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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:53:17 UTC

Update Date

2021-09-26 22:56:12 UTC

HMDB ID

HMDB0246877

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione

Description

1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione, also known as 5'-amino-5'-deoxythymidine monohydrochloride or 5'-amino-2',5'-dideoxythymidine, belongs to the class of organic compounds known as 2',5'-dideoxyribonucleosides. These are nucleosides characterized by a purine or pyrimidine base, which is N-linked to a 2',5'-dideoxyribose moiety. Based on a literature review very few articles have been published on 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-[(2r,4r,5r)-5-(aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0246878
     RDKit          3D
1-[(2S,5S)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione
 32 33  0  0  0  0  0  0  0  0999 V2000
    4.1285    0.8348    1.4113 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1772    0.4289    0.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9194   -0.0951    0.6562 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0677   -0.4587   -0.3182 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2265   -0.9982   -0.0362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8355   -0.4586    1.2421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3098   -0.7964    0.9754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4622   -2.1457    1.2602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3816   -0.6155   -0.5041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8652    0.7912   -0.8791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1744    1.0673   -0.3783 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1265   -0.7599   -1.0357 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4692   -0.3002   -1.5895 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6738   -0.6399   -2.4991 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6754    0.2019   -1.9192 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5519    0.5758   -0.9736 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6953    1.0518   -1.2882 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7127   -0.0244    1.8092 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5878    1.3834    2.2370 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8606    1.5582    1.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6618   -0.1950    1.7036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1721   -2.1148    0.1032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7859    0.6330    1.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5072   -0.9960    2.1309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9834   -0.1555    1.5514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3719   -2.4054    1.5088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0764   -1.3793   -0.9078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8258    0.8131   -2.0033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1514    1.5540   -0.5326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1748    1.7879    0.4046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7355    1.5333   -1.1499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9848    0.3240   -2.9177 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
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  4 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  2  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 15 32  1  0
M  END

  Mrv1652309112101532D          

 17 18  0  0  0  0            999 V2000
    0.1067    4.7652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    4.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    4.3527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    4.7652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    5.5902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8841   -0.4005    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4248    0.3532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  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
 10 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 12 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246877

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN(C2CC(O)C(CN)O2)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N3O4/c1-5-4-13(10(16)12-9(5)15)8-2-6(14)7(3-11)17-8/h4,6-8,14H,2-3,11H2,1H3,(H,12,15,16)

> <INCHI_KEY>
PYWLBQPICCQJFF-UHFFFAOYSA-N

> <FORMULA>
C10H15N3O4

> <MOLECULAR_WEIGHT>
241.247

> <EXACT_MASS>
241.106255975

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.834283542771363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[5-(aminomethyl)-4-hydroxyoxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-1.38

> <JCHEM_LOGP>
-1.592643773347487

> <ALOGPS_LOGS>
-0.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.042493835353884

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.016495872729168

> <JCHEM_PKA_STRONGEST_BASIC>
9.044510202551384

> <JCHEM_POLAR_SURFACE_AREA>
104.89

> <JCHEM_REFRACTIVITY>
57.069500000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.16e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thymidine, 5'-amino-5'-deoxy-

