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 18:47:29 UTC

Update Date

2021-09-26 23:14:17 UTC

HMDB ID

HMDB0257735

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione

Description

1-[4-(azidooxy)-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-methyl-1,2-dihydropyrimidin-2-one belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Based on a literature review very few articles have been published on 1-[4-(azidooxy)-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-methyl-1,2-dihydropyrimidin-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-[(2r,5r)-4-azidooxy-5-(hydroxymethyl)oxolan-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,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-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

HMDB0257735
     RDKit          3D
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione
 33 34  0  0  0  0  0  0  0  0999 V2000
   -3.8498    1.6542   -0.0831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2136    0.3013   -0.0329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8464    0.2035   -0.2006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2133   -0.9843   -0.1661 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2341   -0.9807   -0.3542 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9590   -0.7569    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3115   -0.2861    0.4147 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0681   -1.3902   -0.0595 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3446   -1.5294    0.4221 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1968   -0.6400    0.2511 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.8031    0.4384    0.2474 N   0  0  0  0  0  2  0  0  0  0  0  0
    1.8629    0.4904   -0.8015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7403    1.9505   -0.3525 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0243    2.3698    0.0238 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6380    0.0268   -1.1810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9212   -2.1016    0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3273   -3.2225    0.0684 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2635   -2.0453    0.2040 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9252   -0.8525    0.1727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1793   -0.7884    0.3290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4279    2.2260    0.7860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9408    1.5368   -0.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5233    2.1730   -1.0127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2905    1.1385   -0.3644 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5206   -2.0044   -0.7024 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5037    0.1249    1.4375 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0369   -1.6410    1.5793 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8471    0.3384    1.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6448    0.4386   -1.5773 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1113    2.0141    0.5550 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2947    2.5803   -1.1319 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6165    2.1248   -0.7399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8363   -2.9071    0.3628 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
  8  9  1  0
  9 10  2  0
 10 11  2  0
  7 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  1  0
  4 16  1  0
 16 17  2  0
 16 18  1  0
 18 19  1  0
 19 20  2  0
 19  2  1  0
 15  5  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 18 33  1  0
M  CHG  2  10   1  11  -1
M  END


  Mrv1652309112120472D          

 20 21  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
   -3.0401    0.4394    0.0000 O   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
   -0.7604   -0.4005    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2754   -1.0679    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.2095   -1.7354    0.0000 N   0  5  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
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  2  0  0  0  0
M  CHG  2  19   1  20  -1
M  END
> <DATABASE_ID>
HMDB0257735

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN(C2CC(ON=[N+]=[N-])C(CO)O2)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O5/c1-5-3-15(10(18)12-9(5)17)8-2-6(20-14-13-11)7(4-16)19-8/h3,6-8,16H,2,4H2,1H3,(H,12,17,18)

> <INCHI_KEY>
WSYJDFJOPVQYLZ-UHFFFAOYSA-N

> <FORMULA>
C10H13N5O5

> <MOLECULAR_WEIGHT>
283.244

> <EXACT_MASS>
283.091668539

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
26.32246861116485

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-[4-(azidooxy)-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-0.06

> <JCHEM_LOGP>
0.28628335333333377

> <ALOGPS_LOGS>
-1.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.587814176770394

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.96031474681949

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9806231823224154

> <JCHEM_POLAR_SURFACE_AREA>
117.53

> <JCHEM_REFRACTIVITY>
65.0689

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.28e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[4-(azidooxy)-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-3H-pyrimidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0257735
     RDKit          3D
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione
 33 34  0  0  0  0  0  0  0  0999 V2000
   -3.8498    1.6542   -0.0831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2136    0.3013   -0.0329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8464    0.2035   -0.2006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2133   -0.9843   -0.1661 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2341   -0.9807   -0.3542 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9590   -0.7569    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3115   -0.2861    0.4147 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0681   -1.3902   -0.0595 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3446   -1.5294    0.4221 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1968   -0.6400    0.2511 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.8031    0.4384    0.2474 N   0  0  0  0  0  2  0  0  0  0  0  0
    1.8629    0.4904   -0.8015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7403    1.9505   -0.3525 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0243    2.3698    0.0238 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6380    0.0268   -1.1810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9212   -2.1016    0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3273   -3.2225    0.0684 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2635   -2.0453    0.2040 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9252   -0.8525    0.1727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1793   -0.7884    0.3290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4279    2.2260    0.7860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9408    1.5368   -0.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5233    2.1730   -1.0127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2905    1.1385   -0.3644 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5206   -2.0044   -0.7024 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5037    0.1249    1.4375 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0369   -1.6410    1.5793 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8471    0.3384    1.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6448    0.4386   -1.5773 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1113    2.0141    0.5550 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2947    2.5803   -1.1319 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6165    2.1248   -0.7399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8363   -2.9071    0.3628 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
  8  9  1  0
  9 10  2  0
 10 11  2  0
  7 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  1  0
  4 16  1  0
 16 17  2  0
 16 18  1  0
 18 19  1  0
 19 20  2  0
 19  2  1  0
 15  5  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 18 33  1  0
M  CHG  2  10   1  11  -1
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  O   UNK     0      -5.675   0.820   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -0.793   0.659   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0      -1.419  -0.748   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0      -0.514  -1.993   0.000  0.00  0.00           N+1
HETATM   20  N   UNK     0       0.391  -3.239   0.000  0.00  0.00           N-1
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   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

COMPND    HMDB0257735
HETATM    1  C1  UNL     1      -3.850   1.654  -0.083  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.214   0.301  -0.033  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.846   0.204  -0.201  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.213  -0.984  -0.166  1.00  0.00           N  
HETATM    5  C4  UNL     1       0.234  -0.981  -0.354  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.959  -0.757   0.956  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.312  -0.286   0.415  1.00  0.00           C  
HETATM    8  O1  UNL     1       3.068  -1.390  -0.059  1.00  0.00           O  
HETATM    9  N2  UNL     1       4.345  -1.529   0.422  1.00  0.00           N  
HETATM   10  N3  UNL     1       5.197  -0.640   0.251  1.00  0.00           N1+
HETATM   11  N4  UNL     1       5.803   0.438   0.247  1.00  0.00           N1-
HETATM   12  C7  UNL     1       1.863   0.490  -0.802  1.00  0.00           C  
HETATM   13  C8  UNL     1       1.740   1.950  -0.352  1.00  0.00           C  
HETATM   14  O2  UNL     1       3.024   2.370   0.024  1.00  0.00           O  
HETATM   15  O3  UNL     1       0.638   0.027  -1.181  1.00  0.00           O  
HETATM   16  C9  UNL     1      -1.921  -2.102   0.035  1.00  0.00           C  
HETATM   17  O4  UNL     1      -1.327  -3.223   0.068  1.00  0.00           O  
HETATM   18  N5  UNL     1      -3.263  -2.045   0.204  1.00  0.00           N  
HETATM   19  C10 UNL     1      -3.925  -0.852   0.173  1.00  0.00           C  
HETATM   20  O5  UNL     1      -5.179  -0.788   0.329  1.00  0.00           O  
HETATM   21  H1  UNL     1      -3.428   2.226   0.786  1.00  0.00           H  
HETATM   22  H2  UNL     1      -4.941   1.537  -0.030  1.00  0.00           H  
HETATM   23  H3  UNL     1      -3.523   2.173  -1.013  1.00  0.00           H  
HETATM   24  H4  UNL     1      -1.290   1.139  -0.364  1.00  0.00           H  
HETATM   25  H5  UNL     1       0.521  -2.004  -0.702  1.00  0.00           H  
HETATM   26  H6  UNL     1       0.504   0.125   1.438  1.00  0.00           H  
HETATM   27  H7  UNL     1       1.037  -1.641   1.579  1.00  0.00           H  
HETATM   28  H8  UNL     1       2.847   0.338   1.125  1.00  0.00           H  
HETATM   29  H9  UNL     1       2.645   0.439  -1.577  1.00  0.00           H  
HETATM   30  H10 UNL     1       1.111   2.014   0.555  1.00  0.00           H  
HETATM   31  H11 UNL     1       1.295   2.580  -1.132  1.00  0.00           H  
HETATM   32  H12 UNL     1       3.616   2.125  -0.740  1.00  0.00           H  
HETATM   33  H13 UNL     1      -3.836  -2.907   0.363  1.00  0.00           H  
CONECT    1    2   21   22   23
CONECT    2    3    3   19
CONECT    3    4   24
CONECT    4    5   16
CONECT    5    6   15   25
CONECT    6    7   26   27
CONECT    7    8   12   28
CONECT    8    9
CONECT    9   10   10
CONECT   10   11   11
CONECT   12   13   15   29
CONECT   13   14   30   31
CONECT   14   32
CONECT   16   17   17   18
CONECT   18   19   33
CONECT   19   20   20
END

HMDB0257735
     RDKit          3D
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione
 33 34  0  0  0  0  0  0  0  0999 V2000
   -3.8498    1.6542   -0.0831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2136    0.3013   -0.0329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8464    0.2035   -0.2006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2133   -0.9843   -0.1661 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2341   -0.9807   -0.3542 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9590   -0.7569    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3115   -0.2861    0.4147 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0681   -1.3902   -0.0595 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3446   -1.5294    0.4221 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1968   -0.6400    0.2511 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.8031    0.4384    0.2474 N   0  0  0  0  0  2  0  0  0  0  0  0
    1.8629    0.4904   -0.8015 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7403    1.9505   -0.3525 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0243    2.3698    0.0238 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6380    0.0268   -1.1810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9212   -2.1016    0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3273   -3.2225    0.0684 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2635   -2.0453    0.2040 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9252   -0.8525    0.1727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1793   -0.7884    0.3290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4279    2.2260    0.7860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9408    1.5368   -0.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5233    2.1730   -1.0127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2905    1.1385   -0.3644 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5206   -2.0044   -0.7024 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5037    0.1249    1.4375 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0369   -1.6410    1.5793 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8471    0.3384    1.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6448    0.4386   -1.5773 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1113    2.0141    0.5550 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2947    2.5803   -1.1319 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6165    2.1248   -0.7399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8363   -2.9071    0.3628 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
  8  9  1  0
  9 10  2  0
 10 11  2  0
  7 12  1  0
 12 13  1  0
 13 14  1  0
 12 15  1  0
  4 16  1  0
 16 17  2  0
 16 18  1  0
 18 19  1  0
 19 20  2  0
 19  2  1  0
 15  5  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 18 33  1  0
M  CHG  2  10   1  11  -1
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₁₃N₅O₅

Average Molecular Weight

283.244

Monoisotopic Molecular Weight

283.091668539

IUPAC Name

1-[4-(azidooxy)-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

1-[4-(azidooxy)-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-3H-pyrimidine-2,4-dione

CAS Registry Number

Not Available

SMILES

CC1=CN(C2CC(ON=[N+]=[N-])C(CO)O2)C(=O)NC1=O

InChI Identifier

InChI=1S/C10H13N5O5/c1-5-3-15(10(18)12-9(5)17)8-2-6(20-14-13-11)7(4-16)19-8/h3,6-8,16H,2,4H2,1H3,(H,12,17,18)

InChI Key

WSYJDFJOPVQYLZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Pyrimidone
Pyrimidine
Hydropyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Urea
Organic azide
Lactam
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic zwitterion
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
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)

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	-0.06	ALOGPS
logP	0.29	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	9.96	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	117.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	65.07 m³·mol⁻¹	ChemAxon
Polarizability	26.32 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	161.678	30932474
DeepCCS	[M-H]-	159.32	30932474
DeepCCS	[M-2H]-	192.206	30932474
DeepCCS	[M+Na]+	167.772	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione	CC1=CN(C2CC(ON=[N+]=[N-])C(CO)O2)C(=O)NC1=O	3625.4	Standard polar	33892256
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione	CC1=CN(C2CC(ON=[N+]=[N-])C(CO)O2)C(=O)NC1=O	2289.0	Standard non polar	33892256
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione	CC1=CN(C2CC(ON=[N+]=[N-])C(CO)O2)C(=O)NC1=O	2486.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #1	CC1=CN(C2CC(ON=[N+]=[N-])C(CO[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2592.8	Semi standard non polar	33892256
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #1	CC1=CN(C2CC(ON=[N+]=[N-])C(CO[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	2642.2	Standard non polar	33892256
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TMS,isomer #1	CC1=CN(C2CC(ON=[N+]=[N-])C(CO[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O	3802.2	Standard polar	33892256
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #1	CC1=CN(C2CC(ON=[N+]=[N-])C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3029.9	Semi standard non polar	33892256
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #1	CC1=CN(C2CC(ON=[N+]=[N-])C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3073.9	Standard non polar	33892256
1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione,2TBDMS,isomer #1	CC1=CN(C2CC(ON=[N+]=[N-])C(CO[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3801.2	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,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione GC-MS (Non-derivatized) - 70eV, Positive	splash10-003r-9320000000-d12c95460d934afc2106	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-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,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

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,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione (HMDB0257735)

MOL for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D MOL for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D SDF for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D-SDF for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

PDB for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D PDB for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

SMILES for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

INCHI for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

Structure for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

3D Structure for HMDB0257735 (1-[(2R,5R)-4-Azidooxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra