 10 29  1  1
 11 30  1  0
 12 31  1  0
 12 32  1  0
 13 33  1  0
 14 34  1  0
 17 35  1  0
M  END

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0      34.826 -34.249   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      34.826 -35.789   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      36.160 -36.559   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      37.494 -35.789   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      37.494 -34.249   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      36.160 -33.479   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      36.160 -31.939   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      33.493 -36.559   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      38.848 -33.467   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      38.855 -36.559   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      40.189 -35.789   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      41.522 -36.559   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      42.856 -35.789   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      44.190 -36.559   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      45.523 -35.789   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      46.857 -36.559   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      41.522 -38.099   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      44.190 -38.098   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      42.856 -34.249   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    9                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    2                                                            
CONECT    9    5                                                            
CONECT   10    4   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   19                                                  
CONECT   14   13   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   12                                                            
CONECT   18   14                                                            
CONECT   19   13                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

COMPND    HMDB0011106
HETATM    1  N1  UNL     1       2.579   0.510  -1.884  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.855  -0.408  -0.842  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.049  -0.454   0.270  1.00  0.00           C  
HETATM    4  N2  UNL     1       0.948   0.421   0.359  1.00  0.00           N  
HETATM    5  C3  UNL     1       0.037   0.459   1.479  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.027   1.488   1.287  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.882   1.485   2.393  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.835   1.344   0.038  1.00  0.00           C  
HETATM    9  O2  UNL     1      -2.711   2.454   0.011  1.00  0.00           O  
HETATM   10  C6  UNL     1      -2.694   0.121  -0.019  1.00  0.00           C  
HETATM   11  O3  UNL     1      -2.005  -1.071  -0.005  1.00  0.00           O  
HETATM   12  C7  UNL     1      -3.477   0.172  -1.324  1.00  0.00           C  
HETATM   13  O4  UNL     1      -4.374  -0.882  -1.427  1.00  0.00           O  
HETATM   14  N3  UNL     1       2.382  -1.356   1.212  1.00  0.00           N  
HETATM   15  C8  UNL     1       3.448  -2.173   1.079  1.00  0.00           C  
HETATM   16  O5  UNL     1       3.683  -2.981   2.005  1.00  0.00           O  
HETATM   17  N4  UNL     1       4.251  -2.140  -0.008  1.00  0.00           N  
HETATM   18  C9  UNL     1       3.945  -1.240  -0.983  1.00  0.00           C  
HETATM   19  O6  UNL     1       4.703  -1.227  -1.983  1.00  0.00           O  
HETATM   20  H1  UNL     1       2.427   1.507  -1.621  1.00  0.00           H  
HETATM   21  H2  UNL     1       2.515   0.273  -2.896  1.00  0.00           H  
HETATM   22  H3  UNL     1       0.763   1.088  -0.417  1.00  0.00           H  
HETATM   23  H4  UNL     1       0.549   0.690   2.434  1.00  0.00           H  
HETATM   24  H5  UNL     1      -0.418  -0.535   1.613  1.00  0.00           H  
HETATM   25  H6  UNL     1      -0.554   2.505   1.239  1.00  0.00           H  
HETATM   26  H7  UNL     1      -1.309   1.321   3.192  1.00  0.00           H  
HETATM   27  H8  UNL     1      -1.221   1.436  -0.874  1.00  0.00           H  
HETATM   28  H9  UNL     1      -3.024   2.594   0.950  1.00  0.00           H  
HETATM   29  H10 UNL     1      -3.408   0.164   0.816  1.00  0.00           H  
HETATM   30  H11 UNL     1      -2.351  -1.658   0.739  1.00  0.00           H  
HETATM   31  H12 UNL     1      -2.798   0.117  -2.200  1.00  0.00           H  
HETATM   32  H13 UNL     1      -4.065   1.124  -1.393  1.00  0.00           H  
HETATM   33  H14 UNL     1      -4.863  -0.948  -0.575  1.00  0.00           H  
HETATM   34  H15 UNL     1       1.806  -1.431   2.072  1.00  0.00           H  
HETATM   35  H16 UNL     1       5.077  -2.772  -0.114  1.00  0.00           H  
CONECT    1    2   20   21
CONECT    2    3    3   18
CONECT    3    4   14
CONECT    4    5   22
CONECT    5    6   23   24
CONECT    6    7    8   25
CONECT    7   26
CONECT    8    9   10   27
CONECT    9   28
CONECT   10   11   12   29
CONECT   11   30
CONECT   12   13   31   32
CONECT   13   33
CONECT   14   15   34
CONECT   15   16   16   17
CONECT   17   18   35
CONECT   18   19   19
END

HMDB0011106
     RDKit          3D
5-Amino-6-ribitylamino uracil
 35 35  0  0  0  0  0  0  0  0999 V2000
    2.5793    0.5100   -1.8835 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8547   -0.4078   -0.8419 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0491   -0.4542    0.2697 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.4214    0.3589 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0372    0.4595    1.4786 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0270    1.4883    1.2865 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8824    1.4846    2.3933 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8348    1.3443    0.0379 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7112    2.4545    0.0109 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6935    0.1207   -0.0189 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0054   -1.0714   -0.0049 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4775    0.1722   -1.3244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3735   -0.8824   -1.4273 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3823   -1.3558    1.2121 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4481   -2.1726    1.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6832   -2.9809    2.0053 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2507   -2.1399   -0.0084 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9447   -1.2403   -0.9829 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7033   -1.2271   -1.9833 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4270    1.5072   -1.6208 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5152    0.2734   -2.8962 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7634    1.0880   -0.4172 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5487    0.6898    2.4341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4178   -0.5352    1.6133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5543    2.5049    1.2388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3092    1.3212    3.1920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2212    1.4365   -0.8737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0242    2.5940    0.9499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4082    0.1644    0.8158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3507   -1.6578    0.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7985    0.1175   -2.2000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0652    1.1238   -1.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8633   -0.9482   -0.5746 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8060   -1.4313    2.0717 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0768   -2.7716   -0.1142 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  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  2  0
 18  2  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  6
  7 26  1  0
  8 27  1  6
  9 28  1  0
 10 29  1  1
 11 30  1  0
 12 31  1  0
 12 32  1  0
 13 33  1  0
 14 34  1  0
 17 35  1  0
M  END

Synonyms

Value	Source
5-Amino-6-(D-ribitylamino)uracil	Kegg
6-(1-D-Ribitylamino)-5-amino-2,4-dihydroxypyrimidine	Kegg
6-(1-D-Ribitylamino)-5-aminouracil	Kegg
4-(1-D-Ribitylamino)-5-amino-2,6-dihydroxypyrimidine	Kegg
5-a-RU	HMDB
5-Amino-2,6-dioxo-4-ribitylaminopyrimidine	HMDB
5-Amino-6-(1-D-ribitylamino)uracil	HMDB
5-Amino-6-ribitylamino-2,4-(1H,3H)pyrimidinedione	HMDB
5-Amino-6-ribitylaminouracil	HMDB
5-Arpd	HMDB
a-4-RAP	HMDB
1-[(5-Amino-1,2,3,6-tetrahydro-2,6-dioxo-4-pyrimidinyl)amino]-1-deoxy-D-ribitol	HMDB
4-(1'-D-Ribitylamino)-5-amino-2,6-dihydroxypyrimidine	HMDB
4-(1’-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine	HMDB
4-(Ribitylamino)-5-aminouracil	HMDB
4-Ribitylamino-5-amino-2,6-dihydroxypyrimidine	HMDB
5-Amino-4-D-ribitylaminouracil	HMDB
5-Amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione	HMDB
ARP	HMDB
5-Amino-6-ribitylamino uracil	HMDB

Molecular Formula

C₉H₁₆N₄O₆

Average Mass

276.2465

Monoisotopic Mass

276.106984264

IUPAC Name

5-amino-6-{[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]amino}-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

5-arpd

CAS Registry Number

Not Available

SMILES

NC1=C(NC[C@H](O)[C@H](O)[C@H](O)CO)NC(=O)NC1=O

InChI Identifier

InChI=1S/C9H16N4O6/c10-5-7(12-9(19)13-8(5)18)11-1-3(15)6(17)4(16)2-14/h3-4,6,14-17H,1-2,10H2,(H3,11,12,13,18,19)/t3-,4+,6-/m0/s1

InChI Key

XKQZIXVJVUPORE-RPDRRWSUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Aminopyrimidine
Pyrimidone
Secondary aliphatic/aromatic amine
Hydropyrimidine
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Lactam
Urea
Secondary alcohol
Polyol
Azacycle
Organoheterocyclic compound
Secondary amine
Primary alcohol
Alcohol
Hydrocarbon derivative
Organonitrogen compound
Organic oxide
Organopnictogen compound
Primary amine
Amine
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

hydroxypyrimidine (CHEBI:15934 )
aminouracil (CHEBI:15934 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	14.3 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-4.4	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	8.48	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	177.17 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	71.48 m³·mol⁻¹	ChemAxon
Polarizability	25.82 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

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	306	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; Rat ; Sheep ; Lion ; Chicken	Unknown
Bacteria/Eubacteria	Aquificae	4
Bacteria/Eubacteria	Firmicutes	105	Human ; Human feces; Cattle ; Human subgingival plaque; Human saliva
Bacteria/Eubacteria	Chlamydiae	10	Human ; Sheep ; Cat
Bacteria/Eubacteria	Actinobacteria	49	Cattle ; Human ; Human feces
Bacteria	Proteobacteria	8	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; Rat ; Sheep ; Lion ; Chicken	Unknown
Eukaryota/Fungi	Ascomycota	5	Human feces; Human saliva	Unknown
Archaea/Archaea	Crenarchaeota	15
Archaea/Archaea	Euryarchaeota	29
Bacteria/Eubacteria	Bacteroidetes	11	Human ; Human feces
Bacteria/Eubacteria	Spirochaetes	7	Pig ; Human
Bacteria/Eubacteria	Chloroflexi	6
Bacteria/Eubacteria	Chlorobi	11
Bacteria/Eubacteria	Cyanobacteria	30	Human
Bacteria/Eubacteria	Deinococcus-thermus	5
Bacteria/Eubacteria	Elusimicrobia	1
Bacteria/Eubacteria	Fusobacteria	1	Human ; Human feces
Bacteria/Eubacteria	Gemmatimonadetes	1
Bacteria/Eubacteria	Thermotogae	5
Archaea	Euryarchaeota	1
Bacteria/Eubacteria	Planctomycetes	1
Archaea	Crenarchaeota	1
Bacteria/Eubacteria	Acidobacteria	1
Bacteria	nah	1
Bacteria/Eubacteria	Nitrospirae	1

Exposure Sources

Other Exposures

Source Type	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

HMDB0011106

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030561

KNApSAcK ID

Not Available

Chemspider ID

167930

KEGG Compound ID

C04732

BioCyc ID

AMINO-RIBOSYLAMINO-1H-3H-PYR-DIONE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

193516

PDB ID

Not Available

ChEBI ID

15934

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

WACKER H, HARVEY RA, WINESTOCK CH, PLAUT GW: 4-(1'-D-RIBITYLAMINO)-5-AMINO-2,6-DIHYDROXYPYRIMIDINE, THE SECOND PRODUCT OF THE RIBOFLAVIN SYNTHETASE REACTION. J Biol Chem. 1964 Oct;239:3493-7. [PubMed:14245407 ]

Showing metabocard for 5-amino-6-(D-ribitylamino)uracil (MMDBc0031730)

MOL for #<Metabolite:0x00007f9238bec158>

3D MOL for #<Metabolite:0x00007f9238bec158>

3D SDF for #<Metabolite:0x00007f9238bec158>

3D-SDF for #<Metabolite:0x00007f9238bec158>

PDB for #<Metabolite:0x00007f9238bec158>

3D PDB for #<Metabolite:0x00007f9238bec158>

SMILES for #<Metabolite:0x00007f9238bec158>

INCHI for #<Metabolite:0x00007f9238bec158>

Structure for #<Metabolite:0x00007f9238bec158>

3D Structure for #<Metabolite:0x00007f9238bec158>