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0246878
     RDKit          3D
1-[(2S,5S)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione
 32 33  0  0  0  0  0  0  0  0999 V2000
    4.1285    0.8348    1.4113 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1772    0.4289    0.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9194   -0.0951    0.6562 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0677   -0.4587   -0.3182 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2265   -0.9982   -0.0362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8355   -0.4586    1.2421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3098   -0.7964    0.9754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4622   -2.1457    1.2602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3816   -0.6155   -0.5041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8652    0.7912   -0.8791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1744    1.0673   -0.3783 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1265   -0.7599   -1.0357 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4692   -0.3002   -1.5895 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6738   -0.6399   -2.4991 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6754    0.2019   -1.9192 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5519    0.5758   -0.9736 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6953    1.0518   -1.2882 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7127   -0.0244    1.8092 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5878    1.3834    2.2370 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8606    1.5582    1.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6618   -0.1950    1.7036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1721   -2.1148    0.1032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7859    0.6330    1.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5072   -0.9960    2.1309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9834   -0.1555    1.5514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3719   -2.4054    1.5088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0764   -1.3793   -0.9078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8258    0.8131   -2.0033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1514    1.5540   -0.5326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1748    1.7879    0.4046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7355    1.5333   -1.1499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9848    0.3240   -2.9177 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
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  4 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  2  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 15 32  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       0.199   8.895   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.134   8.125   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.134   6.585   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -2.468   5.815   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -3.802   6.585   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -5.136   5.815   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -3.802   8.125   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -2.468   8.895   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.468  10.435   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.698   1.905   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.238   1.905   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.714   3.370   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -4.143   0.659   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -3.517  -0.748   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      -0.793   0.659   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    2    9                                                  
CONECT    9    8                                                            
CONECT   10    4   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13   10                                                       
CONECT   15   13   16                                                       
CONECT   16   15                                                            
CONECT   17   12                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0246877
HETATM    1  C1  UNL     1      -4.746  -0.421   0.818  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.461   0.292   0.590  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.280  -0.423   0.601  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.074   0.158   0.401  1.00  0.00           N  
HETATM    5  C4  UNL     1       0.129  -0.610   0.420  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.878  -0.606  -0.893  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.167  -1.255  -0.417  1.00  0.00           C  
HETATM    8  O1  UNL     1       3.229  -0.992  -1.261  1.00  0.00           O  
HETATM    9  C7  UNL     1       2.304  -0.626   0.938  1.00  0.00           C  
HETATM   10  C8  UNL     1       3.191   0.615   0.896  1.00  0.00           C  
HETATM   11  N2  UNL     1       4.536   0.287   0.476  1.00  0.00           N  
HETATM   12  O2  UNL     1       1.054  -0.212   1.346  1.00  0.00           O  
HETATM   13  C9  UNL     1      -1.089   1.489   0.188  1.00  0.00           C  
HETATM   14  O3  UNL     1       0.037   2.031   0.001  1.00  0.00           O  
HETATM   15  N3  UNL     1      -2.229   2.214   0.171  1.00  0.00           N  
HETATM   16  C10 UNL     1      -3.435   1.654   0.368  1.00  0.00           C  
HETATM   17  O4  UNL     1      -4.497   2.350   0.349  1.00  0.00           O  
HETATM   18  H1  UNL     1      -4.579  -1.524   0.681  1.00  0.00           H  
HETATM   19  H2  UNL     1      -5.525  -0.136   0.099  1.00  0.00           H  
HETATM   20  H3  UNL     1      -5.050  -0.301   1.880  1.00  0.00           H  
HETATM   21  H4  UNL     1      -2.329  -1.506   0.780  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.122  -1.674   0.622  1.00  0.00           H  
HETATM   23  H6  UNL     1       1.152   0.395  -1.241  1.00  0.00           H  
HETATM   24  H7  UNL     1       0.381  -1.207  -1.672  1.00  0.00           H  
HETATM   25  H8  UNL     1       1.949  -2.341  -0.313  1.00  0.00           H  
HETATM   26  H9  UNL     1       3.398  -1.816  -1.798  1.00  0.00           H  
HETATM   27  H10 UNL     1       2.749  -1.383   1.614  1.00  0.00           H  
HETATM   28  H11 UNL     1       3.190   1.081   1.901  1.00  0.00           H  
HETATM   29  H12 UNL     1       2.805   1.363   0.182  1.00  0.00           H  
HETATM   30  H13 UNL     1       4.769   0.588  -0.475  1.00  0.00           H  
HETATM   31  H14 UNL     1       4.665  -0.730   0.630  1.00  0.00           H  
HETATM   32  H15 UNL     1      -2.167   3.248  -0.002  1.00  0.00           H  
CONECT    1    2   18   19   20
CONECT    2    3    3   16
CONECT    3    4   21
CONECT    4    5   13
CONECT    5    6   12   22
CONECT    6    7   23   24
CONECT    7    8    9   25
CONECT    8   26
CONECT    9   10   12   27
CONECT   10   11   28   29
CONECT   11   30   31
CONECT   13   14   14   15
CONECT   15   16   32
CONECT   16   17   17
END

