NP-MRD: Showing NP-Card for Cytidine diphosphate (NP0000717)

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Record Information

Version

1.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2021-10-07 20:40:18 UTC

NP-MRD ID

NP0000717

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cytidine diphosphate

Description

Cytidine diphosphate, abbreviated CDP, and also known as 5'-CDP, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. It is a cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. CDP exists in all living species, ranging from bacteria to humans. In humans, CDP is involved in cardiolipin biosynthesis. Outside of the human body, CDP has been detected, but not quantified in several different foods, such as carobs, mexican oregano, evergreen huckleberries, green vegetables, and pepper (Capsicum baccatum).

Structure

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

HMDB0001546
     RDKit          3D
CDP
 40 41  0  0  0  0  0  0  0  0999 V2000
    5.7352   -2.3919    2.4140 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5258   -1.8675    1.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4008   -2.6114    1.5364 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3075   -1.9534    0.9586 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3904   -0.6253    0.6552 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1923    0.0340    0.2604 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9090    0.2990   -1.0505 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1620    1.1936   -0.8970 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9165    1.5992   -2.0809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4121    0.3858   -2.6585 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7329   -0.1030   -1.7025 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.2786    0.9986   -0.8501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1103   -1.3773   -0.7236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9544   -0.7762   -2.5941 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1712   -1.1975   -1.4407 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.6100   -1.0945   -0.0156 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3931   -0.0588   -1.6625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7178   -2.7679   -1.6472 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219    2.2641   -0.1027 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2928    3.2816    0.3557 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9997    1.3411    1.0410 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1217    1.2344    1.9108 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4847    0.0718    0.8832 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5671    1.3258    0.5847 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5398   -0.5618    1.4379 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0090   -3.3480    2.2424 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2894   -1.7489    3.0367 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3592   -3.6597    1.7829 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4022   -2.5172    0.7119 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3043   -0.5940    0.6221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8651    0.7132   -0.1157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6604    2.3502   -1.9032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1792    1.9798   -2.8398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2669   -1.2373    0.2250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4508    0.0617   -2.6658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2041   -2.8027   -2.5118 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3747    2.7120   -0.6579 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1487    3.5846    1.2324 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8254    1.6938    1.6030 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2129    1.4118    2.8512 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
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  8 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
  5 23  1  0
 23 24  2  0
 23 25  1  0
 25  2  2  0
 21  6  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  4 29  1  0
  6 30  1  1
  8 31  1  1
  9 32  1  0
  9 33  1  0
 13 34  1  0
 17 35  1  0
 18 36  1  0
 19 37  1  6
 20 38  1  0
 21 39  1  1
 22 40  1  0
M  END


  Mrv1652309042000242D          

 25 26  0  0  0  0            999 V2000
 9998.433210001.5481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.222310001.5399    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.6882 9999.6899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.211410000.9255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.403510000.1010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.1168 9999.6899    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9995.7809 9998.4518    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10002.832110000.1010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.7066 9998.9756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.5312 9998.9756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.5536 9999.7023    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10003.1414 9998.9880    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.269010000.1133    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.9659 9998.9880    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9245 9999.6897    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.210110000.1021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4955 9999.6896    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4955 9998.8646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2100 9998.4521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9245 9998.8647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3096 9999.6069    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.642210000.0919    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.897110000.8765    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.722110000.8765    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.977010000.0919    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  6 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 15 16  1  0  0  0  0
 20 15  1  0  0  0  0
 16  4  2  0  0  0  0
 18  7  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 21 22  1  0  0  0  0
 21 25  1  0  0  0  0
 23  1  1  6  0  0  0
 22 15  1  1  0  0  0
 24  2  1  6  0  0  0
 25  3  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0000717

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
ZWIADYZPOWUWEW-XVFCMESISA-N

> <FORMULA>
C9H15N3O11P2

> <MOLECULAR_WEIGHT>
403.1764

> <EXACT_MASS>
403.018181361

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
31.38641764457615

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.38

> <JCHEM_LOGP>
-3.342881794666666

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2106934533838944

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7787851127589387

> <JCHEM_PKA_STRONGEST_BASIC>
-0.03320007450946405

> <JCHEM_POLAR_SURFACE_AREA>
221.66999999999996

> <JCHEM_REFRACTIVITY>
76.2906

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.01e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
CDP

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001546
     RDKit          3D
CDP
 40 41  0  0  0  0  0  0  0  0999 V2000
    5.7352   -2.3919    2.4140 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5258   -1.8675    1.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4008   -2.6114    1.5364 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3075   -1.9534    0.9586 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3904   -0.6253    0.6552 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1923    0.0340    0.2604 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9090    0.2990   -1.0505 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1620    1.1936   -0.8970 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9165    1.5992   -2.0809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4121    0.3858   -2.6585 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7329   -0.1030   -1.7025 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.2786    0.9986   -0.8501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1103   -1.3773   -0.7236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9544   -0.7762   -2.5941 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1712   -1.1975   -1.4407 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.6100   -1.0945   -0.0156 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3931   -0.0588   -1.6625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7178   -2.7679   -1.6472 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219    2.2641   -0.1027 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2928    3.2816    0.3557 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9997    1.3411    1.0410 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1217    1.2344    1.9108 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4847    0.0718    0.8832 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5671    1.3258    0.5847 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5398   -0.5618    1.4379 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0090   -3.3480    2.2424 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2894   -1.7489    3.0367 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3592   -3.6597    1.7829 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4022   -2.5172    0.7119 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3043   -0.5940    0.6221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8651    0.7132   -0.1157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6604    2.3502   -1.9032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1792    1.9798   -2.8398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2669   -1.2373    0.2250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4508    0.0617   -2.6658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2041   -2.8027   -2.5118 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3747    2.7120   -0.6579 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1487    3.5846    1.2324 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8254    1.6938    1.6030 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2129    1.4118    2.8512 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
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  8 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
  5 23  1  0
 23 24  2  0
 23 25  1  0
 25  2  2  0
 21  6  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  4 29  1  0
  6 30  1  1
  8 31  1  1
  9 32  1  0
  9 33  1  0
 13 34  1  0
 17 35  1  0
 18 36  1  0
 19 37  1  6
 20 38  1  0
 21 39  1  1
 22 40  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  O   UNK     0    8663.7428669.556   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8667.0828669.541   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8667.9518666.088   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8661.4618668.394   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8669.2878666.855   0.000  0.00  0.00           O+0
HETATM    6  P   UNK     0    8670.6188666.088   0.000  0.00  0.00           P+0
HETATM    7  N   UNK     0    8658.7918663.777   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0    8671.9538666.855   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8669.8528664.754   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8671.3928664.754   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0    8673.3008666.111   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0    8672.5318664.778   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8674.6358666.878   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8674.0708664.778   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0    8662.7928666.087   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0    8661.4598666.857   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0    8660.1258666.087   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0    8660.1258664.547   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8661.4598663.777   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8662.7928664.547   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0    8665.3788665.933   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0    8664.1328666.838   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8664.6088668.303   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8666.1488668.303   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8666.6248666.838   0.000  0.00  0.00           C+0
CONECT    1   23                                                            
CONECT    2   24                                                            
CONECT    3    5   25                                                       
CONECT    4   16                                                            
CONECT    5    3    6                                                       
CONECT    6    5    8    9   10                                             
CONECT    7   18                                                            
CONECT    8    6   11                                                       
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11    8   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15   16   20   22                                                  
CONECT   16   17   15    4                                                  
CONECT   17   16   18                                                       
CONECT   18   19   17    7                                                  
CONECT   19   18   20                                                       
CONECT   20   19   15                                                       
CONECT   21   22   25                                                       
CONECT   22   23   21   15                                                  
CONECT   23   22   24    1                                                  
CONECT   24   23   25    2                                                  
CONECT   25   24   21    3                                                  
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

COMPND    HMDB0001546
HETATM    1  N1  UNL     1       5.735  -2.392   2.414  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.526  -1.867   1.775  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.401  -2.611   1.536  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.308  -1.953   0.959  1.00  0.00           C  
HETATM    5  N2  UNL     1       2.390  -0.625   0.655  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.192   0.034   0.260  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.909   0.299  -1.050  1.00  0.00           O  
HETATM    8  C5  UNL     1      -0.162   1.194  -0.897  1.00  0.00           C  
HETATM    9  C6  UNL     1      -0.917   1.599  -2.081  1.00  0.00           C  
HETATM   10  O2  UNL     1      -1.412   0.386  -2.659  1.00  0.00           O  
HETATM   11  P1  UNL     1      -2.733  -0.103  -1.703  1.00  0.00           P  
HETATM   12  O3  UNL     1      -3.279   0.999  -0.850  1.00  0.00           O  
HETATM   13  O4  UNL     1      -2.110  -1.377  -0.724  1.00  0.00           O  
HETATM   14  O5  UNL     1      -3.954  -0.776  -2.594  1.00  0.00           O  
HETATM   15  P2  UNL     1      -5.171  -1.197  -1.441  1.00  0.00           P  
HETATM   16  O6  UNL     1      -4.610  -1.095  -0.016  1.00  0.00           O  
HETATM   17  O7  UNL     1      -6.393  -0.059  -1.663  1.00  0.00           O  
HETATM   18  O8  UNL     1      -5.718  -2.768  -1.647  1.00  0.00           O  
HETATM   19  C7  UNL     1       0.522   2.264  -0.103  1.00  0.00           C  
HETATM   20  O9  UNL     1      -0.293   3.282   0.356  1.00  0.00           O  
HETATM   21  C8  UNL     1       1.000   1.341   1.041  1.00  0.00           C  
HETATM   22  O10 UNL     1      -0.122   1.234   1.911  1.00  0.00           O  
HETATM   23  C9  UNL     1       3.485   0.072   0.883  1.00  0.00           C  
HETATM   24  O11 UNL     1       3.567   1.326   0.585  1.00  0.00           O  
HETATM   25  N3  UNL     1       4.540  -0.562   1.438  1.00  0.00           N  
HETATM   26  H1  UNL     1       6.009  -3.348   2.242  1.00  0.00           H  
HETATM   27  H2  UNL     1       6.289  -1.749   3.037  1.00  0.00           H  
HETATM   28  H3  UNL     1       3.359  -3.660   1.783  1.00  0.00           H  
HETATM   29  H4  UNL     1       1.402  -2.517   0.712  1.00  0.00           H  
HETATM   30  H5  UNL     1       0.304  -0.594   0.622  1.00  0.00           H  
HETATM   31  H6  UNL     1      -0.865   0.713  -0.116  1.00  0.00           H  
HETATM   32  H7  UNL     1      -1.660   2.350  -1.903  1.00  0.00           H  
HETATM   33  H8  UNL     1      -0.179   1.980  -2.840  1.00  0.00           H  
HETATM   34  H9  UNL     1      -2.267  -1.237   0.225  1.00  0.00           H  
HETATM   35  H10 UNL     1      -6.451   0.062  -2.666  1.00  0.00           H  
HETATM   36  H11 UNL     1      -6.204  -2.803  -2.512  1.00  0.00           H  
HETATM   37  H12 UNL     1       1.375   2.712  -0.658  1.00  0.00           H  
HETATM   38  H13 UNL     1       0.149   3.585   1.232  1.00  0.00           H  
HETATM   39  H14 UNL     1       1.825   1.694   1.603  1.00  0.00           H  
HETATM   40  H15 UNL     1       0.213   1.412   2.851  1.00  0.00           H  
CONECT    1    2   26   27
CONECT    2    3   25   25
CONECT    3    4    4   28
CONECT    4    5   29
CONECT    5    6   23
CONECT    6    7   21   30
CONECT    7    8
CONECT    8    9   19   31
CONECT    9   10   32   33
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   34
CONECT   14   15
CONECT   15   16   16   17   18
CONECT   17   35
CONECT   18   36
CONECT   19   20   21   37
CONECT   20   38
CONECT   21   22   39
CONECT   22   40
CONECT   23   24   24   25
END

HMDB0001546
     RDKit          3D
CDP
 40 41  0  0  0  0  0  0  0  0999 V2000
    5.7352   -2.3919    2.4140 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5258   -1.8675    1.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4008   -2.6114    1.5364 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3075   -1.9534    0.9586 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3904   -0.6253    0.6552 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1923    0.0340    0.2604 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9090    0.2990   -1.0505 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1620    1.1936   -0.8970 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9165    1.5992   -2.0809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4121    0.3858   -2.6585 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7329   -0.1030   -1.7025 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.2786    0.9986   -0.8501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1103   -1.3773   -0.7236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9544   -0.7762   -2.5941 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1712   -1.1975   -1.4407 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.6100   -1.0945   -0.0156 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3931   -0.0588   -1.6625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7178   -2.7679   -1.6472 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219    2.2641   -0.1027 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2928    3.2816    0.3557 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9997    1.3411    1.0410 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1217    1.2344    1.9108 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4847    0.0718    0.8832 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5671    1.3258    0.5847 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5398   -0.5618    1.4379 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0090   -3.3480    2.2424 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2894   -1.7489    3.0367 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3592   -3.6597    1.7829 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4022   -2.5172    0.7119 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3043   -0.5940    0.6221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8651    0.7132   -0.1157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6604    2.3502   -1.9032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1792    1.9798   -2.8398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2669   -1.2373    0.2250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4508    0.0617   -2.6658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2041   -2.8027   -2.5118 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3747    2.7120   -0.6579 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1487    3.5846    1.2324 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8254    1.6938    1.6030 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2129    1.4118    2.8512 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
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  8 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
  5 23  1  0
 23 24  2  0
 23 25  1  0
 25  2  2  0
 21  6  1  0
  1 26  1  0
  1 27  1  0
  3 28  1  0
  4 29  1  0
  6 30  1  1
  8 31  1  1
  9 32  1  0
  9 33  1  0
 13 34  1  0
 17 35  1  0
 18 36  1  0
 19 37  1  6
 20 38  1  0
 21 39  1  1
 22 40  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
5'-CDP	ChEBI
Cytidine 5'-diphosphate	ChEBI
Cytidine 5'-diphosphoric acid	ChEBI
Cytidine 5'-pyrophosphate	ChEBI
Cytidine diphosphate	ChEBI
Cytidine, 5'-(trihydrogen pyrophosphate)	ChEBI
CYTIDINE-5'-diphosphATE	ChEBI
Cytidine 5'-pyrophosphoric acid	Generator
Cytidine diphosphoric acid	Generator
Cytidine, 5'-(trihydrogen pyrophosphoric acid)	Generator
CYTIDINE-5'-diphosphoric acid	Generator
Cytidine-diphosphate	HMDB
Diphosphate, cytidine	HMDB

Chemical Formula

C₉H₁₅N₃O₁₁P₂

Average Mass

403.1764 Da

Monoisotopic Mass

403.01818 Da

IUPAC Name

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

Traditional Name

CDP

CAS Registry Number

63-38-7

SMILES

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

InChI Identifier

InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChI Key

ZWIADYZPOWUWEW-XVFCMESISA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Abelmoschus esculentus	FooDB	FooDB
Actinidia chinensis	FooDB	FooDB
Agaricus bisporus	FooDB	FooDB
Agave	FooDB	FooDB
Allium ampeloprasum	FooDB	FooDB
Allium ascalonicum	FooDB	FooDB
Allium cepa	FooDB	FooDB
Allium cepa L.	FooDB	FooDB
Allium fistulosum	FooDB	FooDB
Allium sativum	FooDB	FooDB
Allium schoenoprasum	FooDB	FooDB
Allium tuberosum	FooDB	FooDB
Aloysia triphylla	FooDB	FooDB
Amaranthus	FooDB	FooDB
Amelanchier alnifolia	FooDB	FooDB
Anacardium occidentale	FooDB	FooDB
Ananas comosus	FooDB	FooDB
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anethum graveolens	FooDB	FooDB
Angelica keiskei	FooDB	FooDB
Annona cherimola	FooDB	FooDB
Annona muricata	FooDB	FooDB
Annona reticulata	FooDB	FooDB
Annona squamosa	FooDB	FooDB
Anser anser	FooDB	FooDB
Anthriscus cerefolium	FooDB	FooDB
Apium graveolens	FooDB	FooDB
Apium graveolens var. dulce	FooDB	FooDB
Apium graveolens var. rapaceum	FooDB	FooDB
Apium graveolens var. secalinum	FooDB	FooDB
Arachis hypogaea	FooDB	FooDB
Arctium lappa	FooDB	FooDB
Armoracia rusticana	FooDB	FooDB
Artemisia dracunculus	FooDB	FooDB
Artemisia vulgaris	FooDB	FooDB
Artocarpus altilis	FooDB	FooDB
Artocarpus heterophyllus	FooDB	FooDB
Asparagus officinalis	FooDB	FooDB
Attalea speciosa	FooDB	FooDB
Auricularia auricula-judae	FooDB	FooDB
Auricularia polytricha	FooDB	FooDB
Avena sativa L.	FooDB	FooDB
Averrhoa carambola	FooDB	FooDB
Basella alba	FooDB	FooDB
Benincasa hispida	FooDB	FooDB
Bertholletia excelsa	FooDB	FooDB
Beta vulgaris	FooDB	FooDB
Beta vulgaris ssp. cicla	FooDB	FooDB
Bison bison	FooDB	FooDB
Borago officinalis	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Brassica alboglabra	FooDB	FooDB
Brassica juncea	FooDB	FooDB
Brassica napus	FooDB	FooDB
Brassica napus var. napus	FooDB	FooDB
Brassica oleracea	FooDB	FooDB
Brassica oleracea var. botrytis	FooDB	FooDB
Brassica oleracea var. capitata	FooDB	FooDB
Brassica oleracea var. gemmifera	FooDB	FooDB
Brassica oleracea var. gongylodes	FooDB	FooDB
Brassica oleracea var. italica	FooDB	FooDB
Brassica oleracea var. sabauda	FooDB	FooDB
Brassica oleracea var. viridis	FooDB	FooDB
Brassica rapa	FooDB	FooDB
Brassica rapa ssp. chinensis	FooDB	FooDB
Brassica rapa var. pekinensis	FooDB	FooDB
Brassica rapa var. rapa	FooDB	FooDB
Brassica ruvo	FooDB	FooDB
Brosimum alicastrum	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Byrsonima crassifolia	FooDB	FooDB
Cajanus cajan	FooDB	FooDB
Canarium ovatum	FooDB	FooDB
Cannabis sativa	CannabisDB	Not Available
Cantharellus cibarius	FooDB	FooDB
Capparis spinosa	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Capsicum annuum	FooDB	FooDB
Capsicum annuum L.	FooDB	FooDB
Capsicum annuum var. annuum	FooDB	FooDB
Capsicum chinense	FooDB	FooDB
Capsicum pubescens	FooDB	FooDB
Carica papaya L.	FooDB	FooDB
Carissa macrocarpa	FooDB	FooDB
Carthamus tinctorius	FooDB	FooDB
Carum carvi	FooDB	FooDB
Carya	FooDB	FooDB
Carya illinoinensis	FooDB	FooDB
Castanea	FooDB	FooDB
Castanea crenata	FooDB	FooDB
Castanea mollissima	FooDB	FooDB
Castanea sativa	FooDB	FooDB
Ceratonia siliqua	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Chamaemelum nobile	FooDB	FooDB
Chamerion angustifolium	FooDB	FooDB
Chenopodium album	FooDB	FooDB
Chenopodium quinoa	FooDB	FooDB
Chrysanthemum coronarium	FooDB	FooDB
Cicer arietinum	FooDB	FooDB
Cichorium endivia	FooDB	FooDB
Cichorium intybus	FooDB	FooDB
Cinnamomum	FooDB	FooDB
Cinnamomum aromaticum	FooDB	FooDB
Cinnamomum verum	FooDB	FooDB
Cirsium	FooDB	FooDB
Citrullus lanatus	FooDB	FooDB
Citrus ×limon (L.) Burm. f. (pro sp.)	FooDB	FooDB
Citrus aurantiifolia	FooDB	FooDB
Citrus latifolia	FooDB	FooDB
Citrus limon	FooDB	FooDB
Citrus maxima	FooDB	FooDB
Citrus paradisi	FooDB	FooDB
Citrus reticulata	FooDB	FooDB
Citrus X sinensis (L.) Osbeck (pro. sp.)	FooDB	FooDB
Cocos nucifera	FooDB	FooDB
Coffea arabica L.	FooDB	FooDB
Coffea canephora	FooDB	FooDB
Colocasia esculenta	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Corchorus olitorius	FooDB	FooDB
Coriandrum sativum L.	FooDB	FooDB
Corylus	FooDB	FooDB
Corylus avellana	FooDB	FooDB
Crateva religiosa	FooDB	FooDB
Crocus sativus	FooDB	FooDB
Cucumis melo	FooDB	FooDB
Cucumis metuliferus	FooDB	FooDB
Cucumis sativus L.	FooDB	FooDB
Cucurbita	FooDB	FooDB
Cucurbita maxima	FooDB	FooDB
Cucurbita moschata	FooDB	FooDB
Cuminum cyminum	FooDB	FooDB
Curcuma longa	FooDB	FooDB
Cydonia oblonga	FooDB	FooDB
Cymbopogon citratus	FooDB	FooDB
Cynara cardunculus	FooDB	FooDB
Cynara scolymus	FooDB	FooDB
Daucus carota	FooDB	FooDB
Daucus carota ssp. sativus	FooDB	FooDB
Dimocarpus longan	FooDB	FooDB
Dioscorea	FooDB	FooDB
Dioscorea pentaphylla	FooDB	FooDB
Diospyros	FooDB	FooDB
Diospyros kaki	FooDB	FooDB
Diospyros virginiana	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Durio zibethinus	FooDB	FooDB
Dysphania ambrosioides	FooDB	FooDB
Elaeis	FooDB	FooDB
Eleocharis dulcis	FooDB	FooDB
Elettaria cardamomum	FooDB	FooDB
Empetrum nigrum	FooDB	FooDB
Equus caballus	FooDB	FooDB
Eragrostis tef	FooDB	FooDB
Eriobotrya japonica	FooDB	FooDB
Eruca vesicaria subsp. Sativa	FooDB	FooDB
Eugenia javanica	FooDB	FooDB
Eugenia uniflora	FooDB	FooDB
Eutrema japonicum	FooDB	FooDB
Fagopyrum esculentum	FooDB	FooDB
Fagopyrum tataricum	FooDB	FooDB
Fagus	FooDB	FooDB
Feijoa sellowiana	FooDB	FooDB
Ficus carica	FooDB	FooDB
Flammulina velutipes	FooDB	FooDB
Foeniculum vulgare	FooDB	FooDB
Fragaria x ananassa	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Garcinia mangostana	FooDB	FooDB
Gaylussacia baccata	FooDB	FooDB
Ginkgo biloba	FooDB	FooDB
Glycine max	FooDB	FooDB
Gossypium	FooDB	FooDB
Grifola frondosa	FooDB	FooDB
Hedysarum alpinum	FooDB	FooDB
Helianthus annuus L.	FooDB	FooDB
Helianthus tuberosus	FooDB	FooDB
Hibiscus sabbariffa	FooDB	FooDB
Hippophae rhamnoides	FooDB	FooDB
Hordeum vulgare	FooDB	FooDB
Hyssopus officinalis L.	FooDB	FooDB
Illicium verum	FooDB	FooDB
Ipomoea aquatica	FooDB	FooDB
Ipomoea batatas	FooDB	FooDB
Juglans	FooDB	FooDB
Juglans ailanthifolia	FooDB	FooDB
Juglans cinerea	FooDB	FooDB
Juglans nigra L.	FooDB	FooDB
Juglans regia	FooDB	FooDB
Lablab purpureus	FooDB	FooDB
Lactuca sativa	FooDB	FooDB
Lagenaria siceraria	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Lathyrus sativus	FooDB	FooDB
Laurus nobilis L.	FooDB	FooDB
Lens culinaris	FooDB	FooDB
Lentinus edodes	FooDB	FooDB
Lepidium sativum	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Levisticum officinale	FooDB	FooDB
Linum usitatissimum	FooDB	FooDB
Litchi chinensis	FooDB	FooDB
Luffa aegyptiaca	FooDB	FooDB
Lupinus	FooDB	FooDB
Lupinus albus	FooDB	FooDB
Macadamia	FooDB	FooDB
Macadamia tetraphylla	FooDB	FooDB
Malpighia emarginata	FooDB	FooDB
Malus	FooDB	FooDB
Malus pumila	FooDB	FooDB
Mammea americana	FooDB	FooDB
Mangifera indica	FooDB	FooDB
Manihot esculenta	FooDB	FooDB
Manilkara zapota	FooDB	FooDB
Maranta arundinacea	FooDB	FooDB
Matricaria recutita	FooDB	FooDB
Matteuccia struthiopteris	FooDB	FooDB
Medicago sativa	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Melissa officinalis L.	FooDB	FooDB
Mentha	FooDB	FooDB
Mentha aquatica	FooDB	FooDB
Mentha arvensis	FooDB	FooDB
Mentha spicata	FooDB	FooDB
Mentha x piperita	FooDB	FooDB
Mespilus germanica	FooDB	FooDB
Metroxylon sagu	FooDB	FooDB
Momordica charantia	FooDB	FooDB
Morchellaceae	FooDB	FooDB
Morella rubra	FooDB	FooDB
Moringa oleifera	FooDB	FooDB
Morus	FooDB	FooDB
Morus nigra	FooDB	FooDB
Mus musculus	LOTUS Database	35616633
Musa acuminata	FooDB	FooDB
Musa x paradisiaca	FooDB	FooDB
Myrica	FooDB	FooDB
Myristica fragrans	FooDB	FooDB
Nelumbo	FooDB	FooDB
Nelumbo nucifera	FooDB	FooDB
Nephelium lappaceum	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Nuphar lutea	FooDB	FooDB
Ocimum basilicum	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oenothera biennis	FooDB	FooDB
Olea europaea	FooDB	FooDB
Opuntia	FooDB	FooDB
Opuntia cochenillifera	FooDB	FooDB
Opuntia macrorhiza	FooDB	FooDB
Origanum majorana	FooDB	FooDB
Origanum onites	FooDB	FooDB
Origanum vulgare	FooDB	FooDB
Origanum X majoricum	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Oryza rufipogon	FooDB	FooDB
Oryza sativa	FooDB	FooDB
Ovis aries	FooDB	FooDB
Pachyrhizus erosus	FooDB	FooDB
Panax ginseng	FooDB	FooDB
Pangium edule	FooDB	FooDB
Panicum miliaceum	FooDB	FooDB
Passiflora edulis	FooDB	FooDB
Pastinaca sativa	FooDB	FooDB
Pediomelum esculentum	FooDB	FooDB
Perideridia oregana	FooDB	FooDB
Persea americana	FooDB	FooDB
Petasites japonicus	FooDB	FooDB
Petroselinum crispum	FooDB	FooDB
Phaseolus coccineus	FooDB	FooDB
Phaseolus lunatus	FooDB	FooDB
Phaseolus vulgaris	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Phoenix dactylifera	FooDB	FooDB
Photinia melanocarpa	FooDB	FooDB
Phyllostachys edulis	FooDB	FooDB
Physalis	FooDB	FooDB
Physalis philadelphica var. immaculata	FooDB	FooDB
Phytolacca americana	FooDB	FooDB
Pimenta dioica	FooDB	FooDB
Pimpinella anisum	FooDB	FooDB
Pinus	FooDB	FooDB
Pinus edulis	FooDB	FooDB
Piper nigrum L.	FooDB	FooDB
Pistacia vera	FooDB	FooDB
Pisum sativum	FooDB	FooDB
Pleurotus ostreatus	FooDB	FooDB
Polygonum alpinum	FooDB	FooDB
Portulaca oleracea	FooDB	FooDB
Pouteria sapota	FooDB	FooDB
Prunus armeniaca	FooDB	FooDB
Prunus avium	FooDB	FooDB
Prunus avium L.	FooDB	FooDB
Prunus cerasus	FooDB	FooDB
Prunus domestica	FooDB	FooDB
Prunus dulcis	FooDB	FooDB
Prunus persica	FooDB	FooDB
Prunus persica var. nucipersica	FooDB	FooDB
Prunus persica var. persica	FooDB	FooDB
Prunus tomentosa	FooDB	FooDB
Prunus virginiana	FooDB	FooDB
Psidium cattleianum	FooDB	FooDB
Psidium guajava	FooDB	FooDB
Psophocarpus tetragonolobus	FooDB	FooDB
Punica granatum	FooDB	FooDB
Pyrus communis	FooDB	FooDB
Pyrus pyrifolia	FooDB	FooDB
Quercus	FooDB	FooDB
Raphanus sativus	FooDB	FooDB
Raphanus sativus var. longipinnatus	FooDB	FooDB
Raphanus sativus var. sativus	FooDB	FooDB
Rheum rhabarbarum	FooDB	FooDB
Ribes aureum	FooDB	FooDB
Ribes glandulosum	FooDB	FooDB
Ribes nigrum	FooDB	FooDB
Ribes rubrum	FooDB	FooDB
Ribes uva-crispa	FooDB	FooDB
Rosa	FooDB	FooDB
Rubus arcticus	FooDB	FooDB
Rubus chamaemorus	FooDB	FooDB
Rubus idaeus	FooDB	FooDB
Rubus occidentalis	FooDB	FooDB
Rubus spectabilis	FooDB	FooDB
Rumex	FooDB	FooDB
Rumex acetosa	FooDB	FooDB
Rumex articus	FooDB	FooDB
Sagittaria latifolia	FooDB	FooDB
Salix pulchra	FooDB	FooDB
Salvia elegans	FooDB	FooDB
Salvia hispanica	FooDB	FooDB
Salvia officinalis	FooDB	FooDB
Salvia rosmarinus	FooDB	FooDB
Sambucus nigra	FooDB	FooDB
Sambucus nigra L.	FooDB	FooDB
Satureja hortensis L.	FooDB	FooDB
Satureja montana	FooDB	FooDB
Scorzonera hispanica	FooDB	FooDB
Secale cereale	FooDB	FooDB
Sechium edule	FooDB	FooDB
Sesamum indicum	FooDB	FooDB
Sesbania bispinosa	FooDB	FooDB
Sinapis alba	FooDB	FooDB
Sisymbrium	FooDB	FooDB
Solanum lycopersicum	FooDB	FooDB
Solanum lycopersicum var. cerasiforme	FooDB	FooDB
Solanum lycopersicum var. lycopersicum	FooDB	FooDB
Solanum melongena	FooDB	FooDB
Solanum quitoense	FooDB	FooDB
Solanum tuberosum	FooDB	FooDB
Sorbus aucuparia	FooDB	FooDB
Sorghum bicolor	FooDB	FooDB
Spinacia oleracea	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB
Syzygium aromaticum	FooDB	FooDB
Syzygium cumini	FooDB	FooDB
Syzygium jambos	FooDB	FooDB
Tamarindus indica	FooDB	FooDB
Taraxacum officinale	FooDB	FooDB
Tetragonia tetragonioides	FooDB	FooDB
Thelesperma	FooDB	FooDB
Thymus pulegioides	FooDB	FooDB
Thymus vulgaris	FooDB	FooDB
Tilia cordata	FooDB	FooDB
Tilia L.	FooDB	FooDB
Tragopogon porrifolius	FooDB	FooDB
Trigonella foenum-graecum	FooDB	FooDB
Triticum	FooDB	FooDB
Triticum aestivum	FooDB	FooDB
Triticum durum	FooDB	FooDB
Triticum spelta	FooDB	FooDB
Triticum turanicum	FooDB	FooDB
Typha angustifolia	FooDB	FooDB
Vaccinium	FooDB	FooDB
Vaccinium angustifolium	FooDB	FooDB
Vaccinium angustifolium X Vaccinium corymbosum	FooDB	FooDB
Vaccinium arboreum	FooDB	FooDB
Vaccinium corymbosum	FooDB	FooDB
Vaccinium deliciosum	FooDB	FooDB
Vaccinium elliottii	FooDB	FooDB
Vaccinium macrocarpon	FooDB	FooDB
Vaccinium myrtilloides	FooDB	FooDB
Vaccinium myrtillus	FooDB	FooDB
Vaccinium ovalifolium	FooDB	FooDB
Vaccinium ovatum	FooDB	FooDB
Vaccinium oxycoccos	FooDB	FooDB
Vaccinium parvifolium	FooDB	FooDB
Vaccinium reticulatum	FooDB	FooDB
Vaccinium stamineum	FooDB	FooDB
Vaccinium uliginosum	FooDB	FooDB
Vaccinium vitis-idaea	FooDB	FooDB
Valerianella locusta	FooDB	FooDB
Vanilla	FooDB	FooDB
Verbena officinalis	FooDB	FooDB
Viburnum edule	FooDB	FooDB
Vicia faba	FooDB	FooDB
Vigna aconitifolia	FooDB	FooDB
Vigna angularis	FooDB	FooDB
Vigna mungo	FooDB	FooDB
Vigna radiata	FooDB	FooDB
Vigna umbellata	FooDB	FooDB
Vigna unguiculata	FooDB	FooDB
Vigna unguiculata ssp. cylindrica	FooDB	FooDB
Vigna unguiculata ssp. unguiculata	FooDB	FooDB
Vigna unguiculata var. sesquipedalis	FooDB	FooDB
Vitis	FooDB	FooDB
Vitis aestivalis	FooDB	FooDB
Vitis labrusca	FooDB	FooDB
Vitis rotundifolia	FooDB	FooDB
Vitis vinifera L.	FooDB	FooDB
Xanthosoma sagittifolium	FooDB	FooDB
Zea mays L.	FooDB	FooDB
Zingiber officinale	FooDB	FooDB
Zizania	FooDB	FooDB
Zizania aquatica	FooDB	FooDB
Ziziphus zizyphus	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside diphosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside diphosphate
Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
Organic pyrophosphate
Monosaccharide phosphate
Monoalkyl phosphate
Pyrimidone
Aminopyrimidine
Imidolactam
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

cytidine 5'-phosphate (CHEBI:17239 )
pyrimidine ribonucleoside 5'-diphosphate (CHEBI:17239 )
Ribonucleotides (C00112 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	2.44	Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).

Predicted Properties

Property	Value	Source
Water Solubility	10.1 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-3.3	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.78	ChemAxon
pKa (Strongest Basic)	-0.033	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	221.67 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	76.29 m³·mol⁻¹	ChemAxon
Polarizability	31.39 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0001546

DrugBank ID

DB04555

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17239

Good Scents ID

Not Available

References

General References

Houtkooper RH, Akbari H, van Lenthe H, Kulik W, Wanders RJ, Frentzen M, Vaz FM: Identification and characterization of human cardiolipin synthase. FEBS Lett. 2006 May 29;580(13):3059-64. Epub 2006 Apr 27. [PubMed:16678169 ]
George TP, Cook HW, Byers DM, Palmer FB, Spence MW: Inhibition of phosphatidylcholine and phosphatidylethanolamine biosynthesis by cytochalasin B in cultured glioma cells: potential regulation of biosynthesis by Ca(2+)-dependent mechanisms. Biochim Biophys Acta. 1991 Jul 9;1084(2):185-93. [PubMed:1854804 ]
Riekhof WR, Voelker DR: Uptake and utilization of lyso-phosphatidylethanolamine by Saccharomyces cerevisiae. J Biol Chem. 2006 Dec 1;281(48):36588-96. Epub 2006 Oct 2. [PubMed:17015438 ]
Tsitolovskii LE, Kraevskii AA: [Possible relation between learning and non-template RNA synthesis in neurons]. Zh Vyssh Nerv Deiat Im I P Pavlova. 1982 Mar-Apr;32(2):284-91. [PubMed:6178232 ]
Carstensen S, Pliska-Matyshak G, Bhuvarahamurthy N, Robbins KM, Murthy PP: Biosynthesis and localization of phosphatidyl-scyllo-inositol in barley aleurone cells. Lipids. 1999 Jan;34(1):67-73. [PubMed:10188599 ]
Nowicki M, Muller F, Frentzen M: Cardiolipin synthase of Arabidopsis thaliana. FEBS Lett. 2005 Apr 11;579(10):2161-5. [PubMed:15811335 ]
George TP, Morash SC, Cook HW, Byers DM, Palmer FB, Spence MW: Phosphatidylcholine biosynthesis in cultured glioma cells: evidence for channeling of intermediates. Biochim Biophys Acta. 1989 Aug 22;1004(3):283-91. [PubMed:2758024 ]
Houtkooper RH, Vaz FM: Cardiolipin, the heart of mitochondrial metabolism. Cell Mol Life Sci. 2008 Aug;65(16):2493-506. doi: 10.1007/s00018-008-8030-5. [PubMed:18425414 ]
Lindblad L, Schersten T: Incorporation rate in vitro of choline and methyl-methionine into human hepatic lecithins. Scand J Gastroenterol. 1976;11(6):587-91. [PubMed:981963 ]

Showing NP-Card for Cytidine diphosphate (NP0000717)

MOL for NP0000717 (Cytidine diphosphate)

3D MOL for NP0000717 (Cytidine diphosphate)

3D SDF for NP0000717 (Cytidine diphosphate)

3D-SDF for NP0000717 (Cytidine diphosphate)

PDB for NP0000717 (Cytidine diphosphate)

3D PDB for NP0000717 (Cytidine diphosphate)

SMILES for NP0000717 (Cytidine diphosphate)

INCHI for NP0000717 (Cytidine diphosphate)

Structure for NP0000717 (Cytidine diphosphate)

3D Structure for NP0000717 (Cytidine diphosphate)