MiMeDB: Showing metabocard for dCMP (MMDBc0000564)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:40:38 UTC

Update Date

2024-10-11 01:30:05 UTC

Metabolite ID

MMDBc0000564

Metabolite Identification

Common Name

dCMP

Description

Deoxycytidine monophosphate (dCMP), also known as deoxycytidylic acid or deoxycytidylate in its conjugate acid and conjugate base forms, respectively, is a deoxynucleotide, and one of the four monomers that make up DNA. In a DNA double helix, it will base pair with deoxyguanosine monophosphate. dCMP belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. Deficiency of the enzyme deoxycytidine kinase (EC2.7.1.74) is associated with resistance to antiviral and anticancer chemotherapeutic agents, whereas increased enzyme activity is associated with increased activation of these compounds to cytotoxic nucleoside triphosphate derivatives. dCMP exists in all living species, ranging from bacteria to humans. Within humans, dCMP participates in a number of enzymatic reactions. In particular, dCMP can be converted to dCDP by the enzyme UMP-CMP kinase 2. In addition, dCMP can be converted into deoxycytidine, which is catalyzed by the enzyme cytosolic purine 5'-nucleotidase. In humans, dCMP is involved in the metabolic disorder called ump synthase deficiency (orotic aciduria). Outside of the human body, dCMP has been detected, but not quantified in several different foods, such as turnips, garlics, agaves, garden onions, and italian sweet red peppers. dCMP is a deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions.

Structure

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

HMDB0001202
     RDKit          3D
dCMP
 34 35  0  0  0  0  0  0  0  0999 V2000
   -6.2543    0.4625   -0.0519 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8559    0.3069    0.1421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3413   -0.9517    0.3871 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9832   -1.0889    0.5734 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1276   -0.0523    0.5285 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7351   -0.3059    0.7359 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2759   -1.3639   -0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2291   -1.0765   -0.3069 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9375   -2.1202    0.3039 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3590    0.1787    0.5280 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4284    1.0973   -0.0194 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6491    0.4377    0.1475 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9385    1.3574   -0.4254 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.5186    2.7400   -0.8471 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0800    1.4996    0.8348 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6915    0.6261   -1.7428 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0832    0.7551    0.4060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6534    1.1652    0.2880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8411    2.1395    0.2468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9846    1.3351    0.1003 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6669    0.8178   -0.9427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9573    0.2250    0.7014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0189   -1.8191    0.4294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5988   -2.0928    0.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4809   -0.6265    1.7636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4909   -2.3822    0.0793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7094   -1.0966   -1.2345 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5742   -0.9238   -1.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3112   -2.8992    0.3209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5192   -0.0280    1.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4309    2.0404    0.5246 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2191    1.3210   -1.0812 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1018    0.6591    1.3759 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9043   -0.3367   -1.5669 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  2  0
 17  6  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  6
  9 29  1  0
 10 30  1  1
 11 31  1  0
 11 32  1  0
 15 33  1  0
 16 34  1  0
M  END


  Mrv1652309042000192D          

 20 21  0  0  1  0            999 V2000
    1.3231    0.3051    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5347    0.0480    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9401   -0.2434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4946    1.1106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1063    0.5176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2948   -0.7576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7252    0.0171    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7756   -1.0455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2727    1.3711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7747    0.0274    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5313   -0.7576    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8931    0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5597    0.2811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0180   -1.4157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6747    1.0798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1664   -0.2708    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9857   -0.2708    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9891   -1.0901    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8049   -0.2708    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9891    0.5484    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  2  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  6 11  1  0  0  0  0
  7 12  2  0  0  0  0
 10 13  1  1  0  0  0
 11 14  1  6  0  0  0
 12 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 17 20  2  0  0  0  0
  9 12  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000564

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

> <INCHI_KEY>
NCMVOABPESMRCP-SHYZEUOFSA-N

> <FORMULA>
C9H14N3O7P

> <MOLECULAR_WEIGHT>
307.1971

> <EXACT_MASS>
307.056936329

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.195129069085244

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.13

> <JCHEM_LOGP>
-2.283034970573228

> <ALOGPS_LOGS>
-1.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.2585739758421095

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.279165528098246

> <JCHEM_PKA_STRONGEST_BASIC>
0.16099958039925

> <JCHEM_POLAR_SURFACE_AREA>
154.91

> <JCHEM_REFRACTIVITY>
63.907000000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.09e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dCMP

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001202
     RDKit          3D
dCMP
 34 35  0  0  0  0  0  0  0  0999 V2000
   -6.2543    0.4625   -0.0519 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8559    0.3069    0.1421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3413   -0.9517    0.3871 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9832   -1.0889    0.5734 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1276   -0.0523    0.5285 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7351   -0.3059    0.7359 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2759   -1.3639   -0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2291   -1.0765   -0.3069 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9375   -2.1202    0.3039 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3590    0.1787    0.5280 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4284    1.0973   -0.0194 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6491    0.4377    0.1475 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9385    1.3574   -0.4254 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.5186    2.7400   -0.8471 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0800    1.4996    0.8348 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6915    0.6261   -1.7428 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0832    0.7551    0.4060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6534    1.1652    0.2880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8411    2.1395    0.2468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9846    1.3351    0.1003 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6669    0.8178   -0.9427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9573    0.2250    0.7014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0189   -1.8191    0.4294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5988   -2.0928    0.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4809   -0.6265    1.7636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4909   -2.3822    0.0793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7094   -1.0966   -1.2345 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5742   -0.9238   -1.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3112   -2.8992    0.3209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5192   -0.0280    1.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4309    2.0404    0.5246 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2191    1.3210   -1.0812 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1018    0.6591    1.3759 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9043   -0.3367   -1.5669 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  2  0
 17  6  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  6
  9 29  1  0
 10 30  1  1
 11 31  1  0
 11 32  1  0
 15 33  1  0
 16 34  1  0
M  END

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       2.470   0.570   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.998   0.090   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.622  -0.454   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.790   2.073   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.198   0.966   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.550  -1.414   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       5.087   0.032   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       3.314  -1.952   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.242   2.559   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.446   0.051   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.992  -1.414   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.400   1.536   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.911   0.525   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.900  -2.643   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       6.859   2.016   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      -4.044  -0.505   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0      -5.573  -0.505   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      -5.580  -2.035   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -7.102  -0.505   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -5.580   1.024   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10                                                       
CONECT    6    2   11                                                       
CONECT    7    3   12                                                       
CONECT    8    3                                                            
CONECT    9    4   12                                                       
CONECT   10    5   13   11                                                  
CONECT   11    6   14   10                                                  
CONECT   12    7   15    9                                                  
CONECT   13   10   16                                                       
CONECT   14   11                                                            
CONECT   15   12                                                            
CONECT   16   13   17                                                       
CONECT   17   16   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

COMPND    HMDB0001202
HETATM    1  N1  UNL     1      -6.254   0.463  -0.052  1.00  0.00           N  
HETATM    2  C1  UNL     1      -4.856   0.307   0.142  1.00  0.00           C  
HETATM    3  C2  UNL     1      -4.341  -0.952   0.387  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.983  -1.089   0.573  1.00  0.00           C  
HETATM    5  N2  UNL     1      -2.128  -0.052   0.528  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.735  -0.306   0.736  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.276  -1.364  -0.271  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.229  -1.076  -0.307  1.00  0.00           C  
HETATM    9  O1  UNL     1       1.938  -2.120   0.304  1.00  0.00           O  
HETATM   10  C7  UNL     1       1.359   0.179   0.528  1.00  0.00           C  
HETATM   11  C8  UNL     1       2.428   1.097  -0.019  1.00  0.00           C  
HETATM   12  O2  UNL     1       3.649   0.438   0.148  1.00  0.00           O  
HETATM   13  P1  UNL     1       4.938   1.357  -0.425  1.00  0.00           P  
HETATM   14  O3  UNL     1       4.519   2.740  -0.847  1.00  0.00           O  
HETATM   15  O4  UNL     1       6.080   1.500   0.835  1.00  0.00           O  
HETATM   16  O5  UNL     1       5.691   0.626  -1.743  1.00  0.00           O  
HETATM   17  O6  UNL     1       0.083   0.755   0.406  1.00  0.00           O  
HETATM   18  C9  UNL     1      -2.653   1.165   0.288  1.00  0.00           C  
HETATM   19  O7  UNL     1      -1.841   2.139   0.247  1.00  0.00           O  
HETATM   20  N3  UNL     1      -3.985   1.335   0.100  1.00  0.00           N  
HETATM   21  H1  UNL     1      -6.667   0.818  -0.943  1.00  0.00           H  
HETATM   22  H2  UNL     1      -6.957   0.225   0.701  1.00  0.00           H  
HETATM   23  H3  UNL     1      -5.019  -1.819   0.429  1.00  0.00           H  
HETATM   24  H4  UNL     1      -2.599  -2.093   0.766  1.00  0.00           H  
HETATM   25  H5  UNL     1      -0.481  -0.626   1.764  1.00  0.00           H  
HETATM   26  H6  UNL     1      -0.491  -2.382   0.079  1.00  0.00           H  
HETATM   27  H7  UNL     1      -0.709  -1.097  -1.235  1.00  0.00           H  
HETATM   28  H8  UNL     1       1.574  -0.924  -1.340  1.00  0.00           H  
HETATM   29  H9  UNL     1       1.311  -2.899   0.321  1.00  0.00           H  
HETATM   30  H10 UNL     1       1.519  -0.028   1.598  1.00  0.00           H  
HETATM   31  H11 UNL     1       2.431   2.040   0.525  1.00  0.00           H  
HETATM   32  H12 UNL     1       2.219   1.321  -1.081  1.00  0.00           H  
HETATM   33  H13 UNL     1       6.102   0.659   1.376  1.00  0.00           H  
HETATM   34  H14 UNL     1       5.904  -0.337  -1.567  1.00  0.00           H  
CONECT    1    2   21   22
CONECT    2    3   20   20
CONECT    3    4    4   23
CONECT    4    5   24
CONECT    5    6   18
CONECT    6    7   17   25
CONECT    7    8   26   27
CONECT    8    9   10   28
CONECT    9   29
CONECT   10   11   17   30
CONECT   11   12   31   32
CONECT   12   13
CONECT   13   14   14   15   16
CONECT   15   33
CONECT   16   34
CONECT   18   19   19   20
END

HMDB0001202
     RDKit          3D
dCMP
 34 35  0  0  0  0  0  0  0  0999 V2000
   -6.2543    0.4625   -0.0519 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8559    0.3069    0.1421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3413   -0.9517    0.3871 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9832   -1.0889    0.5734 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1276   -0.0523    0.5285 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7351   -0.3059    0.7359 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2759   -1.3639   -0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2291   -1.0765   -0.3069 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9375   -2.1202    0.3039 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3590    0.1787    0.5280 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4284    1.0973   -0.0194 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6491    0.4377    0.1475 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9385    1.3574   -0.4254 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.5186    2.7400   -0.8471 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0800    1.4996    0.8348 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6915    0.6261   -1.7428 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0832    0.7551    0.4060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6534    1.1652    0.2880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8411    2.1395    0.2468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9846    1.3351    0.1003 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6669    0.8178   -0.9427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9573    0.2250    0.7014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0189   -1.8191    0.4294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5988   -2.0928    0.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4809   -0.6265    1.7636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4909   -2.3822    0.0793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7094   -1.0966   -1.2345 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5742   -0.9238   -1.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3112   -2.8992    0.3209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5192   -0.0280    1.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4309    2.0404    0.5246 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2191    1.3210   -1.0812 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1018    0.6591    1.3759 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9043   -0.3367   -1.5669 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  2  0
 17  6  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  6
  9 29  1  0
 10 30  1  1
 11 31  1  0
 11 32  1  0
 15 33  1  0
 16 34  1  0
M  END

Synonyms

Value	Source
2'-Deoxycytidine 5'-monophosphate	ChEBI
2'-DEOXYCYTIDINE-5'-monophosphATE	ChEBI
Deoxycytidine monophosphate	ChEBI
Deoxycytidylate	ChEBI
Deoxycytidylic acid	ChEBI
2'-Deoxycytidine 5'-monophosphoric acid	Generator
2'-DEOXYCYTIDINE-5'-monophosphoric acid	Generator
Deoxycytidine monophosphoric acid	Generator
2'-Deoxycytosine 5'-monophosphate	HMDB
2'-Deoxycytosine 5'-monophosphoric acid	HMDB
2'-Deoxycytidine-3'-monophosphate	HMDB
2'-Deoxycytidine-5'-monophosphorate	HMDB
2'-Deoxycytidine-5'-phosphate	HMDB
Deoxycytidine-phosphate	HMDB
Acid, deoxycytidylic	HMDB
Deoxycytidylic acids	HMDB
Acids, deoxycytidylic	HMDB
monoPhosphate, deoxycytidine	HMDB

Molecular Formula

C₉H₁₄N₃O₇P

Average Mass

307.1971

Monoisotopic Mass

307.056936329

IUPAC Name

{[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

dCMP

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1

InChI Identifier

InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

InChI Key

NCMVOABPESMRCP-SHYZEUOFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine deoxyribonucleotides

Direct Parent

Pyrimidine 2'-deoxyribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside monophosphate
Aminopyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Imidolactam
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Primary amine
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Alcohol
Amine
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

2'-deoxycytidine phosphate (CHEBI:15918 )
pyrimidine 2'-deoxyribonucleoside 5'-monophosphate (CHEBI:15918 )
Deoxyribonucleotides (C00239 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	10.9 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-2.3	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.28	ChemAxon
pKa (Strongest Basic)	0.16	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	154.91 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	63.91 m³·mol⁻¹	ChemAxon
Polarizability	26.2 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

Spectra

Not Available

Biological Properties

Cellular Locations

Lysosome
Mitochondria
Nucleus

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191677	5'-nucleotidase	Unknown	P21589	Homo sapiens
MMDBp0191678	Deoxycytidylate deaminase	Unknown	P32321	Homo sapiens
MMDBp0191679	UMP-CMP kinase	Unknown	P30085	Homo sapiens
MMDBp0191680	Cytosolic 5'-nucleotidase 1B	Unknown	Q96P26	Homo sapiens
MMDBp0191681	Cytosolic 5'-nucleotidase 1A	Unknown	Q9BXI3	Homo sapiens
MMDBp0191682	5'(3')-deoxyribonucleotidase, cytosolic type	Unknown	Q8TCD5	Homo sapiens
MMDBp0191683	Deoxycytidine kinase	Enzyme	P27707	Homo sapiens
MMDBp0191684	5'(3')-deoxyribonucleotidase, mitochondrial	Unknown	Q9NPB1	Homo sapiens
MMDBp0193860	Cytosolic 5'-nucleotidase 3	Enzyme	Q9H0P0	Homo sapiens
MMDBp0193932	Cytosolic purine 5'-nucleotidase	Unknown	P49902	Homo sapiens
MMDBp0194184	UMP-CMP kinase 2, mitochondrial	Enzyme	Q5EBM0	Homo sapiens
MMDBp0196729	dCTP pyrophosphatase 1	Unknown	Q9H773

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0024645	Deoxycytidine	dCMP	Deoxyadenosine/deoxycytidine kinase	Phosphorylation	RHEA	34755880
MMDBr0026053	Deoxycytidine	Uridine 5'-diphosphate	Deoxyadenosine/deoxycytidine kinase	Phosphorylation	RHEA	34755880
MMDBr0026054	Deoxycytidine	Uridine 5'-diphosphate	Deoxyadenosine/deoxycytidine kinase	Phosphorylation	RHEA	34755880
MMDBr0026055	Deoxycytidine	dCMP	Deoxyadenosine/deoxycytidine kinase	Phosphorylation	RHEA	34755880
MMDBr0026056	Deoxycytidine	Guanosine 3',5'-bis(diphosphate)	Deoxyadenosine/deoxycytidine kinase	Phosphorylation	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Actinobacteria	126	Human ; Human feces; Human saliva; Human supragingival plaque; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human mucosa; Human subgingival plaque; Cattle	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	460	Human ; Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool; Catfish	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Archaea	Euryarchaeota	1	Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Proteobacteria	390	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Rat ; Sheep ; Chicken ; American dog tick	Metabolic reconstruction
Bacteria	Actinobacteria	15	Human ; Human feces; Human saliva; Human supragingival plaque; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human mucosa; Human subgingival plaque; Cattle	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	131	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	28	Human ; Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool; Catfish	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	11	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Rat ; Sheep ; Chicken ; American dog tick	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	13	Human feces; Human ; Relapsing fever tick	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	23	Human feces; Goat ; Human ; Pig	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Viruses/Heunggongvirae	Uroviricota	5
Eukaryota/Fungi	Ascomycota	3	Human feces; Human saliva	Unknown
Archaea/Archaea	Crenarchaeota	17		Metabolic reconstruction
Bacteria/Eubacteria	Aquificae	2
Archaea/Archaea	Euryarchaeota	34		Metabolic reconstruction
Bacteria/Eubacteria	Chlamydiae	10	Human ; Sheep ; Cat
Bacteria/Eubacteria	Chloroflexi	3
Bacteria/Eubacteria	Chlorobi	3
Bacteria/Eubacteria	Deinococcus-thermus	5
Eukaryota/Fungi	Microsporidia	3
Bacteria/Eubacteria	Thermotogae	8
Bacteria	Tenericutes	1	Human feces; Goat ; Human ; Pig	Metabolic reconstruction
Bacteria/Eubacteria	Acidobacteria	1
Bacteria/Eubacteria	Nitrospirae	1
Bacteria/Eubacteria	Cyanobacteria	26
Bacteria	nah	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0001202

DrugBank ID

DB03798

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022488

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

15918

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Zegers BJ, Stoop JW, Staal GE, Wadman SK: An approach to the restoration of T cell function in a purine nucleoside phosphorylase deficient patient. Ciba Found Symp. 1978;(68):231-53. doi: 10.1002/9780470720516.ch15. [PubMed:115663 ]
Dientsbier Z, Buric L, Bechyne M, Kovarikova H, Foltynova V, Mostecky H: Deoxypyrimidineuria in the course of chemotherapy in M. Hodgkin. Neoplasma. 1976;23(6):645-65. [PubMed:1004661 ]
Broder S: Pharmacodynamics of 2',3'-dideoxycytidine: an inhibitor of human immunodeficiency virus. Am J Med. 1990 May 21;88(5B):2S-7S. doi: 10.1016/0002-9343(90)90413-8. [PubMed:1692446 ]
Abbruzzese JL, Grunewald R, Weeks EA, Gravel D, Adams T, Nowak B, Mineishi S, Tarassoff P, Satterlee W, Raber MN, et al.: A phase I clinical, plasma, and cellular pharmacology study of gemcitabine. J Clin Oncol. 1991 Mar;9(3):491-8. doi: 10.1200/JCO.1991.9.3.491. [PubMed:1999720 ]
Mills GC, Schmalstieg FC, Goldblum RM: Urinary excretion of modified purines and nucleosides in immunodeficient children. Biochem Med. 1985 Aug;34(1):37-51. doi: 10.1016/0006-2944(85)90060-2. [PubMed:4052062 ]
Shejbal J, Arient M, Kovarikova H: Estimation of deoxycytidine in the urine of humans and laboratory animals. Clin Chim Acta. 1967 May;16(2):324-5. doi: 10.1016/0009-8981(67)90199-4. [PubMed:4962141 ]
Chen IW, Kereiakes JG, Friedman BI, Saenger EL: Colorimetric analysis of deoxycytidine in urine after separation by ion-exchange column chromatography. Anal Biochem. 1968 May;23(2):230-40. doi: 10.1016/0003-2697(68)90354-0. [PubMed:5657794 ]
Arient M, Dienstbier Z, Shejbal J: The post-irradiation excretion of deoxycytidine by urine in man. Minerva Fisiconucl. 1966;10(1):57-60. [PubMed:5956823 ]
Itoh K, Aida S, Ishiwata S, Yamaguchi T, Ishida N, Mizugaki M: Immunochemical detection of urinary 5-methyl-2'-deoxycytidine as a potential biologic marker for leukemia. Clin Chim Acta. 1995 Jan 31;234(1-2):37-45. doi: 10.1016/0009-8981(94)05986-3. [PubMed:7758221 ]
Mazurets AF, Kubyshkin VF, Dziuba MV: [The cytochemical characteristics of the blood polymorphonuclear leukocytes in dilated cardiomyopathy and an inflammatory myocardial lesion]. Lik Sprava. 1994 Jul-Aug;(7-8):109-12. [PubMed:7900329 ]
Lebedev PA: [Selenium deficiency in patients with cardiovascular diseases and its correction with the drug "selena"]. Patol Fiziol Eksp Ter. 1996 Jul-Sep;(3):5-7. [PubMed:8966057 ]
Zambonin CG, Palmisano F: Electrospray ionization mass spectrometry of 5-methyl-2'-deoxycytidine and its determination in urine by liquid chromatography/electrospray ionization tandem mass spectrometry. Rapid Commun Mass Spectrom. 1999;13(21):2160-5. doi: 10.1002/(SICI)1097-0231(19991115)13:21<2160::AID-RCM768>3.0.CO;2-D. [PubMed:10523775 ]
Zambonin CG, Aresta A, Palmisano F, Specchia G, Liso V: Liquid chromatographic determination of urinary 5-methyl-2'-deoxycytidine and pseudouridine as potential biological markers for leukaemia. J Pharm Biomed Anal. 1999 Dec;21(5):1045-51. doi: 10.1016/s0731-7085(99)00221-6. [PubMed:10703973 ]
Masuda N, Matsui K, Yamamoto N, Nogami T, Nakagawa K, Negoro S, Takeda K, Takifuji N, Yamada M, Kudoh S, Okuda T, Nemoto S, Ogawa K, Myobudani H, Nihira S, Fukuoka M: Phase I trial of oral 2'-deoxy-2'-methylidenecytidine: on a daily x 14-day schedule. Clin Cancer Res. 2000 Jun;6(6):2288-94. [PubMed:10873079 ]
Chen HJ, Lin TC, Hong CL, Chiang LC: Analysis of 3,N(4)-ethenocytosine in DNA and in human urine by isotope dilution gas chromatography/negative ion chemical ionization/mass spectrometry. Chem Res Toxicol. 2001 Dec;14(12):1612-9. doi: 10.1021/tx015551x. [PubMed:11743744 ]
de Bono JS, Stephenson J Jr, Baker SD, Hidalgo M, Patnaik A, Hammond LA, Weiss G, Goetz A, Siu L, Simmons C, Jolivet J, Rowinsky EK: Troxacitabine, an L-stereoisomeric nucleoside analog, on a five-times-daily schedule: a phase I and pharmacokinetic study in patients with advanced solid malignancies. J Clin Oncol. 2002 Jan 1;20(1):96-109. doi: 10.1200/JCO.2002.20.1.96. [PubMed:11773159 ]
Dudley E, Lemiere F, Van Dongen W, Langridge JI, El-Sharkawi S, Games DE, Esmans EL, Newton RP: Analysis of urinary nucleosides. III. Identification of 5'-deoxycytidine in urine of a patient with head and neck cancer. Rapid Commun Mass Spectrom. 2003;17(11):1132-6. doi: 10.1002/rcm.1034. [PubMed:12772268 ]
Sottani C, Zucchetti M, Zaffaroni M, Bettinelli M, Minoia C: Validated procedure for simultaneous trace level determination of the anti-cancer agent gemcitabine and its metabolite in human urine by high-performance liquid chromatography with tandem mass spectrometry. Rapid Commun Mass Spectrom. 2004;18(10):1017-23. doi: 10.1002/rcm.1436. [PubMed:15150823 ]
Chen HJ, Wu CF, Hong CL, Chang CM: Urinary excretion of 3,N4-etheno-2'-deoxycytidine in humans as a biomarker of oxidative stress: association with cigarette smoking. Chem Res Toxicol. 2004 Jul;17(7):896-903. doi: 10.1021/tx0342013. [PubMed:15257614 ]
Tuma P, Samcova E, Kvasnicova V: Improved detection limit for a direct determination of 8-hydroxy-2'-deoxyguanosine in untreated urine samples by capillary electrophoresis with optical detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Dec 25;813(1-2):255-61. doi: 10.1016/j.jchromb.2004.09.049. [PubMed:15556541 ]

Showing metabocard for dCMP (MMDBc0000564)

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3D PDB for #<Metabolite:0x00005645ca156f60>

SMILES for #<Metabolite:0x00005645ca156f60>

INCHI for #<Metabolite:0x00005645ca156f60>

Structure for #<Metabolite:0x00005645ca156f60>

3D Structure for #<Metabolite:0x00005645ca156f60>