HMDB0246878
     RDKit          3D
1-[(2S,5S)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione
 32 33  0  0  0  0  0  0  0  0999 V2000
    4.1285    0.8348    1.4113 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1772    0.4289    0.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9194   -0.0951    0.6562 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0677   -0.4587   -0.3182 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2265   -0.9982   -0.0362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8355   -0.4586    1.2421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3098   -0.7964    0.9754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4622   -2.1457    1.2602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3816   -0.6155   -0.5041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8652    0.7912   -0.8791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1744    1.0673   -0.3783 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1265   -0.7599   -1.0357 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4692   -0.3002   -1.5895 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6738   -0.6399   -2.4991 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6754    0.2019   -1.9192 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5519    0.5758   -0.9736 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6953    1.0518   -1.2882 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7127   -0.0244    1.8092 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5878    1.3834    2.2370 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8606    1.5582    1.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6618   -0.1950    1.7036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1721   -2.1148    0.1032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7859    0.6330    1.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5072   -0.9960    2.1309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9834   -0.1555    1.5514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3719   -2.4054    1.5088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0764   -1.3793   -0.9078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8258    0.8131   -2.0033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1514    1.5540   -0.5326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1748    1.7879    0.4046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7355    1.5333   -1.1499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9848    0.3240   -2.9177 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
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  4 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  2  0
 16  2  1  0
 12  5  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 15 32  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
5'-Amino-5'-deoxythymidine monohydrochloride	HMDB
5'-Amino-2',5'-dideoxythymidine	HMDB
5'-Amino-5'-deoxythymidine monoacetate	HMDB
5'-Amino-5'-deoxythymidine	HMDB
5-ADDOT	HMDB

Chemical Formula

C₁₀H₁₅N₃O₄

Average Molecular Weight

241.247

Monoisotopic Molecular Weight

241.106255975

IUPAC Name

1-[5-(aminomethyl)-4-hydroxyoxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

thymidine, 5'-amino-5'-deoxy-

CAS Registry Number

Not Available

SMILES

CC1=CN(C2CC(O)C(CN)O2)C(=O)NC1=O

InChI Identifier

InChI=1S/C10H15N3O4/c1-5-4-13(10(16)12-9(5)15)8-2-6(14)7(3-11)17-8/h4,6-8,14H,2-3,11H2,1H3,(H,12,15,16)

InChI Key

PYWLBQPICCQJFF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2',5'-dideoxyribonucleosides. These are nucleosides characterized by a purine or pyrimidine base, which is N-linked to a 2',5'-dideoxyribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

2',5'-dideoxyribonucleosides

Sub Class

Not Available

Direct Parent

2',5'-dideoxyribonucleosides

Alternative Parents

Substituents

2',5'-dideoxyribonucleoside
Pyrimidone
Hydropyrimidine
Pyrimidine
Tetrahydrofuran
Vinylogous amide
Heteroaromatic compound
Lactam
Secondary alcohol
Urea
Organoheterocyclic compound
Azacycle
Oxacycle
Amine
Alcohol
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organic oxide
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

