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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-05-22 14:17:42 UTC

Update Date

2021-09-14 15:46:08 UTC

HMDB ID

HMDB0002224

Secondary Accession Numbers

HMDB02224

Metabolite Identification

Common Name

5-Methyldeoxycytidine

Description

5-Methyldeoxycytidine is a dinucleotide. Methylation of cytosine-guanine dinucleotide sequences (CpG dinucleotides) catalyzed by DNA methyltransferase, particularly in the 5′-promoter regions of mammalian genes, forms 5-methyldeoxycytidine (5-mdc) whose levels may regulate gene expression. Levels of 5-mdc and the expression of nm23-H1 (an anti-metastatic gene identified in and human cancer lines) are highly correlated with human hepatoma cells with different invasion activities. DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents. The levels of 5-mdc in the urine of patients with breast cancer is not significantly different than controls. (PMID: 17044778 , 17264127 , 16799933 ).

Structure

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

HMDB0002224
     RDKit          3D
5-Methyldeoxycytidine
 32 33  0  0  0  0  0  0  0  0999 V2000
   -3.5017    1.4311    1.4289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8255    0.5205    0.4850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4804    0.6677    0.2323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7868   -0.1133   -0.6089 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5831   -0.0247   -0.9168 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3110    1.1991   -0.6282 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6455    0.6891   -0.0614 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7216    1.3700   -0.6088 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5870   -0.7608   -0.5115 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5140   -1.6361    0.2936 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8197   -1.2912   -0.0107 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2449   -1.0747   -0.2356 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5034   -1.0960   -1.2244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9377   -1.8904   -2.0410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8026   -1.2613   -0.9995 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5145   -0.4878   -0.1594 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8925   -0.6589    0.0826 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5509    1.1445    1.5571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9932    1.4839    2.4160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5058    2.4706    1.0034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9606    1.4447    0.7323 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7182   -0.2873   -2.0079 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9193    1.8984    0.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5952    1.7425   -1.5728 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6339    0.7714    1.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2383    1.8748    0.0738 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8045   -0.7851   -1.5795 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3035   -2.6853   -0.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2941   -1.5080    1.3688 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1150   -1.7084   -0.8531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5678   -0.4784   -0.6811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2256   -0.9605    1.0101 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  2  0
 16 17  1  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  6
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  6
 10 28  1  0
 10 29  1  0
 11 30  1  0
 17 31  1  0
 17 32  1  0
M  END


  Mrv0541 02231219262D          

 17 18  0  0  1  0            999 V2000
   17.9364   -6.9742    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3716   -8.4262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9868   -8.3401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8399   -5.6643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2690   -5.6643    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.5544   -4.4267    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.2690   -3.1893    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8564   -7.7589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2690   -6.4893    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.6014   -6.9742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6815   -7.7589    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.1662   -8.4262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9834   -5.2517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5544   -5.2517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9834   -4.4267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2690   -4.0143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6978   -4.0143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  1 11  1  0  0  0  0
  2  8  1  0  0  0  0
  3 12  1  0  0  0  0
  4 14  2  0  0  0  0
  9  5  1  6  0  0  0
  5 13  1  0  0  0  0
  5 14  1  0  0  0  0
  6 14  1  0  0  0  0
  6 16  2  0  0  0  0
  7 16  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
  9 10  1  0  0  0  0
 11 12  1  6  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002224

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N3O4/c1-5-3-13(10(16)12-9(5)11)8-2-6(15)7(4-14)17-8/h3,6-8,14-15H,2,4H2,1H3,(H2,11,12,16)/t6?,7-,8-/m1/s1

> <INCHI_KEY>
LUCHPKXVUGJYGU-SPDVFEMOSA-N

> <FORMULA>
C10H15N3O4

> <MOLECULAR_WEIGHT>
241.2438

> <EXACT_MASS>
241.106255983

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
23.341430172428066

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.71

> <JCHEM_LOGP>
-1.5013287319999995

> <ALOGPS_LOGS>
-1.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.787549172762255

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.894901399805956

> <JCHEM_PKA_STRONGEST_BASIC>
0.4056210110378124

> <JCHEM_POLAR_SURFACE_AREA>
108.37999999999998

> <JCHEM_REFRACTIVITY>
57.3912

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0002224
     RDKit          3D
5-Methyldeoxycytidine
 32 33  0  0  0  0  0  0  0  0999 V2000
   -3.5017    1.4311    1.4289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8255    0.5205    0.4850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4804    0.6677    0.2323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7868   -0.1133   -0.6089 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5831   -0.0247   -0.9168 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3110    1.1991   -0.6282 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6455    0.6891   -0.0614 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7216    1.3700   -0.6088 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5870   -0.7608   -0.5115 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5140   -1.6361    0.2936 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8197   -1.2912   -0.0107 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2449   -1.0747   -0.2356 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5034   -1.0960   -1.2244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9377   -1.8904   -2.0410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8026   -1.2613   -0.9995 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5145   -0.4878   -0.1594 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8925   -0.6589    0.0826 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5509    1.1445    1.5571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9932    1.4839    2.4160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5058    2.4706    1.0034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9606    1.4447    0.7323 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7182   -0.2873   -2.0079 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9193    1.8984    0.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5952    1.7425   -1.5728 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6339    0.7714    1.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2383    1.8748    0.0738 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8045   -0.7851   -1.5795 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3035   -2.6853   -0.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2941   -1.5080    1.3688 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1150   -1.7084   -0.8531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5678   -0.4784   -0.6811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2256   -0.9605    1.0101 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  2  0
 16 17  1  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  6
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  6
 10 28  1  0
 10 29  1  0
 11 30  1  0
 17 31  1  0
 17 32  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      33.481 -13.019   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      30.560 -15.729   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      35.442 -15.568   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      29.568 -10.573   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      32.235 -10.573   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      30.902  -8.263   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      32.235  -5.953   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      31.465 -14.483   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      32.235 -12.113   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      30.989 -13.019   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      33.005 -14.483   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      33.910 -15.729   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.569  -9.803   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      30.902  -9.803   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      33.569  -8.263   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      32.235  -7.493   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      34.903  -7.493   0.000  0.00  0.00           C+0
CONECT    1    9   11                                                       
CONECT    2    8                                                            
CONECT    3   12                                                            
CONECT    4   14                                                            
CONECT    5    9   13   14                                                  
CONECT    6   14   16                                                       
CONECT    7   16                                                            
CONECT    8    2   10   11                                                  
CONECT    9    1    5   10                                                  
CONECT   10    8    9                                                       
CONECT   11    1    8   12                                                  
CONECT   12    3   11                                                       
CONECT   13    5   15                                                       
CONECT   14    4    5    6                                                  
CONECT   15   13   16   17                                                  
CONECT   16    6    7   15                                                  
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0002224
HETATM    1  C1  UNL     1      -3.502   1.431   1.429  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.826   0.520   0.485  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.480   0.668   0.232  1.00  0.00           C  
HETATM    4  N1  UNL     1      -0.787  -0.113  -0.609  1.00  0.00           N  
HETATM    5  C4  UNL     1       0.583  -0.025  -0.917  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.311   1.199  -0.628  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.646   0.689  -0.061  1.00  0.00           C  
HETATM    8  O1  UNL     1       3.722   1.370  -0.609  1.00  0.00           O  
HETATM    9  C7  UNL     1       2.587  -0.761  -0.512  1.00  0.00           C  
HETATM   10  C8  UNL     1       3.514  -1.636   0.294  1.00  0.00           C  
HETATM   11  O2  UNL     1       4.820  -1.291  -0.011  1.00  0.00           O  
HETATM   12  O3  UNL     1       1.245  -1.075  -0.236  1.00  0.00           O  
HETATM   13  C9  UNL     1      -1.503  -1.096  -1.224  1.00  0.00           C  
HETATM   14  O4  UNL     1      -0.938  -1.890  -2.041  1.00  0.00           O  
HETATM   15  N2  UNL     1      -2.803  -1.261  -0.999  1.00  0.00           N  
HETATM   16  C10 UNL     1      -3.514  -0.488  -0.159  1.00  0.00           C  
HETATM   17  N3  UNL     1      -4.893  -0.659   0.083  1.00  0.00           N  
HETATM   18  H1  UNL     1      -4.551   1.144   1.557  1.00  0.00           H  
HETATM   19  H2  UNL     1      -2.993   1.484   2.416  1.00  0.00           H  
HETATM   20  H3  UNL     1      -3.506   2.471   1.003  1.00  0.00           H  
HETATM   21  H4  UNL     1      -0.961   1.445   0.732  1.00  0.00           H  
HETATM   22  H5  UNL     1       0.718  -0.287  -2.008  1.00  0.00           H  
HETATM   23  H6  UNL     1       0.919   1.898   0.093  1.00  0.00           H  
HETATM   24  H7  UNL     1       1.595   1.742  -1.573  1.00  0.00           H  
HETATM   25  H8  UNL     1       2.634   0.771   1.060  1.00  0.00           H  
HETATM   26  H9  UNL     1       4.238   1.875   0.074  1.00  0.00           H  
HETATM   27  H10 UNL     1       2.804  -0.785  -1.579  1.00  0.00           H  
HETATM   28  H11 UNL     1       3.303  -2.685  -0.000  1.00  0.00           H  
HETATM   29  H12 UNL     1       3.294  -1.508   1.369  1.00  0.00           H  
HETATM   30  H13 UNL     1       5.115  -1.708  -0.853  1.00  0.00           H  
HETATM   31  H14 UNL     1      -5.568  -0.478  -0.681  1.00  0.00           H  
HETATM   32  H15 UNL     1      -5.226  -0.961   1.010  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
CONECT   13   14   14   15
CONECT   15   16   16
CONECT   16   17
CONECT   17   31   32
END

HMDB0002224
     RDKit          3D
5-Methyldeoxycytidine
 32 33  0  0  0  0  0  0  0  0999 V2000
   -3.5017    1.4311    1.4289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8255    0.5205    0.4850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4804    0.6677    0.2323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7868   -0.1133   -0.6089 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5831   -0.0247   -0.9168 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3110    1.1991   -0.6282 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6455    0.6891   -0.0614 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7216    1.3700   -0.6088 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5870   -0.7608   -0.5115 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5140   -1.6361    0.2936 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8197   -1.2912   -0.0107 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2449   -1.0747   -0.2356 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5034   -1.0960   -1.2244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9377   -1.8904   -2.0410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8026   -1.2613   -0.9995 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5145   -0.4878   -0.1594 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8925   -0.6589    0.0826 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5509    1.1445    1.5571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9932    1.4839    2.4160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5058    2.4706    1.0034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9606    1.4447    0.7323 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7182   -0.2873   -2.0079 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9193    1.8984    0.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5952    1.7425   -1.5728 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6339    0.7714    1.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2383    1.8748    0.0738 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8045   -0.7851   -1.5795 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3035   -2.6853   -0.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2941   -1.5080    1.3688 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1150   -1.7084   -0.8531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5678   -0.4784   -0.6811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2256   -0.9605    1.0101 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  2  0
 16 17  1  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  6
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  9 27  1  6
 10 28  1  0
 10 29  1  0
 11 30  1  0
 17 31  1  0
 17 32  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2'-Deoxy-5-methylcytidine	HMDB
5-Methyl-2'-deoxycytidine	HMDB
5-Methyldeoxycytidine	MeSH

Chemical Formula

C₁₀H₁₅N₃O₄

Average Molecular Weight

241.2438

Monoisotopic Molecular Weight

241.106255983

IUPAC Name

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

Traditional Name

4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one

CAS Registry Number

838-07-3

SMILES

CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N

InChI Identifier

InChI=1S/C10H15N3O4/c1-5-3-13(10(16)12-9(5)11)8-2-6(15)7(4-14)17-8/h3,6-8,14-15H,2,4H2,1H3,(H2,11,12,16)/t6?,7-,8-/m1/s1

InChI Key

LUCHPKXVUGJYGU-SPDVFEMOSA-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
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Endogenous (HMDB: HMDB0002224)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

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
Water Solubility	10.8 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-1.5	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	0.41	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	108.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	57.39 m³·mol⁻¹	ChemAxon
Polarizability	23.34 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
DarkChem	[M+H]+	153.797	31661259
DarkChem	[M-H]-	150.143	31661259
DeepCCS	[M+H]+	152.969	30932474
DeepCCS	[M-H]-	150.573	30932474
DeepCCS	[M-2H]-	184.474	30932474
DeepCCS	[M+Na]+	159.488	30932474
AllCCS	[M+H]+	155.3	32859911
AllCCS	[M+H-H2O]+	151.5	32859911
AllCCS	[M+NH4]+	158.8	32859911
AllCCS	[M+Na]+	159.8	32859911
AllCCS	[M-H]-	154.8	32859911
AllCCS	[M+Na-2H]-	155.0	32859911
AllCCS	[M+HCOO]-	155.2	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	1.79 minutes	32390414
Predicted by Siyang on May 30, 2022	9.2369 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.44 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	72.3 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	539.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	220.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	82.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	155.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	59.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	283.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	256.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	433.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	600.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	90.0 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	775.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	166.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	181.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	495.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	281.1 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	166.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Methyldeoxycytidine	CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N	3657.4	Standard polar	33892256
5-Methyldeoxycytidine	CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N	2261.1	Standard non polar	33892256
5-Methyldeoxycytidine	CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N	2550.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Methyldeoxycytidine,1TMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO)O2)C(=O)N=C1N	2372.6	Semi standard non polar	33892256
5-Methyldeoxycytidine,1TMS,isomer #2	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N	2370.9	Semi standard non polar	33892256
5-Methyldeoxycytidine,1TMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N[Si](C)(C)C	2447.6	Semi standard non polar	33892256
5-Methyldeoxycytidine,2TMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N	2359.3	Semi standard non polar	33892256
5-Methyldeoxycytidine,2TMS,isomer #2	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO)O2)C(=O)N=C1N[Si](C)(C)C	2423.7	Semi standard non polar	33892256
5-Methyldeoxycytidine,2TMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N[Si](C)(C)C	2416.2	Semi standard non polar	33892256
5-Methyldeoxycytidine,2TMS,isomer #4	CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2403.0	Semi standard non polar	33892256
5-Methyldeoxycytidine,3TMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N[Si](C)(C)C	2389.1	Semi standard non polar	33892256
5-Methyldeoxycytidine,3TMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N[Si](C)(C)C	2439.6	Standard non polar	33892256
5-Methyldeoxycytidine,3TMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N[Si](C)(C)C	3063.2	Standard polar	33892256
5-Methyldeoxycytidine,3TMS,isomer #2	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2402.4	Semi standard non polar	33892256
5-Methyldeoxycytidine,3TMS,isomer #2	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2558.8	Standard non polar	33892256
5-Methyldeoxycytidine,3TMS,isomer #2	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	3040.8	Standard polar	33892256
5-Methyldeoxycytidine,3TMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2409.1	Semi standard non polar	33892256
5-Methyldeoxycytidine,3TMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2542.8	Standard non polar	33892256
5-Methyldeoxycytidine,3TMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2964.9	Standard polar	33892256
5-Methyldeoxycytidine,4TMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2412.8	Semi standard non polar	33892256
5-Methyldeoxycytidine,4TMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2555.8	Standard non polar	33892256
5-Methyldeoxycytidine,4TMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C)[Si](C)(C)C	2732.7	Standard polar	33892256
5-Methyldeoxycytidine,1TBDMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C(=O)N=C1N	2639.0	Semi standard non polar	33892256
5-Methyldeoxycytidine,1TBDMS,isomer #2	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N	2647.5	Semi standard non polar	33892256
5-Methyldeoxycytidine,1TBDMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N[Si](C)(C)C(C)(C)C	2677.9	Semi standard non polar	33892256
5-Methyldeoxycytidine,2TBDMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N	2835.7	Semi standard non polar	33892256
5-Methyldeoxycytidine,2TBDMS,isomer #2	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C(=O)N=C1N[Si](C)(C)C(C)(C)C	2862.6	Semi standard non polar	33892256
5-Methyldeoxycytidine,2TBDMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N[Si](C)(C)C(C)(C)C	2861.7	Semi standard non polar	33892256
5-Methyldeoxycytidine,2TBDMS,isomer #4	CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2839.6	Semi standard non polar	33892256
5-Methyldeoxycytidine,3TBDMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N[Si](C)(C)C(C)(C)C	3065.0	Semi standard non polar	33892256
5-Methyldeoxycytidine,3TBDMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N[Si](C)(C)C(C)(C)C	3084.9	Standard non polar	33892256
5-Methyldeoxycytidine,3TBDMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N[Si](C)(C)C(C)(C)C	3246.9	Standard polar	33892256
5-Methyldeoxycytidine,3TBDMS,isomer #2	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3071.5	Semi standard non polar	33892256
5-Methyldeoxycytidine,3TBDMS,isomer #2	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3176.5	Standard non polar	33892256
5-Methyldeoxycytidine,3TBDMS,isomer #2	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3196.8	Standard polar	33892256
5-Methyldeoxycytidine,3TBDMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3064.0	Semi standard non polar	33892256
5-Methyldeoxycytidine,3TBDMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3164.1	Standard non polar	33892256
5-Methyldeoxycytidine,3TBDMS,isomer #3	CC1=CN([C@H]2CC(O)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3161.7	Standard polar	33892256
5-Methyldeoxycytidine,4TBDMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3265.6	Semi standard non polar	33892256
5-Methyldeoxycytidine,4TBDMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3326.9	Standard non polar	33892256
5-Methyldeoxycytidine,4TBDMS,isomer #1	CC1=CN([C@H]2CC(O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3087.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methyldeoxycytidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9420000000-4af773e99af76af961ea	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methyldeoxycytidine GC-MS (2 TMS) - 70eV, Positive	splash10-0006-9014000000-1fd11a88c9a0762a6b1d	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methyldeoxycytidine 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 - 5-Methyldeoxycytidine 10V, Positive-QTOF	splash10-004i-0900000000-d1d23649ec4fa9201eba	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 20V, Positive-QTOF	splash10-004i-2900000000-d21a1bb287e1d523b6c2	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 40V, Positive-QTOF	splash10-004i-3900000000-b4f3cca0a164fdbc5031	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 10V, Negative-QTOF	splash10-0a4j-0920000000-6aa55dc948aac874e1a0	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 20V, Negative-QTOF	splash10-0uk9-2920000000-6d51e08eb5820a748902	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 40V, Negative-QTOF	splash10-007p-9400000000-77fb64e0199129096777	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 10V, Negative-QTOF	splash10-00dl-0970000000-a011cf5a5c3613811717	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 20V, Negative-QTOF	splash10-00dl-9600000000-ee60e868c938ff348f09	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 40V, Negative-QTOF	splash10-006y-9500000000-81204e67016c197ad16f	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 10V, Positive-QTOF	splash10-004i-0900000000-a1c51dd1d9ae2dee6e38	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 20V, Positive-QTOF	splash10-00b9-2900000000-7c9c6f54bbfba0acc135	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methyldeoxycytidine 40V, Positive-QTOF	splash10-0059-6900000000-9559671d86d852719546	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	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

FDB022917

KNApSAcK ID

Not Available

Chemspider ID

12719

KEGG Compound ID

C03592

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13279

PDB ID

Not Available

ChEBI ID

27964

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Vorbrueggen, Helmut; Krolikiewicz, Konrad. 2'-Deoxy-5-methylcytidine: Amination of thymidine. Nucleic Acid Chem. (1978), 1 227-9.

Material Safety Data Sheet (MSDS)

Not Available

General References

Cho SH, Jung BH, Lee SH, Lee WY, Kong G, Chung BC: Direct determination of nucleosides in the urine of patients with breast cancer using column-switching liquid chromatography-tandem mass spectrometry. Biomed Chromatogr. 2006 Nov;20(11):1229-36. [PubMed:16799933 ]
Yang TH, Hu ML: Intracellular levels of S-adenosylhomocysteine but not homocysteine are highly correlated to the expression of nm23-H1 and the level of 5-methyldeoxycytidine in human hepatoma cells with different invasion activities. Nutr Cancer. 2006;55(2):224-31. [PubMed:17044778 ]
Liu Z, Liu S, Xie Z, Blum W, Perrotti D, Paschka P, Klisovic R, Byrd J, Chan KK, Marcucci G: Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method. Nucleic Acids Res. 2007;35(5):e31. Epub 2007 Jan 30. [PubMed:17264127 ]

Showing metabocard for 5-Methyldeoxycytidine (HMDB0002224)

MOL for HMDB0002224 (5-Methyldeoxycytidine)

3D MOL for HMDB0002224 (5-Methyldeoxycytidine)

3D SDF for HMDB0002224 (5-Methyldeoxycytidine)

3D-SDF for HMDB0002224 (5-Methyldeoxycytidine)

PDB for HMDB0002224 (5-Methyldeoxycytidine)

3D PDB for HMDB0002224 (5-Methyldeoxycytidine)

SMILES for HMDB0002224 (5-Methyldeoxycytidine)

INCHI for HMDB0002224 (5-Methyldeoxycytidine)

Structure for HMDB0002224 (5-Methyldeoxycytidine)

3D Structure for HMDB0002224 (5-Methyldeoxycytidine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra