MiMeDB: Showing metabocard for 2'-Deoxycytidine 5'-diphosphate (MMDBc0057145)

Microbial

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-11-09 19:14:47 UTC

Update Date

2025-10-07 16:09:52 UTC

Metabolite ID

MMDBc0057145

Metabolite Identification

Common Name

2'-Deoxycytidine 5'-diphosphate

Description

2'-Deoxycytidine 5'-diphosphate is a nucleotide metabolite belonging to the class of deoxyribonucleotides, which are essential components of DNA synthesis. Its chemical structure consists of a deoxyribose sugar, a cytosine base, and two phosphate groups attached to the 5' position of the sugar. This compound plays a crucial role in the synthesis of DNA as it serves as a precursor for the formation of 2'-deoxycytidine 5'-triphosphate (dCTP), which is incorporated into DNA during replication and repair processes. The conversion of 2'-deoxycytidine 5'-diphosphate to dCTP is facilitated by the action of nucleoside diphosphate kinases. Additionally, a simple and rapid capillary electrophoretic method was developed for simultaneous determination of sub-micromolar 2'-deoxycytidine 5'-diphosphate (dCDP) and 2'-deoxycytidine 5'-triphosphate (dCTP) levels in enzyme assays without using radioactively labeled substrates, highlighting its relevance in biochemical assays and research (PMID:22212996 ).

Structure

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

HMDB0001245
     RDKit          3D
dCDP
 39 40  0  0  0  0  0  0  0  0999 V2000
    6.5890   -1.4988   -1.6142 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3577   -1.1332   -1.0326 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3710   -0.6342    0.2699 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1826   -0.2714    0.8571 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9868   -0.3791    0.2177 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8198    0.0302    0.9326 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6274    1.5172    0.7815 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1242    1.6202    0.5699 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4303    2.6222    1.3494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3240    0.2501    1.0097 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7191   -0.0782    0.5641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9076    0.0147   -0.7907 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5417   -0.3930   -1.0952 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.9768    0.0550   -2.4537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7888   -2.0509   -0.8582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4471    0.4136    0.1036 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0925    0.2396   -0.1238 P   0  0  0  0  0  5  0  0  0  0  0  0
   -6.4665    0.0817   -1.5895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8827    1.6425    0.4459 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7255   -1.0578    0.7781 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6446   -0.5666    0.4675 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0102   -0.8609   -1.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8944   -0.9628   -1.6289 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1672   -1.2302   -1.6425 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9435   -2.4747   -1.6191 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1625   -0.7493   -2.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3289   -0.5463    0.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2192    0.1127    1.8677 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9459   -0.2753    1.9933 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1951    1.9428   -0.0698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9264    1.9805    1.7615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0336    1.7818   -0.5168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3470    2.7851    1.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2679    0.2090    2.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4017    0.6419    1.0589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9803   -1.0749    0.9350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7964   -2.1883    0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2162    2.3455    0.7041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1507   -1.8605    0.7004 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
 16 17  1  0
 17 18  2  0
 17 19  1  0
 17 20  1  0
 10 21  1  0
  5 22  1  0
 22 23  2  0
 22 24  1  0
 24  2  2  0
 21  6  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  4 28  1  0
  6 29  1  1
  7 30  1  0
  7 31  1  0
  8 32  1  6
  9 33  1  0
 10 34  1  1
 11 35  1  0
 11 36  1  0
 15 37  1  0
 19 38  1  0
 20 39  1  0
M  END


  Mrv1652309042000192D          

 24 25  0  0  1  0            999 V2000
    2.1343    0.3505    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3438    0.0928    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7530   -0.1993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3062    1.1583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7011    0.5636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1032   -0.7148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5400    0.0619    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5880   -1.0036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0864    1.4194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0309    0.0722    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2750   -0.7148    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7084    0.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7561    0.3265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2131   -1.3747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4920    1.1239    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3645   -0.2268    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1859   -0.2268    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0072   -0.2268    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1893   -1.0482    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1893    0.5946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8321   -0.2234    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8356   -1.0448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6536   -0.2234    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8356    0.5980    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
 18 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 21 24  2  0  0  0  0
  9 12  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057145

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

> <INCHI_KEY>
FTDHDKPUHBLBTL-SHYZEUOFSA-N

> <FORMULA>
C9H15N3O10P2

> <MOLECULAR_WEIGHT>
387.177

> <EXACT_MASS>
387.023266739

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
30.767607896278484

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <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}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-1.48

> <JCHEM_LOGP>
-2.590131106588101

> <ALOGPS_LOGS>
-1.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2110547045641784

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7869997246775

> <JCHEM_PKA_STRONGEST_BASIC>
0.29647546987304596

> <JCHEM_POLAR_SURFACE_AREA>
201.43999999999997

> <JCHEM_REFRACTIVITY>
74.7799

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.13e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dCDP

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001245
     RDKit          3D
dCDP
 39 40  0  0  0  0  0  0  0  0999 V2000
    6.5890   -1.4988   -1.6142 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3577   -1.1332   -1.0326 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3710   -0.6342    0.2699 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1826   -0.2714    0.8571 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9868   -0.3791    0.2177 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8198    0.0302    0.9326 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6274    1.5172    0.7815 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1242    1.6202    0.5699 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4303    2.6222    1.3494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3240    0.2501    1.0097 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7191   -0.0782    0.5641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9076    0.0147   -0.7907 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5417   -0.3930   -1.0952 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.9768    0.0550   -2.4537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7888   -2.0509   -0.8582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4471    0.4136    0.1036 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0925    0.2396   -0.1238 P   0  0  0  0  0  5  0  0  0  0  0  0
   -6.4665    0.0817   -1.5895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8827    1.6425    0.4459 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7255   -1.0578    0.7781 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6446   -0.5666    0.4675 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0102   -0.8609   -1.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8944   -0.9628   -1.6289 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1672   -1.2302   -1.6425 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9435   -2.4747   -1.6191 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1625   -0.7493   -2.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3289   -0.5463    0.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2192    0.1127    1.8677 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9459   -0.2753    1.9933 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1951    1.9428   -0.0698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9264    1.9805    1.7615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0336    1.7818   -0.5168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3470    2.7851    1.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2679    0.2090    2.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4017    0.6419    1.0589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9803   -1.0749    0.9350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7964   -2.1883    0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2162    2.3455    0.7041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1507   -1.8605    0.7004 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
 16 17  1  0
 17 18  2  0
 17 19  1  0
 17 20  1  0
 10 21  1  0
  5 22  1  0
 22 23  2  0
 22 24  1  0
 24  2  2  0
 21  6  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  4 28  1  0
  6 29  1  1
  7 30  1  0
  7 31  1  0
  8 32  1  6
  9 33  1  0
 10 34  1  1
 11 35  1  0
 11 36  1  0
 15 37  1  0
 19 38  1  0
 20 39  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       3.984   0.654   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.508   0.173   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.139  -0.372   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.305   2.162   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.309   1.052   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.059  -1.334   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       6.608   0.116   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       4.831  -1.873   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       5.761   2.650   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.058   0.135   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.513  -1.334   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.922   1.623   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.411   0.609   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.398  -2.566   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       8.385   2.098   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      -2.547  -0.423   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0      -4.080  -0.423   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      -5.613  -0.423   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -4.087  -1.957   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -4.087   1.110   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0      -7.153  -0.417   0.000  0.00  0.00           P+0
HETATM   22  O   UNK     0      -7.160  -1.950   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -8.687  -0.417   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -7.160   1.116   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   21                                                       
CONECT   19   17                                                            
CONECT   20   17                                                            
CONECT   21   18   22   23   24                                             
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   21                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

COMPND    HMDB0001245
HETATM    1  N1  UNL     1       6.589  -1.499  -1.614  1.00  0.00           N  
HETATM    2  C1  UNL     1       5.358  -1.133  -1.033  1.00  0.00           C  
HETATM    3  C2  UNL     1       5.371  -0.634   0.270  1.00  0.00           C  
HETATM    4  C3  UNL     1       4.183  -0.271   0.857  1.00  0.00           C  
HETATM    5  N2  UNL     1       2.987  -0.379   0.218  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.820   0.030   0.933  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.627   1.517   0.781  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.124   1.620   0.570  1.00  0.00           C  
HETATM    9  O1  UNL     1      -0.430   2.622   1.349  1.00  0.00           O  
HETATM   10  C7  UNL     1      -0.324   0.250   1.010  1.00  0.00           C  
HETATM   11  C8  UNL     1      -1.719  -0.078   0.564  1.00  0.00           C  
HETATM   12  O2  UNL     1      -1.908   0.015  -0.791  1.00  0.00           O  
HETATM   13  P1  UNL     1      -3.542  -0.393  -1.095  1.00  0.00           P  
HETATM   14  O3  UNL     1      -3.977   0.055  -2.454  1.00  0.00           O  
HETATM   15  O4  UNL     1      -3.789  -2.051  -0.858  1.00  0.00           O  
HETATM   16  O5  UNL     1      -4.447   0.414   0.104  1.00  0.00           O  
HETATM   17  P2  UNL     1      -6.092   0.240  -0.124  1.00  0.00           P  
HETATM   18  O6  UNL     1      -6.466   0.082  -1.589  1.00  0.00           O  
HETATM   19  O7  UNL     1      -6.883   1.642   0.446  1.00  0.00           O  
HETATM   20  O8  UNL     1      -6.725  -1.058   0.778  1.00  0.00           O  
HETATM   21  O9  UNL     1       0.645  -0.567   0.468  1.00  0.00           O  
HETATM   22  C9  UNL     1       3.010  -0.861  -1.029  1.00  0.00           C  
HETATM   23  O10 UNL     1       1.894  -0.963  -1.629  1.00  0.00           O  
HETATM   24  N3  UNL     1       4.167  -1.230  -1.642  1.00  0.00           N  
HETATM   25  H1  UNL     1       6.944  -2.475  -1.619  1.00  0.00           H  
HETATM   26  H2  UNL     1       7.162  -0.749  -2.057  1.00  0.00           H  
HETATM   27  H3  UNL     1       6.329  -0.546   0.786  1.00  0.00           H  
HETATM   28  H4  UNL     1       4.219   0.113   1.868  1.00  0.00           H  
HETATM   29  H5  UNL     1       1.946  -0.275   1.993  1.00  0.00           H  
HETATM   30  H6  UNL     1       2.195   1.943  -0.070  1.00  0.00           H  
HETATM   31  H7  UNL     1       1.926   1.981   1.761  1.00  0.00           H  
HETATM   32  H8  UNL     1      -0.034   1.782  -0.517  1.00  0.00           H  
HETATM   33  H9  UNL     1      -1.347   2.785   1.010  1.00  0.00           H  
HETATM   34  H10 UNL     1      -0.268   0.209   2.104  1.00  0.00           H  
HETATM   35  H11 UNL     1      -2.402   0.642   1.059  1.00  0.00           H  
HETATM   36  H12 UNL     1      -1.980  -1.075   0.935  1.00  0.00           H  
HETATM   37  H13 UNL     1      -3.796  -2.188   0.143  1.00  0.00           H  
HETATM   38  H14 UNL     1      -6.216   2.345   0.704  1.00  0.00           H  
HETATM   39  H15 UNL     1      -6.151  -1.861   0.700  1.00  0.00           H  
CONECT    1    2   25   26
CONECT    2    3   24   24
CONECT    3    4    4   27
CONECT    4    5   28
CONECT    5    6   22
CONECT    6    7   21   29
CONECT    7    8   30   31
CONECT    8    9   10   32
CONECT    9   33
CONECT   10   11   21   34
CONECT   11   12   35   36
CONECT   12   13
CONECT   13   14   14   15   16
CONECT   15   37
CONECT   16   17
CONECT   17   18   18   19   20
CONECT   19   38
CONECT   20   39
CONECT   22   23   23   24
END

HMDB0001245
     RDKit          3D
dCDP
 39 40  0  0  0  0  0  0  0  0999 V2000
    6.5890   -1.4988   -1.6142 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3577   -1.1332   -1.0326 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3710   -0.6342    0.2699 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1826   -0.2714    0.8571 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9868   -0.3791    0.2177 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8198    0.0302    0.9326 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6274    1.5172    0.7815 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1242    1.6202    0.5699 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4303    2.6222    1.3494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3240    0.2501    1.0097 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7191   -0.0782    0.5641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9076    0.0147   -0.7907 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5417   -0.3930   -1.0952 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.9768    0.0550   -2.4537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7888   -2.0509   -0.8582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4471    0.4136    0.1036 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0925    0.2396   -0.1238 P   0  0  0  0  0  5  0  0  0  0  0  0
   -6.4665    0.0817   -1.5895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8827    1.6425    0.4459 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7255   -1.0578    0.7781 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6446   -0.5666    0.4675 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0102   -0.8609   -1.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8944   -0.9628   -1.6289 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1672   -1.2302   -1.6425 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9435   -2.4747   -1.6191 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1625   -0.7493   -2.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3289   -0.5463    0.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2192    0.1127    1.8677 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9459   -0.2753    1.9933 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1951    1.9428   -0.0698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9264    1.9805    1.7615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0336    1.7818   -0.5168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3470    2.7851    1.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2679    0.2090    2.1036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4017    0.6419    1.0589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9803   -1.0749    0.9350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7964   -2.1883    0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2162    2.3455    0.7041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1507   -1.8605    0.7004 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
 16 17  1  0
 17 18  2  0
 17 19  1  0
 17 20  1  0
 10 21  1  0
  5 22  1  0
 22 23  2  0
 22 24  1  0
 24  2  2  0
 21  6  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  4 28  1  0
  6 29  1  1
  7 30  1  0
  7 31  1  0
  8 32  1  6
  9 33  1  0
 10 34  1  1
 11 35  1  0
 11 36  1  0
 15 37  1  0
 19 38  1  0
 20 39  1  0
M  END

Synonyms

Value	Source
2'-Deoxycytidine 5'-diphosphate	ChEBI
2'-Deoxycytidine diphosphate	ChEBI
D-1beta-Ribofuranosylcytosine diphosphate	ChEBI
Deoxycytidine diphosphate	ChEBI
2'-Deoxycytidine 5'-diphosphoric acid	Generator
2'-Deoxycytidine diphosphoric acid	Generator
D-1b-Ribofuranosylcytosine diphosphate	Generator
D-1b-Ribofuranosylcytosine diphosphoric acid	Generator
D-1beta-Ribofuranosylcytosine diphosphoric acid	Generator
D-1Β-ribofuranosylcytosine diphosphate	Generator
D-1Β-ribofuranosylcytosine diphosphoric acid	Generator
Deoxycytidine diphosphoric acid	Generator
2'-Deoxy-cytidine 5'-pyrophosphate	HMDB
2'-Deoxy-cytidine pyrophosphate	HMDB
2'-Deoxycytidine-5'-diphosphate	HMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinone	HMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinone	HMDB
delta-1beta-Ribofuranosylcytosine diphosphate	HMDB
Deoxy-CDP	HMDB
Deoxycytidine 5'-diphosphate	HMDB

Molecular Formula

C₉H₁₅N₃O₁₀P₂

Average Mass

387.177

Monoisotopic Mass

387.023266739

IUPAC Name

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

Traditional Name

dCDP

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

InChI Key

FTDHDKPUHBLBTL-SHYZEUOFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organic oxoanionic compounds

Sub Class

Organic pyrophosphates

Direct Parent

Organic pyrophosphates

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside 5'-diphosphate (CHEBI:28846 )
2'-deoxycytidine phosphate (CHEBI:28846 )
Deoxyribonucleotides (C00705 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	11.3 g/L	ALOGPS
logP	-1.5	ALOGPS
logP	-2.6	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	1.79	ChemAxon
pKa (Strongest Basic)	0.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	201.44 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	74.78 m³·mol⁻¹	ChemAxon
Polarizability	30.77 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	splash10-002e-7912000000-ef0991eaee32b505e016	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0006-9851100000-62426a0730b483cea09b	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
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 - LC-ESI-QTOF , negative	splash10-0570-9418000000-2d9af3073a3dc2deba5d	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-056r-9511000000-84defb0c7de79c169ebf	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000i-0409000000-e5af2ab8466aa7c560d3	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0a4i-0903000000-1de5fa4ac24e19830f39	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0009000000-4aa3ce1bf37251d7fc83	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9435000000-55592321586c623c4830	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-0a4i-0903000000-1de5fa4ac24e19830f39	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-056r-9411000000-84bbde6c497548c746d1	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-63f9c6b289fb024c58fa	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-e584f4f2cb1a8a01a7e7	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-3910000000-d34603d21a6d1d52ae1f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-52ac41f181e1d5fbf96a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000f-4209000000-ea241dab90201ce7963e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9601000000-55120f468bf1ebba66cd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-bd81788fb13a599a4f60	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-63028e00ccb9887f46f5	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1900000000-9b943638c706a10be8db	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3910000000-f5ebfcca0e4ec5d76afa	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0409000000-47d71d5707b30d7b3ad5	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9324000000-25bfbc45e3248b83b219	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-16	View Spectrum

Biological Properties

Cellular Locations

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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
MMDBr0026058	L-Cystine	L-Cysteine	Vitamin B12-dependent ribonucleoside-diphosphate reductase	Reduction	RHEA	34755880
MMDBr0026086	2'-Deoxycytidine 5'-diphosphate	Deoxycytidine 5'-triphosphate	Nucleoside diphosphate 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

Exposure Sources

Other Exposures

Source Type	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

HMDB0001245

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022510

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Deoxycytidine_diphosphate

METLIN ID

6105

PubChem Compound

150855

PDB ID

Not Available

ChEBI ID

28846

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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'-diphosphate (MMDBc0057145)

MOL for #<Metabolite:0x00007f8dc0505780>

3D MOL for #<Metabolite:0x00007f8dc0505780>

3D SDF for #<Metabolite:0x00007f8dc0505780>

3D-SDF for #<Metabolite:0x00007f8dc0505780>

PDB for #<Metabolite:0x00007f8dc0505780>

3D PDB for #<Metabolite:0x00007f8dc0505780>

SMILES for #<Metabolite:0x00007f8dc0505780>

INCHI for #<Metabolite:0x00007f8dc0505780>

Structure for #<Metabolite:0x00007f8dc0505780>

3D Structure for #<Metabolite:0x00007f8dc0505780>