MiMeDB: Showing metabocard for 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (MMDBc0029980)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:49:16 UTC

Update Date

2022-08-31 17:38:17 UTC

Metabolite ID

MMDBc0029980

Metabolite Identification

Common Name

2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol

Description

2-phospho-4-(cytidine 5'-diphospho)-2-c-methyl-D-erythritol is a member of the chemical class known as Pyrimidine Ribonucleoside Diphosphates. These are pyrimidine ribobucleotides with diphosphate group linked to the ribose moiety.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303082006172D          

 42 43  0  0  0  0            999 V2000
    3.1878    2.2594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3905   -4.3317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9056   -3.6642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8917   -1.2036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9767    1.9821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6779    3.8286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6763   -1.4585    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1482    2.7890    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2110   -4.2454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3437   -0.9736    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0112   -1.4585    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7562   -2.2431    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0616   -2.8243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9328    3.0440    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6959   -4.9129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5466   -3.4918    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2412   -2.9106    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8709    4.0001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351    3.3411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3437   -0.1486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7958   -1.2036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3972   -2.0706    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0605    4.9129    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.6959    3.9344    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.0820    4.2774    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3193   -0.9263    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.1905    0.6429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8275    0.7486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2135    1.0917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7202   -0.3966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1920    1.7271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9312   -2.2431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7174    3.2989    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8490    0.1132    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8890    4.1059    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0644   -0.1416    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.0205    0.9202    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5472   -0.6437    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7613    2.2370    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0788   -0.5990    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5945   -2.0419    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3817   -2.9782    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  7  4  1  1  0  0  0
  8  5  1  0  0  0  0
  9  2  1  0  0  0  0
 10  7  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 14  1  1  1  0  0  0
 14  6  1  0  0  0  0
 14  8  1  0  0  0  0
 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 16 13  2  0  0  0  0
 17  3  1  0  0  0  0
 12 17  1  1  0  0  0
 17 13  1  0  0  0  0
 18  6  1  0  0  0  0
  8 19  1  6  0  0  0
 10 20  1  6  0  0  0
 11 21  1  6  0  0  0
 22 13  1  0  0  0  0
 30  4  1  0  0  0  0
 31  5  1  0  0  0  0
 32  7  1  0  0  0  0
 32 12  1  0  0  0  0
 14 33  1  6  0  0  0
 35 23  1  0  0  0  0
 35 24  1  0  0  0  0
 35 25  2  0  0  0  0
 35 33  1  0  0  0  0
 36 26  1  0  0  0  0
 36 27  2  0  0  0  0
 36 30  1  0  0  0  0
 36 34  1  0  0  0  0
 37 28  1  0  0  0  0
 37 29  2  0  0  0  0
 37 31  1  0  0  0  0
 37 34  1  0  0  0  0
  7 38  1  6  0  0  0
  8 39  1  6  0  0  0
 10 40  1  1  0  0  0
 11 41  1  1  0  0  0
 12 42  1  6  0  0  0
M  CHG  4  22  -1  23  -1  24  -1  26  -1
M  END


  Mrv1652303082006172D          

 42 43  0  0  0  0            999 V2000
    3.1878    2.2594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3905   -4.3317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9056   -3.6642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8917   -1.2036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9767    1.9821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6779    3.8286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6763   -1.4585    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1482    2.7890    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2110   -4.2454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3437   -0.9736    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0112   -1.4585    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7562   -2.2431    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0616   -2.8243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9328    3.0440    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6959   -4.9129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5466   -3.4918    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2412   -2.9106    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8709    4.0001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351    3.3411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3437   -0.1486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7958   -1.2036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3972   -2.0706    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0605    4.9129    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.6959    3.9344    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.0820    4.2774    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3193   -0.9263    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.1905    0.6429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8275    0.7486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2135    1.0917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7202   -0.3966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1920    1.7271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9312   -2.2431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7174    3.2989    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8490    0.1132    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8890    4.1059    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0644   -0.1416    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.0205    0.9202    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5472   -0.6437    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7613    2.2370    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0788   -0.5990    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5945   -2.0419    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3817   -2.9782    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  7  4  1  1  0  0  0
  8  5  1  0  0  0  0
  9  2  1  0  0  0  0
 10  7  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 14  1  1  1  0  0  0
 14  6  1  0  0  0  0
 14  8  1  0  0  0  0
 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 16 13  2  0  0  0  0
 17  3  1  0  0  0  0
 12 17  1  1  0  0  0
 17 13  1  0  0  0  0
 18  6  1  0  0  0  0
  8 19  1  6  0  0  0
 10 20  1  6  0  0  0
 11 21  1  6  0  0  0
 22 13  1  0  0  0  0
 30  4  1  0  0  0  0
 31  5  1  0  0  0  0
 32  7  1  0  0  0  0
 32 12  1  0  0  0  0
 14 33  1  6  0  0  0
 35 23  1  0  0  0  0
 35 24  1  0  0  0  0
 35 25  2  0  0  0  0
 35 33  1  0  0  0  0
 36 26  1  0  0  0  0
 36 27  2  0  0  0  0
 36 30  1  0  0  0  0
 36 34  1  0  0  0  0
 37 28  1  0  0  0  0
 37 29  2  0  0  0  0
 37 31  1  0  0  0  0
 37 34  1  0  0  0  0
  7 38  1  6  0  0  0
  8 39  1  6  0  0  0
 10 40  1  1  0  0  0
 11 41  1  1  0  0  0
 12 42  1  6  0  0  0
M  CHG  4  22  -1  23  -1  24  -1  26  -1
M  END
> <DATABASE_ID>
MMDBc0029980

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(COP(O)(=O)OP([O-])(=O)OC[C@@]1([H])O[C@@]([H])(N2C=CC(=N)N=C2[O-])[C@]([H])(O)[C@]1([H])O)[C@](C)(CO)OP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H26N3O17P3/c1-14(6-18,33-35(23,24)25)8(19)5-31-37(28,29)34-36(26,27)30-4-7-10(20)11(21)12(32-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21H,4-6H2,1H3,(H,26,27)(H,28,29)(H2,15,16,22)(H2,23,24,25)/p-4/t7-,8-,10-,11-,12-,14+/m1/s1

> <INCHI_KEY>
HTJXTKBIUVFUAR-XHIBXCGHSA-J

> <FORMULA>
C14H22N3O17P3

> <MOLECULAR_WEIGHT>
597.257

> <EXACT_MASS>
597.018401574

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
47.38437759005175

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-5-[({[(2R,3S)-2,4-dihydroxy-3-methyl-3-(phosphonooxy)butoxy](hydroxy)phosphoryl phosphono}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-olate

> <ALOGPS_LOGP>
-1.03

> <JCHEM_LOGP>
-5.27321193468311

> <ALOGPS_LOGS>
-1.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
2.554869476207795

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0509760192695161

> <JCHEM_PKA_STRONGEST_BASIC>
1.847679681656192

> <JCHEM_POLAR_SURFACE_AREA>
330.2000000000001

> <JCHEM_REFRACTIVITY>
133.09899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.55e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-5-({[(2R,3S)-2,4-dihydroxy-3-methyl-3-(phosphonooxy)butoxy(hydroxy)phosphoryl phosphono]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-iminopyrimidin-2-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       5.951   4.218   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.329  -8.086   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.424  -6.840   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.665  -2.247   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.690   3.700   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.999   7.147   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.129  -2.723   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.010   5.206   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -7.861  -7.925   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.375  -1.817   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.621  -2.723   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -5.145  -4.187   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -7.582  -5.272   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.475   5.682   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -8.766  -9.171   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -8.487  -6.518   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      -6.050  -5.433   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       3.492   7.467   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.866   6.237   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -4.375  -0.277   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -7.085  -2.247   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -8.208  -3.865   0.000  0.00  0.00           O-1
HETATM   23  O   UNK     0       7.580   9.171   0.000  0.00  0.00           O-1
HETATM   24  O   UNK     0       8.766   7.344   0.000  0.00  0.00           O-1
HETATM   25  O   UNK     0       5.753   7.984   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.596  -1.729   0.000  0.00  0.00           O-1
HETATM   27  O   UNK     0      -0.356   1.200   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       3.411   1.397   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.399   2.038   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -1.344  -0.740   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       2.225   3.224   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -3.605  -4.187   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       6.939   6.158   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       1.585   0.211   0.000  0.00  0.00           O+0
HETATM   35  P   UNK     0       7.259   7.664   0.000  0.00  0.00           P+0
HETATM   36  P   UNK     0       0.120  -0.264   0.000  0.00  0.00           P+0
HETATM   37  P   UNK     0       1.905   1.718   0.000  0.00  0.00           P+0
HETATM   38  H   UNK     0      -2.888  -1.202   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0       5.154   4.176   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0      -5.747  -1.118   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0      -6.710  -3.812   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0      -4.446  -5.559   0.000  0.00  0.00           H+0
CONECT    1   14                                                            
CONECT    2    3    9                                                       
CONECT    3    2   17                                                       
CONECT    4    7   30                                                       
CONECT    5    8   31                                                       
CONECT    6   14   18                                                       
CONECT    7    4   10   32   38                                             
CONECT    8    5   14   19   39                                             
CONECT    9    2   15   16                                                  
CONECT   10    7   11   20   40                                             
CONECT   11   10   12   21   41                                             
CONECT   12   11   17   32   42                                             
CONECT   13   16   17   22                                                  
CONECT   14    1    6    8   33                                             
CONECT   15    9                                                            
CONECT   16    9   13                                                       
CONECT   17    3   12   13                                                  
CONECT   18    6                                                            
CONECT   19    8                                                            
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22   13                                                            
CONECT   23   35                                                            
CONECT   24   35                                                            
CONECT   25   35                                                            
CONECT   26   36                                                            
CONECT   27   36                                                            
CONECT   28   37                                                            
CONECT   29   37                                                            
CONECT   30    4   36                                                       
CONECT   31    5   37                                                       
CONECT   32    7   12                                                       
CONECT   33   14   35                                                       
CONECT   34   36   37                                                       
CONECT   35   23   24   25   33                                             
CONECT   36   26   27   30   34                                             
CONECT   37   28   29   31   34                                             
CONECT   38    7                                                            
CONECT   39    8                                                            
CONECT   40   10                                                            
CONECT   41   11                                                            
CONECT   42   12                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   86    0
END

Synonyms

Value	Source
4-CDP-2-C-Methyl-D-erythritol 2-phosphate	ChEBI
4-CDP-2-C-Methyl-D-erythritol 2-phosphate tetraanion	ChEBI
4-CDP-2-C-Methyl-D-erythritol 2-phosphoric acid	Generator
4-CDP-2-C-Methyl-D-erythritol 2-phosphoric acid tetraanion	Generator
4-CDP-2-c-Methyl-D-erythritol 2-phosphoric acid(4-)	Generator

Molecular Formula

C₁₄H₂₂N₃O₁₇P₃

Average Mass

597.257

Monoisotopic Mass

597.018401574

IUPAC Name

1-[(2R,3R,4S,5R)-5-[({[(2R,3S)-2,4-dihydroxy-3-methyl-3-(phosphonooxy)butoxy](hydroxy)phosphoryl phosphono}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-olate

Traditional Name

1-[(2R,3R,4S,5R)-5-({[(2R,3S)-2,4-dihydroxy-3-methyl-3-(phosphonooxy)butoxy(hydroxy)phosphoryl phosphono]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-iminopyrimidin-2-olate

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(COP(O)(=O)OP([O-])(=O)OC[C@@]1([H])O[C@@]([H])(N2C=CC(=N)N=C2[O-])[C@]([H])(O)[C@]1([H])O)[C@](C)(CO)OP([O-])([O-])=O

InChI Identifier

InChI=1S/C14H26N3O17P3/c1-14(6-18,33-35(23,24)25)8(19)5-31-37(28,29)34-36(26,27)30-4-7-10(20)11(21)12(32-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21H,4-6H2,1H3,(H,26,27)(H,28,29)(H2,15,16,22)(H2,23,24,25)/p-4/t7-,8-,10-,11-,12-,14+/m1/s1

InChI Key

HTJXTKBIUVFUAR-XHIBXCGHSA-J

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

nucleotide-sugar oxoanion (CHEBI:57919 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	35.5 g/L	ALOGPS
logP	-1	ALOGPS
logP	-5.3	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	1.05	ChemAxon
pKa (Strongest Basic)	1.85	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	330.2 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	133.1 m³·mol⁻¹	ChemAxon
Polarizability	47.38 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

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum

Biological Properties

Cellular Locations

Not Available

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
MMDBr0013768	4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol	2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	Phosphorylation	RHEA	34755880
MMDBr0013769	4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol	2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	Phosphorylation	RHEA	34755880
MMDBr0014392	2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	2-C-Methyl-D-erythritol-2,4-cyclodiphosphate	Bifunctional enzyme IspD/IspF	Synthesis	RHEA	34755880
MMDBr0018654	Adenosine triphosphate	Hydrogen Ion	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	Phosphorylation	PathBank	31602464
MMDBr0018655	2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	Cytidine monophosphate	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	Synthesis	PathBank	31602464

Health Effects and Bioactivity

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

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	372	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; River trout ; Rat ; Dog ; Lion ; Chicken ; Sheep ; Turkey	Unknown
Bacteria	Cyanobacteria	32	Human
Bacteria	Firmicutes	113	Human feces; Human ; Catfish ; Cattle
Bacteria	Aquificae	4
Bacteria	Actinobacteria	53	Human ; Human feces; Cattle
Bacteria	Bacteroidetes	10	Human ; Human feces
Bacteria	Chlamydiae	10	Human ; Sheep ; Cat
Bacteria	Chlorobi	11
Bacteria	Chloroflexi	3
Bacteria	Deinococcus-thermus	4
Bacteria	Thermotogae	10
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Spirochaetes	10	Human ; Pig
Bacteria	Verrucomicrobia	2	Human ; Human feces
Bacteria	Planctomycetes	1
Bacteria	Acidobacteria	2
Bacteria	nah	1
Bacteria	Nitrospirae	1
Bacteria	Tenericutes	4	Human
Bacteria/NULL	Proteobacteria	2	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; River trout ; Rat ; Dog ; Lion ; Chicken ; Sheep ; Turkey	Unknown
Bacteria	Elusimicrobia	1
Bacteria	Gemmatimonadetes	1

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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46878430

PDB ID

Not Available

ChEBI ID

57919

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (MMDBc0029980)

MOL for #<Metabolite:0x000055d246ebb8b0>

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3D PDB for #<Metabolite:0x000055d246ebb8b0>

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Structure for #<Metabolite:0x000055d246ebb8b0>

3D Structure for #<Metabolite:0x000055d246ebb8b0>