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	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.4	ALOGPS
logP	-1.6	ChemAxon
logS	-0.53	ALOGPS
pKa (Strongest Acidic)	10.02	ChemAxon
pKa (Strongest Basic)	9.04	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	104.89 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	57.07 m³·mol⁻¹	ChemAxon
Polarizability	23.83 Å³	ChemAxon
Number of Rings	2	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
DeepCCS	[M+H]+	150.106	30932474
DeepCCS	[M-H]-	147.71	30932474
DeepCCS	[M-2H]-	181.03	30932474
DeepCCS	[M+Na]+	156.092	30932474
AllCCS	[M+H]+	154.6	32859911
AllCCS	[M+H-H2O]+	150.8	32859911
AllCCS	[M+NH4]+	158.1	32859911
AllCCS	[M+Na]+	159.1	32859911
AllCCS	[M-H]-	154.9	32859911
AllCCS	[M+Na-2H]-	155.0	32859911
AllCCS	[M+HCOO]-	155.3	32859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN)O2)C(=O)[NH]C1=O	2385.9	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN)O2)C(=O)[NH]C1=O	2385.3	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN)O2)C(=O)[NH]C1=O	3522.9	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TMS,isomer #2	CC1=CN(C2CC(O)C(CN[Si](C)(C)C)O2)C(=O)[NH]C1=O	2473.8	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TMS,isomer #2	CC1=CN(C2CC(O)C(CN[Si](C)(C)C)O2)C(=O)[NH]C1=O	2554.8	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TMS,isomer #2	CC1=CN(C2CC(O)C(CN[Si](C)(C)C)O2)C(=O)[NH]C1=O	3588.4	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TMS,isomer #3	CC1=CN(C2CC(O)C(CN)O2)C(=O)N([Si](C)(C)C)C1=O	2369.5	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TMS,isomer #3	CC1=CN(C2CC(O)C(CN)O2)C(=O)N([Si](C)(C)C)C1=O	2443.6	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TMS,isomer #3	CC1=CN(C2CC(O)C(CN)O2)C(=O)N([Si](C)(C)C)C1=O	3658.7	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN[Si](C)(C)C)O2)C(=O)[NH]C1=O	2489.0	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN[Si](C)(C)C)O2)C(=O)[NH]C1=O	2534.4	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN[Si](C)(C)C)O2)C(=O)[NH]C1=O	3118.5	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C)C(CN)O2)C(=O)N([Si](C)(C)C)C1=O	2415.5	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C)C(CN)O2)C(=O)N([Si](C)(C)C)C1=O	2491.4	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C)C(CN)O2)C(=O)N([Si](C)(C)C)C1=O	3205.7	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)[NH]C1=O	2536.7	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)[NH]C1=O	2693.1	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)[NH]C1=O	3361.7	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #4	CC1=CN(C2CC(O)C(CN[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2474.2	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #4	CC1=CN(C2CC(O)C(CN[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2594.7	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #4	CC1=CN(C2CC(O)C(CN[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	3286.9	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)[NH]C1=O	2556.0	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)[NH]C1=O	2684.1	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)[NH]C1=O	2960.4	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C)C(CN[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2535.6	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C)C(CN[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2590.5	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C)C(CN[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2845.8	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2558.7	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2749.0	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	3078.7	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,4TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2603.8	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,4TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2729.1	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,4TMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C)C(CN([Si](C)(C)C)[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2727.7	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN)O2)C(=O)[NH]C1=O	2655.8	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN)O2)C(=O)[NH]C1=O	2619.1	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN)O2)C(=O)[NH]C1=O	3539.9	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TBDMS,isomer #2	CC1=CN(C2CC(O)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	2757.0	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TBDMS,isomer #2	CC1=CN(C2CC(O)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	2753.7	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TBDMS,isomer #2	CC1=CN(C2CC(O)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	3581.0	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TBDMS,isomer #3	CC1=CN(C2CC(O)C(CN)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2603.4	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TBDMS,isomer #3	CC1=CN(C2CC(O)C(CN)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2661.3	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,1TBDMS,isomer #3	CC1=CN(C2CC(O)C(CN)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3581.6	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	2984.3	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	2960.6	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	3222.0	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2896.8	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2914.9	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3218.7	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	3020.8	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	3097.5	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	3389.4	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #4	CC1=CN(C2CC(O)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2957.1	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #4	CC1=CN(C2CC(O)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3008.2	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #4	CC1=CN(C2CC(O)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3281.5	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	3284.5	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	3274.2	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O	3164.8	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TBDMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3188.3	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TBDMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3204.2	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TBDMS,isomer #2	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3084.6	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TBDMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3269.2	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TBDMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3336.7	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,3TBDMS,isomer #3	CC1=CN(C2CC(O)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3211.9	Standard polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,4TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3524.1	Semi standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,4TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3485.8	Standard non polar	33892256
1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione,4TBDMS,isomer #1	CC1=CN(C2CC(O[Si](C)(C)C(C)(C)C)C(CN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3055.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-9200000000-b171f2dacc9853dde388	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione 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 - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione 10V, Positive-QTOF	splash10-002f-1890000000-b592f78ec430ceb27aaf	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione 20V, Positive-QTOF	splash10-004i-5910000000-68cc4703d33a6dffdb44	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione 40V, Positive-QTOF	splash10-056r-9800000000-eaae5fb9758b0671b852	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione 10V, Negative-QTOF	splash10-0006-1590000000-d8fceff0972617aab9f8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione 20V, Negative-QTOF	splash10-002f-9300000000-555ed9b2a12717cd58fd	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione 40V, Negative-QTOF	splash10-002f-9800000000-9412c7586302dbe0819b	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

263077

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

297924

PDB ID

Not Available

ChEBI ID

Not Available

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione (HMDB0246877)

MOL for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D MOL for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D SDF for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D-SDF for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

PDB for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D PDB for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

SMILES for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

INCHI for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

Structure for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D Structure for HMDB0246877 (1-[(2R,4R,5R)-5-(Aminomethyl)-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra