Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 15:38:59 UTC

Update Date

2021-09-26 23:10:56 UTC

HMDB ID

HMDB0255802

Secondary Accession Numbers

None

Metabolite Identification

Common Name

4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one

Description

1-[5-(hydroxymethyl)oxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3. Based on a literature review very few articles have been published on 1-[5-(hydroxymethyl)oxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 4-amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one 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

HMDB0255802
     RDKit          3D
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
 28 29  0  0  0  0  0  0  0  0999 V2000
    5.0148   -0.2712    0.5114 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6318   -0.2822    0.1429 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7383   -1.0905    0.8172 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4202   -1.0415    0.3983 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0311   -0.2484   -0.6120 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3393   -0.2218   -1.0199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8157    1.1901   -1.3339 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2248    1.1700   -0.7773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4368   -0.2819   -0.5048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5641   -0.5605    0.4502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4439    0.0812    1.6519 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2013   -0.6728    0.0060 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9155    0.5329   -1.2583 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5490    1.2875   -2.2186 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1972    0.4932   -0.8598 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7480    0.0699   -0.1445 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2660   -0.6138    1.4532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0530   -1.7299    1.6322 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7163   -1.6853    0.9375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4957   -0.9133   -1.8738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8214    1.3229   -2.4158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1836    1.9312   -0.7876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9010    1.5760   -1.5527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2708    1.8017    0.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6016   -0.7978   -1.4550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5258   -0.3434   -0.0557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5554   -1.6728    0.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9000    0.9705    1.5772 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  5 13  1  0
 13 14  2  0
 13 15  1  0
 15  2  2  0
 12  6  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  0
  8 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
M  END

  Mrv1533004241520322D          

 15 16  0  0  0  0            999 V2000
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323   -4.5956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3390   -2.3346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6377   -5.1768    0.0000 N   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  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  2  0  0  0  0
 11 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255802

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(=O)N(C=C1)C1CCC(CO)O1

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N3O3/c10-7-3-4-12(9(14)11-7)8-2-1-6(5-13)15-8/h3-4,6,8,13H,1-2,5H2,(H2,10,11,14)

> <INCHI_KEY>
WREGKURFCTUGRC-UHFFFAOYSA-N

> <FORMULA>
C9H13N3O3

> <MOLECULAR_WEIGHT>
211.221

> <EXACT_MASS>
211.095691291

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
20.978349450239556

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.29

> <JCHEM_LOGP>
-1.1882264563333331

> <ALOGPS_LOGS>
-1.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.21725074537269

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.673289182384618

> <JCHEM_PKA_STRONGEST_BASIC>
0.4696473165568924

> <JCHEM_POLAR_SURFACE_AREA>
88.15

> <JCHEM_REFRACTIVITY>
52.240199999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.05e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cytidine, 2',3'-dideoxy-

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0255802
     RDKit          3D
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
 28 29  0  0  0  0  0  0  0  0999 V2000
    5.0148   -0.2712    0.5114 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6318   -0.2822    0.1429 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7383   -1.0905    0.8172 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4202   -1.0415    0.3983 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0311   -0.2484   -0.6120 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3393   -0.2218   -1.0199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8157    1.1901   -1.3339 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2248    1.1700   -0.7773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4368   -0.2819   -0.5048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5641   -0.5605    0.4502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4439    0.0812    1.6519 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2013   -0.6728    0.0060 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9155    0.5329   -1.2583 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5490    1.2875   -2.2186 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1972    0.4932   -0.8598 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7480    0.0699   -0.1445 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2660   -0.6138    1.4532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0530   -1.7299    1.6322 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7163   -1.6853    0.9375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4957   -0.9133   -1.8738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8214    1.3229   -2.4158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1836    1.9312   -0.7876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9010    1.5760   -1.5527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2708    1.8017    0.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6016   -0.7978   -1.4550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5258   -0.3434   -0.0557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5554   -1.6728    0.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9000    0.9705    1.5772 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  5 13  1  0
 13 14  2  0
 13 15  1  0
 15  2  2  0
 12  6  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  0
  8 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
M  END

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.088  -3.215   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0      -0.342  -5.926   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       0.285  -7.333   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.620  -8.578   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.152  -8.417   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -2.778  -7.011   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -1.873  -5.765   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.499  -4.358   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0      -3.057  -9.663   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    3    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8   14                                                  
CONECT   14   13                                                            
CONECT   15   11                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

COMPND    HMDB0255802
HETATM    1  N1  UNL     1       5.015  -0.271   0.511  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.632  -0.282   0.143  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.738  -1.090   0.817  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.420  -1.041   0.398  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.031  -0.248  -0.612  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.339  -0.222  -1.020  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.816   1.190  -1.334  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.225   1.170  -0.777  1.00  0.00           C  
HETATM    9  C7  UNL     1      -2.437  -0.282  -0.505  1.00  0.00           C  
HETATM   10  C8  UNL     1      -3.564  -0.561   0.450  1.00  0.00           C  
HETATM   11  O1  UNL     1      -3.444   0.081   1.652  1.00  0.00           O  
HETATM   12  O2  UNL     1      -1.201  -0.673   0.006  1.00  0.00           O  
HETATM   13  C9  UNL     1       1.916   0.533  -1.258  1.00  0.00           C  
HETATM   14  O3  UNL     1       1.549   1.288  -2.219  1.00  0.00           O  
HETATM   15  N3  UNL     1       3.197   0.493  -0.860  1.00  0.00           N  
HETATM   16  H1  UNL     1       5.748   0.070  -0.145  1.00  0.00           H  
HETATM   17  H2  UNL     1       5.266  -0.614   1.453  1.00  0.00           H  
HETATM   18  H3  UNL     1       3.053  -1.730   1.632  1.00  0.00           H  
HETATM   19  H4  UNL     1       0.716  -1.685   0.938  1.00  0.00           H  
HETATM   20  H5  UNL     1      -0.496  -0.913  -1.874  1.00  0.00           H  
HETATM   21  H6  UNL     1      -0.821   1.323  -2.416  1.00  0.00           H  
HETATM   22  H7  UNL     1      -0.184   1.931  -0.788  1.00  0.00           H  
HETATM   23  H8  UNL     1      -2.901   1.576  -1.553  1.00  0.00           H  
HETATM   24  H9  UNL     1      -2.271   1.802   0.155  1.00  0.00           H  
HETATM   25  H10 UNL     1      -2.602  -0.798  -1.455  1.00  0.00           H  
HETATM   26  H11 UNL     1      -4.526  -0.343  -0.056  1.00  0.00           H  
HETATM   27  H12 UNL     1      -3.555  -1.673   0.629  1.00  0.00           H  
HETATM   28  H13 UNL     1      -3.900   0.970   1.577  1.00  0.00           H  
CONECT    1    2   16   17
CONECT    2    3   15   15
CONECT    3    4    4   18
CONECT    4    5   19
CONECT    5    6   13
CONECT    6    7   12   20
CONECT    7    8   21   22
CONECT    8    9   23   24
CONECT    9   10   12   25
CONECT   10   11   26   27
CONECT   11   28
CONECT   13   14   14   15
END

HMDB0255802
     RDKit          3D
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
 28 29  0  0  0  0  0  0  0  0999 V2000
    5.0148   -0.2712    0.5114 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6318   -0.2822    0.1429 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7383   -1.0905    0.8172 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4202   -1.0415    0.3983 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0311   -0.2484   -0.6120 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3393   -0.2218   -1.0199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8157    1.1901   -1.3339 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2248    1.1700   -0.7773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4368   -0.2819   -0.5048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5641   -0.5605    0.4502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4439    0.0812    1.6519 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2013   -0.6728    0.0060 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9155    0.5329   -1.2583 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5490    1.2875   -2.2186 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1972    0.4932   -0.8598 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7480    0.0699   -0.1445 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2660   -0.6138    1.4532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0530   -1.7299    1.6322 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7163   -1.6853    0.9375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4957   -0.9133   -1.8738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8214    1.3229   -2.4158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1836    1.9312   -0.7876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9010    1.5760   -1.5527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2708    1.8017    0.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6016   -0.7978   -1.4550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5258   -0.3434   -0.0557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5554   -1.6728    0.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9000    0.9705    1.5772 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
  5 13  1  0
 13 14  2  0
 13 15  1  0
 15  2  2  0
 12  6  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  0
  8 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2',3'-Dideoxycytidine	MeSH
HIVID roche	MeSH
2',3' Dideoxycytidine	MeSH
Hivid	MeSH
Zalcitabine	MeSH
Dideoxycytidine	MeSH
DDC (Antiviral)	MeSH

Chemical Formula

C₉H₁₃N₃O₃

Average Molecular Weight

211.221

Monoisotopic Molecular Weight

211.095691291

IUPAC Name

4-amino-1-[5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

cytidine, 2',3'-dideoxy-

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)C1CCC(CO)O1

InChI Identifier

InChI=1S/C9H13N3O3/c10-7-3-4-12(9(14)11-7)8-2-1-6(5-13)15-8/h3-4,6,8,13H,1-2,5H2,(H2,10,11,14)

InChI Key

WREGKURFCTUGRC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2',3'-dideoxyribonucleosides. Pyrimidine 2',3'-dideoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at positions 2 and 3.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2',3'-dideoxyribonucleosides

Direct Parent

Pyrimidine 2',3'-dideoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2',3'-dideoxyribonucleoside
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Alcohol
Amine
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	-1.3	ALOGPS
logP	-1.2	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	14.67	ChemAxon
pKa (Strongest Basic)	0.47	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	88.15 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.24 m³·mol⁻¹	ChemAxon
Polarizability	20.98 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]+	154.621	30932474
DeepCCS	[M-H]-	152.263	30932474
DeepCCS	[M-2H]-	186.83	30932474
DeepCCS	[M+Na]+	161.658	30932474
AllCCS	[M+H]+	147.8	32859911
AllCCS	[M+H-H2O]+	143.7	32859911
AllCCS	[M+NH4]+	151.5	32859911
AllCCS	[M+Na]+	152.6	32859911
AllCCS	[M-H]-	148.0	32859911
AllCCS	[M+Na-2H]-	148.2	32859911
AllCCS	[M+HCOO]-	148.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one	NC1=NC(=O)N(C=C1)C1CCC(CO)O1	3416.1	Standard polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one	NC1=NC(=O)N(C=C1)C1CCC(CO)O1	1999.5	Standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one	NC1=NC(=O)N(C=C1)C1CCC(CO)O1	2298.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CCC(CO[Si](C)(C)C)O2)C=C1	2222.9	Semi standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CCC(CO[Si](C)(C)C)O2)C=C1	2284.9	Standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CCC(CO[Si](C)(C)C)O2)C=C1	2924.0	Standard polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N(C2CCC(CO)O2)C=C1)[Si](C)(C)C	2229.3	Semi standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N(C2CCC(CO)O2)C=C1)[Si](C)(C)C	2368.7	Standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N(C2CCC(CO)O2)C=C1)[Si](C)(C)C	2985.5	Standard polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,3TMS,isomer #1	C[Si](C)(C)OCC1CCC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O1	2212.0	Semi standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,3TMS,isomer #1	C[Si](C)(C)OCC1CCC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O1	2380.7	Standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,3TMS,isomer #1	C[Si](C)(C)OCC1CCC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O1	2618.5	Standard polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CCC(CO[Si](C)(C)C(C)(C)C)O2)C=C1	2670.5	Semi standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CCC(CO[Si](C)(C)C(C)(C)C)O2)C=C1	2712.3	Standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CCC(CO[Si](C)(C)C(C)(C)C)O2)C=C1	3030.4	Standard polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(C2CCC(CO)O2)C=C1)[Si](C)(C)C(C)(C)C	2665.9	Semi standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(C2CCC(CO)O2)C=C1)[Si](C)(C)C(C)(C)C	2808.3	Standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(C2CCC(CO)O2)C=C1)[Si](C)(C)C(C)(C)C	3030.5	Standard polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CCC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O1	2857.5	Semi standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CCC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O1	3012.9	Standard non polar	33892256
4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CCC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O1	2875.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-005c-9600000000-2b4de4867a39d5e3055b	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	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

5516

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5718

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 4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one (HMDB0255802)

MOL for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

3D MOL for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

3D SDF for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

3D-SDF for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

PDB for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

3D PDB for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

SMILES for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

INCHI for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

Structure for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

3D Structure for HMDB0255802 (4-Amino-1-[5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

NMR Spectra