MiMeDB: Showing metabocard for Cytidine 2',3'-cyclic phosphate (MMDBc0000650)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:51:56 UTC

Update Date

2024-04-30 19:33:25 UTC

Metabolite ID

MMDBc0000650

Metabolite Identification

Common Name

Cytidine 2',3'-cyclic phosphate

Description

Cytidine 2',3'-cyclic phosphate is a cytidine nucleotide containing a pyrophosphate group esterified to C2 and C3(cyclic) of the sugar moiety. A cyclic nucleotide is any nucleotide in which the phosphate group is bonded to two of the sugar's hydroxyl groups, forming a cyclical or ring structure. 2',3' cyclic CMP is a substrate for 2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37). This enzyme (also called CNP) catalyzes the chemical reaction: nucleoside 2',3'-cyclic phosphate + H2O <-> nucleoside 2'-phosphate. CNP is a myelin-associated enzyme that makes up 4% of total CNS myelin protein, and is thought to undergo significant age-associated changes. The absence of CNP causes axonal swelling and neuronal degeneration. The biological role of cyclic 2',3' monophosphates is not clear, although it is thought to have something to do with neuronal stasis or development.

Structure

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

HMDB0011691
     RDKit          3D
Cytidine 2',3'-cyclic phosphate
 32 34  0  0  0  0  0  0  0  0999 V2000
    5.4361   -0.9862   -0.3934 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0732   -0.6220   -0.2819 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6896    0.1677    0.7749 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3666    0.5332    0.9009 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135    0.1409    0.0133 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0931    0.5438    0.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6068    0.9059   -0.9461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9425    0.9784   -0.5978 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4157    2.4072   -0.4342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7673    2.3536   -0.0856 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0970    0.2992    0.7385 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1723   -0.5209    0.8470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6623   -1.9332    0.0733 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.3739   -2.0772   -1.2359 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8710   -3.2298    1.1021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0089   -1.5658   -0.1572 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8365   -0.5438    0.7487 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8288   -0.6320   -1.0083 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9436   -0.9962   -1.8324 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1249   -1.0071   -1.1572 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1494   -0.2128   -0.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7810   -1.9559   -0.4468 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4506    0.4891    1.4956 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0976    1.1518    1.7386 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0054    1.3918    0.9105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5611    0.5133   -1.3783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8909    2.8414    0.4630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2766    3.0180   -1.3254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3615    2.4468   -0.8632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9870    1.0319    1.5651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0833   -4.0732    0.6724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5387   -0.8580    1.7531 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
  8 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 16 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  2  0
 17  6  1  0
 17 11  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  6 25  1  0
  8 26  1  6
  9 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  1
 15 31  1  0
 17 32  1  1
M  END


  Mrv0541 02241201502D          

 20 22  0  0  1  0            999 V2000
   10.3600   -7.4485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5316   -8.2555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.5754   -7.1936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9185   -8.8075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9624   -7.7456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1339   -8.5526    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.0900   -9.6145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3162   -8.5104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9837   -8.0255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5712   -9.2950    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.6511   -8.5104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.3962   -9.2950    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.1778   -7.4907    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.3162  -10.0797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6511  -10.0797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4357   -8.2555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6073   -7.4485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9837  -10.5646    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   12.3962  -11.2791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5712  -11.2791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  4  2  0  0  0  0
  9  8  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 12 11  1  0  0  0  0
  2  8  1  0  0  0  0
 13  5  1  0  0  0  0
 10 14  1  1  0  0  0
 12 15  1  1  0  0  0
 11 16  1  6  0  0  0
 17 16  1  0  0  0  0
 19 18  2  0  0  0  0
 20 18  1  0  0  0  0
 14 18  1  0  0  0  0
 18 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000650

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(=O)N(C=C1)C1O[C@H](CO)[C@H]2OP(O)(=O)O[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N3O7P/c10-5-1-2-12(9(14)11-5)8-7-6(4(3-13)17-8)18-20(15,16)19-7/h1-2,4,6-8,13H,3H2,(H,15,16)(H2,10,11,14)/t4-,6-,7-,8?/m1/s1

> <INCHI_KEY>
NMPZCCZXCOMSDQ-ZRTZXPPTSA-N

> <FORMULA>
C9H12N3O7P

> <MOLECULAR_WEIGHT>
305.1812

> <EXACT_MASS>
305.041286265

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
25.76071278729555

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(3aR,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxo-tetrahydro-2H-2λ⁵-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-4-amino-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.78

> <JCHEM_LOGP>
-2.2562422969105067

> <ALOGPS_LOGS>
-1.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.584903044550341

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.6486125153578648

> <JCHEM_PKA_STRONGEST_BASIC>
1.764223084638504

> <JCHEM_POLAR_SURFACE_AREA>
143.91

> <JCHEM_REFRACTIVITY>
61.6387

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(3aR,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxo-tetrahydro-2λ⁵-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-4-aminopyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0011691
     RDKit          3D
Cytidine 2',3'-cyclic phosphate
 32 34  0  0  0  0  0  0  0  0999 V2000
    5.4361   -0.9862   -0.3934 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0732   -0.6220   -0.2819 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6896    0.1677    0.7749 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3666    0.5332    0.9009 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135    0.1409    0.0133 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0931    0.5438    0.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6068    0.9059   -0.9461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9425    0.9784   -0.5978 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4157    2.4072   -0.4342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7673    2.3536   -0.0856 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0970    0.2992    0.7385 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1723   -0.5209    0.8470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6623   -1.9332    0.0733 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.3739   -2.0772   -1.2359 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8710   -3.2298    1.1021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0089   -1.5658   -0.1572 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8365   -0.5438    0.7487 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8288   -0.6320   -1.0083 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9436   -0.9962   -1.8324 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1249   -1.0071   -1.1572 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1494   -0.2128   -0.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7810   -1.9559   -0.4468 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4506    0.4891    1.4956 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0976    1.1518    1.7386 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0054    1.3918    0.9105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5611    0.5133   -1.3783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8909    2.8414    0.4630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2766    3.0180   -1.3254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3615    2.4468   -0.8632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9870    1.0319    1.5651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0833   -4.0732    0.6724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5387   -0.8580    1.7531 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
  8 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 16 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  2  0
 17  6  1  0
 17 11  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  6 25  1  0
  8 26  1  6
  9 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  1
 15 31  1  0
 17 32  1  1
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      19.339 -13.904   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      19.659 -15.410   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      17.874 -13.428   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      18.515 -16.441   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.730 -14.458   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      17.050 -15.965   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      18.835 -17.947   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      21.124 -15.886   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      22.370 -14.981   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      21.600 -17.351   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.615 -15.886   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      23.140 -17.351   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      15.265 -13.983   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0      21.124 -18.815   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      23.615 -18.815   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      25.080 -15.410   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      25.400 -13.904   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0      22.370 -19.721   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0      23.140 -21.054   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      21.600 -21.054   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4    8                                                  
CONECT    3    1    5                                                       
CONECT    4    2    6    7                                                  
CONECT    5    3    6   13                                                  
CONECT    6    4    5                                                       
CONECT    7    4                                                            
CONECT    8    9   10    2                                                  
CONECT    9    8   11                                                       
CONECT   10    8   12   14                                                  
CONECT   11    9   12   16                                                  
CONECT   12   10   11   15                                                  
CONECT   13    5                                                            
CONECT   14   10   18                                                       
CONECT   15   12   18                                                       
CONECT   16   11   17                                                       
CONECT   17   16                                                            
CONECT   18   19   20   14   15                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

COMPND    HMDB0011691
HETATM    1  N1  UNL     1       5.436  -0.986  -0.393  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.073  -0.622  -0.282  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.690   0.168   0.775  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.367   0.533   0.901  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.413   0.141   0.013  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.093   0.544   0.196  1.00  0.00           C  
HETATM    7  O1  UNL     1      -0.607   0.906  -0.946  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.943   0.978  -0.598  1.00  0.00           C  
HETATM    9  C6  UNL     1      -2.416   2.407  -0.434  1.00  0.00           C  
HETATM   10  O2  UNL     1      -3.767   2.354  -0.086  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.097   0.299   0.738  1.00  0.00           C  
HETATM   12  O3  UNL     1      -3.172  -0.521   0.847  1.00  0.00           O  
HETATM   13  P1  UNL     1      -2.662  -1.933   0.073  1.00  0.00           P  
HETATM   14  O4  UNL     1      -3.374  -2.077  -1.236  1.00  0.00           O  
HETATM   15  O5  UNL     1      -2.871  -3.230   1.102  1.00  0.00           O  
HETATM   16  O6  UNL     1      -1.009  -1.566  -0.157  1.00  0.00           O  
HETATM   17  C8  UNL     1      -0.837  -0.544   0.749  1.00  0.00           C  
HETATM   18  C9  UNL     1       1.829  -0.632  -1.008  1.00  0.00           C  
HETATM   19  O7  UNL     1       0.944  -0.996  -1.832  1.00  0.00           O  
HETATM   20  N3  UNL     1       3.125  -1.007  -1.157  1.00  0.00           N  
HETATM   21  H1  UNL     1       6.149  -0.213  -0.424  1.00  0.00           H  
HETATM   22  H2  UNL     1       5.781  -1.956  -0.447  1.00  0.00           H  
HETATM   23  H3  UNL     1       4.451   0.489   1.496  1.00  0.00           H  
HETATM   24  H4  UNL     1       2.098   1.152   1.739  1.00  0.00           H  
HETATM   25  H5  UNL     1       0.005   1.392   0.910  1.00  0.00           H  
HETATM   26  H6  UNL     1      -2.561   0.513  -1.378  1.00  0.00           H  
HETATM   27  H7  UNL     1      -1.891   2.841   0.463  1.00  0.00           H  
HETATM   28  H8  UNL     1      -2.277   3.018  -1.325  1.00  0.00           H  
HETATM   29  H9  UNL     1      -4.361   2.447  -0.863  1.00  0.00           H  
HETATM   30  H10 UNL     1      -1.987   1.032   1.565  1.00  0.00           H  
HETATM   31  H11 UNL     1      -3.083  -4.073   0.672  1.00  0.00           H  
HETATM   32  H12 UNL     1      -0.539  -0.858   1.753  1.00  0.00           H  
CONECT    1    2   21   22
CONECT    2    3   20   20
CONECT    3    4    4   23
CONECT    4    5   24
CONECT    5    6   18
CONECT    6    7   17   25
CONECT    7    8
CONECT    8    9   11   26
CONECT    9   10   27   28
CONECT   10   29
CONECT   11   12   17   30
CONECT   12   13
CONECT   13   14   14   15   16
CONECT   15   31
CONECT   16   17
CONECT   17   32
CONECT   18   19   19   20
END

HMDB0011691
     RDKit          3D
Cytidine 2',3'-cyclic phosphate
 32 34  0  0  0  0  0  0  0  0999 V2000
    5.4361   -0.9862   -0.3934 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0732   -0.6220   -0.2819 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6896    0.1677    0.7749 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3666    0.5332    0.9009 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135    0.1409    0.0133 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0931    0.5438    0.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6068    0.9059   -0.9461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9425    0.9784   -0.5978 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4157    2.4072   -0.4342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7673    2.3536   -0.0856 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0970    0.2992    0.7385 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1723   -0.5209    0.8470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6623   -1.9332    0.0733 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.3739   -2.0772   -1.2359 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8710   -3.2298    1.1021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0089   -1.5658   -0.1572 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8365   -0.5438    0.7487 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8288   -0.6320   -1.0083 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9436   -0.9962   -1.8324 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1249   -1.0071   -1.1572 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1494   -0.2128   -0.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7810   -1.9559   -0.4468 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4506    0.4891    1.4956 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0976    1.1518    1.7386 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0054    1.3918    0.9105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5611    0.5133   -1.3783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8909    2.8414    0.4630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2766    3.0180   -1.3254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3615    2.4468   -0.8632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9870    1.0319    1.5651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0833   -4.0732    0.6724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5387   -0.8580    1.7531 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
  8 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 16 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  2  0
 17  6  1  0
 17 11  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  6 25  1  0
  8 26  1  6
  9 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  1
 15 31  1  0
 17 32  1  1
M  END

Synonyms

Value	Source
Cytidine 2',3'-cyclic phosphoric acid	Generator
2',3' Cyclic CMP	HMDB
2',3' Cyclic-CMP	HMDB
Cyclic(2',3')-CMP	HMDB
Cytidine-2',3'-cyclophosphate	HMDB

Molecular Formula

C₉H₁₂N₃O₇P

Average Mass

305.1812

Monoisotopic Mass

305.041286265

IUPAC Name

1-[(3aR,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxo-tetrahydro-2H-2λ⁵-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-4-amino-1,2-dihydropyrimidin-2-one

Traditional Name

1-[(3aR,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxo-tetrahydro-2λ⁵-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-4-aminopyrimidin-2-one

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)C1O[C@H](CO)[C@H]2OP(O)(=O)O[C@@H]12

InChI Identifier

InChI=1S/C9H12N3O7P/c10-5-1-2-12(9(14)11-5)8-7-6(4(3-13)17-8)18-20(15,16)19-7/h1-2,4,6-8,13H,3H2,(H,15,16)(H2,10,11,14)/t4-,6-,7-,8?/m1/s1

InChI Key

NMPZCCZXCOMSDQ-ZRTZXPPTSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2',3'-cyclic pyrimidine nucleotides. These are pyrimidine nucleotides in which the oxygen atoms linked to the C2 and C3 carbon atoms of the ribose moiety are both bonded the same phosphorus atom of the phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Cyclic pyrimidine nucleotides

Direct Parent

2',3'-cyclic pyrimidine nucleotides

Alternative Parents

Substituents

2',3'-cyclic pyrimidine ribonucleotide
Ribonucleoside 3'-phosphate
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
1,3_dioxaphospholane
Organoheterocyclic compound
Oxacycle
Azacycle
Organic oxide
Primary alcohol
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organic nitrogen compound
Primary amine
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	20.5 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.3	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	-0.65	ChemAxon
pKa (Strongest Basic)	1.76	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	143.91 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	61.64 m³·mol⁻¹	ChemAxon
Polarizability	25.76 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces
Placenta

Tissue Locations

Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0193538	2',3'-cyclic-nucleotide 3'-phosphodiesterase	Enzyme	P09543	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0026035	Cytidine 2',3'-cyclic phosphate	Cytidine 2'-monophosphate	2',3'-cyclic-nucleotide 3'-phosphodiesterase	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	RHEA	34755880
MMDBr0026050	Cytidine 2',3'-cyclic phosphate	Cytidine 3'-monophosphate	2',3'-cyclic-nucleotide 2'-phosphodiesterase	Hydrolysis of nucleotide; Dephosphorylation	RHEA	34755880

Health Effects and Bioactivity

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

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Bacteroidetes	1	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Proteobacteria	1		Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Placenta	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0011691

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028378

KNApSAcK ID

Not Available

Chemspider ID

35032090

KEGG Compound ID

C00127

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Glutathione disulfide

METLIN ID

Not Available

PubChem Compound

53481030

PDB ID

Not Available

ChEBI ID

177258

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for Cytidine 2',3'-cyclic phosphate (MMDBc0000650)

MOL for #<Metabolite:0x00007f92386a6f40>

3D MOL for #<Metabolite:0x00007f92386a6f40>

3D SDF for #<Metabolite:0x00007f92386a6f40>

3D-SDF for #<Metabolite:0x00007f92386a6f40>

PDB for #<Metabolite:0x00007f92386a6f40>

3D PDB for #<Metabolite:0x00007f92386a6f40>

SMILES for #<Metabolite:0x00007f92386a6f40>

INCHI for #<Metabolite:0x00007f92386a6f40>

Structure for #<Metabolite:0x00007f92386a6f40>

3D Structure for #<Metabolite:0x00007f92386a6f40>