MiMeDB: Showing metabocard for 2'-Deoxycytidine 5'-phosphate (MMDBc0057214)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-11-10 21:48:40 UTC

Update Date

2022-12-15 22:52:23 UTC

Metabolite ID

MMDBc0057214

Metabolite Identification

Common Name

2'-Deoxycytidine 5'-phosphate

Description

dCMP, also known as deoxycytidylate, 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. dCMP is an extremely weak basic (essentially neutral) compound (based on its pKa). 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 into dCDP; which is mediated by the enzyme UMP-CMP kinase 2, mitochondrial. In addition, dCMP can be converted into deoxycytidine; which is mediated 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 tronchuda cabbages, american cranberries, common oregano, longans, and soy beans. This could make dCMP a potential biomarker for the consumption of these foods. A pyrimidine 2'-deoxyribonucleoside 5'-monophosphate having cytosine as the nucleobase.

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>
MMDBc0057214

> <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

Not Available

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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9410000000-f31bf162f5f972b9cf42	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-03dm-9522000000-d25b21eb547d23c4886d	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-0900000000-01bb64efeca205daaf6e	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-1900000000-13c56ec900e188e10ddb	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-03di-5900000000-4e6dd8fdc8a4142269a2	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-004j-9402000000-6a9e4b2e32058773f6bf	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, negative	splash10-0006-9000000000-3b4572f2c8e51186f7e5	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-bc40821757dbbe57a7c2	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1900000000-9052cfbf31794c457d3b	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-004j-9400000000-1f2a185e05aed001e983	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-5209000000-b46ae8ade9397163198a	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-004j-9300000000-c6505ac4fafc2bc54910	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-2d1a73d09ad4b06da15f	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-03fr-3910000000-ee0cc0c7897818415edc	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-2900000000-7e33f3b263e35a18c2e0	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-03dj-9400000000-4ab96ba8107b5f1820a6	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3900000000-56a3ecce668ff56b702c	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0900000000-986f256cdcdf8c8d2f9f	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0006-9000000000-d236c094fbaf8d2136b4	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-dd904e0c162b36055113	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-4cc5b5143e38514f3010	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-3b0a0a6948a49378ff1c	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-a901f489d4e9b8516bf2	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-6900000000-d9e59981c244792a2f76	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a6r-9367000000-d5c1062e5203ec9699d4	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9110000000-20768d2b834097ac11d7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-29f2d493f3f68928488b	2016-09-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Lysosome
Mitochondria
Nucleus

Biospecimen Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0026021	2'-Deoxycytidine 5'-phosphate	2'-Deoxycytidine 5'-diphosphate	Deoxynucleotide monophosphate kinase	Phosphorylation	RHEA	34755880
MMDBr0026076	2'-Deoxycytidine 5'-phosphate	Deoxycytidine	5'-nucleotidase SurE 1	Hydrolysis of nucleotide	RHEA	34755880
MMDBr0026090	Deoxycytidine 5'-triphosphate	2'-Deoxycytidine 5'-phosphate	Nucleoside triphosphate pyrophosphatase	Purine metabolism and pyrimidine metabolism; Hydrolysis of pyrophosphate; Dephosphorylation	RHEA	34755880
MMDBr0026094	Deoxycytidine 5'-triphosphate	2'-Deoxycytidine 5'-phosphate	Inosine triphosphate pyrophosphatase	Purine metabolism and pyrimidine metabolism	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

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

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

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 2'-Deoxycytidine 5'-phosphate (MMDBc0057214)

MOL for #<Metabolite:0x000055d24b0019a0>

3D MOL for #<Metabolite:0x000055d24b0019a0>

3D SDF for #<Metabolite:0x000055d24b0019a0>

3D-SDF for #<Metabolite:0x000055d24b0019a0>

PDB for #<Metabolite:0x000055d24b0019a0>

3D PDB for #<Metabolite:0x000055d24b0019a0>

SMILES for #<Metabolite:0x000055d24b0019a0>

INCHI for #<Metabolite:0x000055d24b0019a0>

Structure for #<Metabolite:0x000055d24b0019a0>

3D Structure for #<Metabolite:0x000055d24b0019a0>