MiMeDB: Showing metabocard for 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol (MMDBc0030011)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:50:36 UTC

Update Date

2022-08-31 17:38:39 UTC

MiMeDB ID

MMDBc0030011

Metabolite Identification

Common Name

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

Description

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. CDP-ME is an intermediate in the mevalonate-independent pathway for isoprenoid biosynthesis in a number of prokaryotic organisms, algae, the plant plastids and the malaria parasite. (PMID 11427897 ) In the MEP pathway, 4-diphosphocytidyl-2-C-methyl-D-erythritol is formed from 2-C-methyl-D-erythritol 4-phosphate (MEP) and CTP in a reaction catalyzed by a 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase (IspD). (PMID 17921290 ) Diphosphocytidyl-methylerythritol (DPCME) synthetase is involved in the mevalonate-independent pathway of isoprenoid biosynthesis, where it catalyses the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from 2-C-methyl-D-erythritol 4-phosphate and CTP. (PMID 11468415 )

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303082006192D          

 38 39  0  0  0  0            999 V2000
    3.0814    4.2321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9870   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5021   -3.2607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4882   -0.8001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3802    2.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1209    3.7024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2728   -1.0550    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5517    3.1925    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8075   -3.8419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9403   -0.5701    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6077   -1.0550    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3528   -1.8396    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6582   -2.4208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3363    3.4475    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2924   -4.5094    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1431   -3.0883    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8377   -2.5071    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2924    4.5094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9386    3.7446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9403    0.2548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3923   -0.8001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9937   -1.6672    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.5912    2.6629    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7228   -0.5228    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.2129    1.0464    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2310    1.1521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6170    1.4952    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3167    0.0068    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5955    2.1306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5278   -1.8396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2525    0.5167    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4679    0.2617    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.4240    1.3237    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1438   -0.2402    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1648    2.6405    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6753   -0.1955    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1911   -1.6384    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9782   -2.5747    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
 14 23  1  1  0  0  0
 28  4  1  0  0  0  0
 29  5  1  0  0  0  0
 30  7  1  0  0  0  0
 30 12  1  0  0  0  0
 32 24  1  0  0  0  0
 32 25  2  0  0  0  0
 32 28  1  0  0  0  0
 32 31  1  0  0  0  0
 33 26  1  0  0  0  0
 33 27  2  0  0  0  0
 33 29  1  0  0  0  0
 33 31  1  0  0  0  0
  7 34  1  6  0  0  0
  8 35  1  6  0  0  0
 10 36  1  1  0  0  0
 11 37  1  1  0  0  0
 12 38  1  6  0  0  0
M  CHG  2  22  -1  24  -1
M  END


  Mrv1652303082006192D          

 38 39  0  0  0  0            999 V2000
    3.0814    4.2321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9870   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5021   -3.2607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4882   -0.8001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3802    2.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1209    3.7024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2728   -1.0550    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5517    3.1925    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8075   -3.8419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9403   -0.5701    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6077   -1.0550    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3528   -1.8396    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6582   -2.4208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3363    3.4475    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2924   -4.5094    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1431   -3.0883    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8377   -2.5071    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2924    4.5094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9386    3.7446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9403    0.2548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3923   -0.8001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9937   -1.6672    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.5912    2.6629    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7228   -0.5228    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.2129    1.0464    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2310    1.1521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6170    1.4952    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3167    0.0068    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5955    2.1306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5278   -1.8396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2525    0.5167    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4679    0.2617    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.4240    1.3237    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1438   -0.2402    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1648    2.6405    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6753   -0.1955    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1911   -1.6384    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9782   -2.5747    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
 14 23  1  1  0  0  0
 28  4  1  0  0  0  0
 29  5  1  0  0  0  0
 30  7  1  0  0  0  0
 30 12  1  0  0  0  0
 32 24  1  0  0  0  0
 32 25  2  0  0  0  0
 32 28  1  0  0  0  0
 32 31  1  0  0  0  0
 33 26  1  0  0  0  0
 33 27  2  0  0  0  0
 33 29  1  0  0  0  0
 33 31  1  0  0  0  0
  7 34  1  6  0  0  0
  8 35  1  6  0  0  0
 10 36  1  1  0  0  0
 11 37  1  1  0  0  0
 12 38  1  6  0  0  0
M  CHG  2  22  -1  24  -1
M  END
> <DATABASE_ID>
MMDBc0030011

> <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)(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/p-2/t7-,8-,10-,11-,12-,14+/m1/s1

> <INCHI_KEY>
YFAUKWZNPVBCFF-XHIBXCGHSA-L

> <FORMULA>
C14H23N3O14P2

> <MOLECULAR_WEIGHT>
519.294

> <EXACT_MASS>
519.066623588

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
43.584131205357565

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.73

> <JCHEM_LOGP>
-4.611989542530284

> <ALOGPS_LOGS>
-1.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.5406688718482373

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7734910875909096

> <JCHEM_PKA_STRONGEST_BASIC>
3.342646991099132

> <JCHEM_POLAR_SURFACE_AREA>
278.01

> <JCHEM_REFRACTIVITY>
124.46949999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.52e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy((2R,3S)-2,3,4-trihydroxy-3-methylbutoxy)phosphoryl phosphono]oxy}methyl)oxolan-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       5.752   7.900   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.576  -7.333   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.671  -6.087   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.911  -1.494   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.443   4.453   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.692   6.911   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.376  -1.969   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.763   5.959   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -7.107  -7.172   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.622  -1.064   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.868  -1.969   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.392  -3.434   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.829  -4.519   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.228   6.435   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -8.012  -8.418   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -7.734  -5.765   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      -5.297  -4.680   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       8.012   8.418   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       3.619   6.990   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -3.622   0.476   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -6.332  -1.494   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -7.455  -3.112   0.000  0.00  0.00           O-1
HETATM   23  O   UNK     0       6.704   4.971   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.349  -0.976   0.000  0.00  0.00           O-1
HETATM   25  O   UNK     0       0.397   1.953   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       4.165   2.151   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       1.152   2.791   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -0.591   0.013   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       2.978   3.977   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -2.852  -3.434   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       2.338   0.965   0.000  0.00  0.00           O+0
HETATM   32  P   UNK     0       0.873   0.489   0.000  0.00  0.00           P+0
HETATM   33  P   UNK     0       2.658   2.471   0.000  0.00  0.00           P+0
HETATM   34  H   UNK     0      -2.135  -0.448   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0       5.908   4.929   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0      -4.994  -0.365   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0      -5.957  -3.058   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0      -3.693  -4.806   0.000  0.00  0.00           H+0
CONECT    1   14                                                            
CONECT    2    3    9                                                       
CONECT    3    2   17                                                       
CONECT    4    7   28                                                       
CONECT    5    8   29                                                       
CONECT    6   14   18                                                       
CONECT    7    4   10   30   34                                             
CONECT    8    5   14   19   35                                             
CONECT    9    2   15   16                                                  
CONECT   10    7   11   20   36                                             
CONECT   11   10   12   21   37                                             
CONECT   12   11   17   30   38                                             
CONECT   13   16   17   22                                                  
CONECT   14    1    6    8   23                                             
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   14                                                            
CONECT   24   32                                                            
CONECT   25   32                                                            
CONECT   26   33                                                            
CONECT   27   33                                                            
CONECT   28    4   32                                                       
CONECT   29    5   33                                                       
CONECT   30    7   12                                                       
CONECT   31   32   33                                                       
CONECT   32   24   25   28   31                                             
CONECT   33   26   27   29   31                                             
CONECT   34    7                                                            
CONECT   35    8                                                            
CONECT   36   10                                                            
CONECT   37   11                                                            
CONECT   38   12                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   78    0
END

Synonyms

Value	Source
4-CDP-2-C-Methyl-D-erythritol	ChEBI
4-CDP-2-C-Methyl-D-erythritol dianion	ChEBI
5'-O-{[({[(2R,3S)-2,3,4-trihydroxy-3-methylbutyl]oxy}phosphinato)oxy]phosphinato}cytidine	ChEBI
4-DPCME	MeSH
4-Diphosphocytidyl-2-C-methylerythritol	MeSH
4-Diphosphocytidyl-2C-methyl-D-erythritol	MeSH

Chemical Formula

C₁₄H₂₃N₃O₁₄P₂

Average Molecular Weight

519.294

Monoisotopic Molecular Weight

519.066623588

IUPAC Name

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

Traditional Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy((2R,3S)-2,3,4-trihydroxy-3-methylbutoxy)phosphoryl phosphono]oxy}methyl)oxolan-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)(O)CO

InChI Identifier

InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/p-2/t7-,8-,10-,11-,12-,14+/m1/s1

InChI Key

YFAUKWZNPVBCFF-XHIBXCGHSA-L

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

nucleotide-sugar oxoanion (CHEBI:57823 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	25.2 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-4.6	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	3.34	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	278.01 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	124.47 m³·mol⁻¹	ChemAxon
Polarizability	43.58 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
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	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

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
	Proteobacteria	369	Human ; Pig ; Cattle ; Chicken ; Human Feces; Rat ; Sheep ; Lion ; Dog	Unknown;
	Cyanobacteria	34	Human
	Acidobacteria	2
	Firmicutes	110	Human Feces; Human ; Catfish ; Cattle
	Aquificae	4
	Bacteroidetes	10	Human
	Actinobacteria	47	Human ; Cattle ; Human Feces
	Chlamydiae	10	Human ; Cat
	Chlorobi	11
	Chloroflexi	3
	Deinococcus-Thermus	4
	Dictyoglomi	1
	Elusimicrobia	1
	Fusobacteria	1	Human
	Spirochaetes	9	Human
	Thermotogae	9
	Planctomycetes	1
		1
	Verrucomicrobia	1
	Nitrospirae	1
	Tenericutes	3	Human
NULL	Proteobacteria	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

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

24970669

PDB ID

Not Available

ChEBI ID

57823

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 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol (MMDBc0030011)

MOL for #<Metabolite:0x0000564abfbd2aa8>

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3D Structure for #<Metabolite:0x0000564abfbd2aa8>