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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-08-27 00:45:33 UTC

Update Date

2021-09-14 15:19:35 UTC

HMDB ID

HMDB0242131

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one

Description

1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. Based on a literature review very few articles have been published on 1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one.

Structure

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

HMDB0242131
     RDKit          3D
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methyl...
 33 34  0  0  0  0  0  0  0  0999 V2000
    4.1832   -0.0743    0.8808 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1092    0.1388   -0.0691 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3991    0.4470   -1.3372 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6316    0.5626   -1.7484 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3515    0.6438   -2.2183 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0579    0.5113   -1.7404 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7888    0.2006   -0.4608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5265    0.0646    0.0304 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4687    0.8472   -0.6037 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7028    0.2848   -0.4395 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7246    1.2266    0.1463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8837    2.3292   -0.6899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5433   -0.9687    0.3946 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4218   -1.9203   -0.0600 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0966   -1.3213    0.0220 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1837   -1.8845   -1.2296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8275    0.0143    0.3759 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6405   -0.2767    1.5781 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7661    0.8749    0.9387 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8272   -0.9323    0.5407 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7879   -0.3803    1.8682 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8055    0.8035   -2.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5123    0.8978   -3.2678 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1968    0.6513   -2.3736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5271    0.3918    1.1109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0597   -0.0419   -1.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3415    1.5914    1.1121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7135    0.7344    0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3932    3.0126   -0.1542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6297   -0.7675    1.4771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0035   -2.8050   -0.2321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6889   -1.9873    0.7938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9765   -2.8685   -1.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17  2  1  0
 15  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  8 25  1  1
 10 26  1  6
 11 27  1  0
 11 28  1  0
 12 29  1  0
 13 30  1  1
 14 31  1  0
 15 32  1  1
 16 33  1  0
M  END


  Mrv1652308272102552D          

 22 23  0  0  1  0            999 V2000
   -0.2721   -2.4936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5477    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0161    0.3129    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -1.1299    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7132   -2.0662    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  5  4  1  1  0  0  0
  6  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 11  6  2  0  0  0  0
 12  1  1  0  0  0  0
 12  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13  3  1  0  0  0  0
  9 13  1  6  0  0  0
 13 10  1  0  0  0  0
 14  4  1  0  0  0  0
  7 15  1  6  0  0  0
  8 16  1  6  0  0  0
 17 10  2  0  0  0  0
 18  5  1  0  0  0  0
 18  9  1  0  0  0  0
  5 19  1  6  0  0  0
  7 20  1  1  0  0  0
  8 21  1  1  0  0  0
  9 22  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0242131

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@]1(CO)O[C@]([H])(N2C=CC(=N)N(C)C2=O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N3O5/c1-12-6(11)2-3-13(10(12)17)9-8(16)7(15)5(4-14)18-9/h2-3,5,7-9,11,14-16H,4H2,1H3/t5-,7-,8-,9+/m1/s1

> <INCHI_KEY>
RDPUKVRQKWBSPK-YYNOVJQHSA-N

> <FORMULA>
C10H15N3O5

> <MOLECULAR_WEIGHT>
257.246

> <EXACT_MASS>
257.101170595

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
24.339117329607667

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methyl-1,2,3,4-tetrahydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.71

> <JCHEM_LOGP>
-1.817037896

> <ALOGPS_LOGS>
-1.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.933965309537061

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.55383331073508

> <JCHEM_PKA_STRONGEST_BASIC>
-0.017893755025646274

> <JCHEM_POLAR_SURFACE_AREA>
117.32000000000001

> <JCHEM_REFRACTIVITY>
69.9343

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.43e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0242131
     RDKit          3D
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methyl...
 33 34  0  0  0  0  0  0  0  0999 V2000
    4.1832   -0.0743    0.8808 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1092    0.1388   -0.0691 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3991    0.4470   -1.3372 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6316    0.5626   -1.7484 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3515    0.6438   -2.2183 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0579    0.5113   -1.7404 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7888    0.2006   -0.4608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5265    0.0646    0.0304 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4687    0.8472   -0.6037 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7028    0.2848   -0.4395 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7246    1.2266    0.1463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8837    2.3292   -0.6899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5433   -0.9687    0.3946 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4218   -1.9203   -0.0600 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0966   -1.3213    0.0220 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1837   -1.8845   -1.2296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8275    0.0143    0.3759 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6405   -0.2767    1.5781 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7661    0.8749    0.9387 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8272   -0.9323    0.5407 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7879   -0.3803    1.8682 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8055    0.8035   -2.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5123    0.8978   -3.2678 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1968    0.6513   -2.3736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5271    0.3918    1.1109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0597   -0.0419   -1.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3415    1.5914    1.1121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7135    0.7344    0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3932    3.0126   -0.1542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6297   -0.7675    1.4771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0035   -2.8050   -0.2321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6889   -1.9873    0.7938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9765   -2.8685   -1.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17  2  1  0
 15  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  8 25  1  1
 10 26  1  6
 11 27  1  0
 11 28  1  0
 12 29  1  0
 13 30  1  1
 14 31  1  0
 15 32  1  1
 16 33  1  0
M  END

HEADER    PROTEIN                                 27-AUG-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-AUG-21         0                                  
HETATM    1  C   UNK     0      -0.508  -4.655   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.182  -6.383   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.087  -5.138   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.846  -0.544   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.650  -6.222   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.929  -3.570   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.745  -7.468   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       1.024  -4.816   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       3.460  -3.731   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       8.166   0.962   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       5.136   1.425   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.425  -0.544   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.302  -2.163   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       5.906  -2.485   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       6.622   0.501   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.763   0.584   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       2.801  -2.109   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       5.065  -3.857   0.000  0.00  0.00           H+0
CONECT    1   12                                                            
CONECT    2    3    6                                                       
CONECT    3    2   13                                                       
CONECT    4    5   14                                                       
CONECT    5    4    7   18   19                                             
CONECT    6    2   11   12                                                  
CONECT    7    5    8   15   20                                             
CONECT    8    7    9   16   21                                             
CONECT    9    8   13   18   22                                             
CONECT   10   12   13   17                                                  
CONECT   11    6                                                            
CONECT   12    1    6   10                                                  
CONECT   13    3    9   10                                                  
CONECT   14    4                                                            
CONECT   15    7                                                            
CONECT   16    8                                                            
CONECT   17   10                                                            
CONECT   18    5    9                                                       
CONECT   19    5                                                            
CONECT   20    7                                                            
CONECT   21    8                                                            
CONECT   22    9                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

COMPND    HMDB0242131
HETATM    1  C1  UNL     1       4.183  -0.074   0.881  1.00  0.00           C  
HETATM    2  N1  UNL     1       3.109   0.139  -0.069  1.00  0.00           N  
HETATM    3  C2  UNL     1       3.399   0.447  -1.337  1.00  0.00           C  
HETATM    4  N2  UNL     1       4.632   0.563  -1.748  1.00  0.00           N  
HETATM    5  C3  UNL     1       2.351   0.644  -2.218  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.058   0.511  -1.740  1.00  0.00           C  
HETATM    7  N3  UNL     1       0.789   0.201  -0.461  1.00  0.00           N  
HETATM    8  C5  UNL     1      -0.527   0.065   0.030  1.00  0.00           C  
HETATM    9  O1  UNL     1      -1.469   0.847  -0.604  1.00  0.00           O  
HETATM   10  C6  UNL     1      -2.703   0.285  -0.440  1.00  0.00           C  
HETATM   11  C7  UNL     1      -3.725   1.227   0.146  1.00  0.00           C  
HETATM   12  O2  UNL     1      -3.884   2.329  -0.690  1.00  0.00           O  
HETATM   13  C8  UNL     1      -2.543  -0.969   0.395  1.00  0.00           C  
HETATM   14  O3  UNL     1      -3.422  -1.920  -0.060  1.00  0.00           O  
HETATM   15  C9  UNL     1      -1.097  -1.321   0.022  1.00  0.00           C  
HETATM   16  O4  UNL     1      -1.184  -1.884  -1.230  1.00  0.00           O  
HETATM   17  C10 UNL     1       1.828   0.014   0.376  1.00  0.00           C  
HETATM   18  O5  UNL     1       1.640  -0.277   1.578  1.00  0.00           O  
HETATM   19  H1  UNL     1       4.766   0.875   0.939  1.00  0.00           H  
HETATM   20  H2  UNL     1       4.827  -0.932   0.541  1.00  0.00           H  
HETATM   21  H3  UNL     1       3.788  -0.380   1.868  1.00  0.00           H  
HETATM   22  H4  UNL     1       4.806   0.804  -2.743  1.00  0.00           H  
HETATM   23  H5  UNL     1       2.512   0.898  -3.268  1.00  0.00           H  
HETATM   24  H6  UNL     1       0.197   0.651  -2.374  1.00  0.00           H  
HETATM   25  H7  UNL     1      -0.527   0.392   1.111  1.00  0.00           H  
HETATM   26  H8  UNL     1      -3.060  -0.042  -1.454  1.00  0.00           H  
HETATM   27  H9  UNL     1      -3.341   1.591   1.112  1.00  0.00           H  
HETATM   28  H10 UNL     1      -4.713   0.734   0.220  1.00  0.00           H  
HETATM   29  H11 UNL     1      -4.393   3.013  -0.154  1.00  0.00           H  
HETATM   30  H12 UNL     1      -2.630  -0.767   1.477  1.00  0.00           H  
HETATM   31  H13 UNL     1      -3.003  -2.805  -0.232  1.00  0.00           H  
HETATM   32  H14 UNL     1      -0.689  -1.987   0.794  1.00  0.00           H  
HETATM   33  H15 UNL     1      -0.977  -2.869  -1.135  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3   17
CONECT    3    4    4    5
CONECT    4   22
CONECT    5    6    6   23
CONECT    6    7   24
CONECT    7    8   17
CONECT    8    9   15   25
CONECT    9   10
CONECT   10   11   13   26
CONECT   11   12   27   28
CONECT   12   29
CONECT   13   14   15   30
CONECT   14   31
CONECT   15   16   32
CONECT   16   33
CONECT   17   18   18
END

HMDB0242131
     RDKit          3D
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methyl...
 33 34  0  0  0  0  0  0  0  0999 V2000
    4.1832   -0.0743    0.8808 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1092    0.1388   -0.0691 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3991    0.4470   -1.3372 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6316    0.5626   -1.7484 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3515    0.6438   -2.2183 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0579    0.5113   -1.7404 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7888    0.2006   -0.4608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5265    0.0646    0.0304 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4687    0.8472   -0.6037 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7028    0.2848   -0.4395 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7246    1.2266    0.1463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8837    2.3292   -0.6899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5433   -0.9687    0.3946 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4218   -1.9203   -0.0600 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0966   -1.3213    0.0220 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1837   -1.8845   -1.2296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8275    0.0143    0.3759 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6405   -0.2767    1.5781 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7661    0.8749    0.9387 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8272   -0.9323    0.5407 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7879   -0.3803    1.8682 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8055    0.8035   -2.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5123    0.8978   -3.2678 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1968    0.6513   -2.3736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5271    0.3918    1.1109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0597   -0.0419   -1.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3415    1.5914    1.1121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7135    0.7344    0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3932    3.0126   -0.1542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6297   -0.7675    1.4771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0035   -2.8050   -0.2321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6889   -1.9873    0.7938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9765   -2.8685   -1.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17  2  1  0
 15  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  8 25  1  1
 10 26  1  6
 11 27  1  0
 11 28  1  0
 12 29  1  0
 13 30  1  1
 14 31  1  0
 15 32  1  1
 16 33  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₁₅N₃O₅

Average Molecular Weight

257.246

Monoisotopic Molecular Weight

257.101170595

IUPAC Name

1-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methyl-1,2,3,4-tetrahydropyrimidin-2-one

Traditional Name

1-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one

CAS Registry Number

Not Available

SMILES

[H][C@]1(CO)O[C@]([H])(N2C=CC(=N)N(C)C2=O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C10H15N3O5/c1-12-6(11)2-3-13(10(12)17)9-8(16)7(15)5(4-14)18-9/h2-3,5,7-9,11,14-16H,4H2,1H3/t5-,7-,8-,9+/m1/s1

InChI Key

RDPUKVRQKWBSPK-YYNOVJQHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Urea
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Not Available

Not Available

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	-1.7	ALOGPS
logP	-1.8	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	-0.018	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	117.32 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	69.93 m³·mol⁻¹	ChemAxon
Polarizability	24.34 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]+	160.579	30932474
DeepCCS	[M-H]-	158.194	30932474
DeepCCS	[M-2H]-	193.395	30932474
DeepCCS	[M+Na]+	169.03	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one	[H][C@]1(CO)O[C@]([H])(N2C=CC(=N)N(C)C2=O)[C@]([H])(O)[C@]1([H])O	3789.1	Standard polar	33892256
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one	[H][C@]1(CO)O[C@]([H])(N2C=CC(=N)N(C)C2=O)[C@]([H])(O)[C@]1([H])O	2299.5	Standard non polar	33892256
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one	[H][C@]1(CO)O[C@]([H])(N2C=CC(=N)N(C)C2=O)[C@]([H])(O)[C@]1([H])O	2543.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one,4TMS,isomer #1	CN1C(=N[Si](C)(C)C)C=CN([C@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O	2412.3	Semi standard non polar	33892256
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one,4TMS,isomer #1	CN1C(=N[Si](C)(C)C)C=CN([C@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O	2647.9	Standard non polar	33892256
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one,4TMS,isomer #1	CN1C(=N[Si](C)(C)C)C=CN([C@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C1=O	2895.3	Standard polar	33892256
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one,4TBDMS,isomer #1	CN1C(=N[Si](C)(C)C(C)(C)C)C=CN([C@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C1=O	3299.8	Semi standard non polar	33892256
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one,4TBDMS,isomer #1	CN1C(=N[Si](C)(C)C(C)(C)C)C=CN([C@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C1=O	3395.1	Standard non polar	33892256
1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one,4TBDMS,isomer #1	CN1C(=N[Si](C)(C)C(C)(C)C)C=CN([C@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C1=O	3256.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-0abc-9410000000-54a6d66a129aba98d330	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one 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-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one 10V, Positive-QTOF	splash10-004i-0900000000-df3f72a3679ceae847f1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one 20V, Positive-QTOF	splash10-004j-9700000000-5dcd13d6e856f8b32ec2	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one 40V, Positive-QTOF	splash10-057i-9800000000-13a0cef8b136ecae6aba	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one 10V, Negative-QTOF	splash10-05fu-6920000000-9d4e90067e3c2435846e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one 20V, Negative-QTOF	splash10-0007-9200000000-4902f649b54484346566	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one 40V, Negative-QTOF	splash10-0006-9000000000-d55c8f98b65c6082f0c3	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

30988560

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

159649

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

Kong SW, Hernandez-Ferrer C: Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2020;25:587-598. [PubMed:31797630 ]

Showing metabocard for 1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one (HMDB0242131)

MOL for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

3D MOL for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

3D SDF for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

3D-SDF for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

PDB for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

3D PDB for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

SMILES for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

INCHI for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

Structure for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

3D Structure for HMDB0242131 (1-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-3-methylpyrimidin-2-one)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra