MiMeDB: Showing metabocard for 3'-CMP (MMDBc0030008)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:50:29 UTC

Update Date

2022-08-31 17:38:37 UTC

Metabolite ID

MMDBc0030008

Metabolite Identification

Common Name

3'-CMP

Description

Cytidine monophosphate, also known as 3'-cytidylic acid and abbreviated CMP, is an ester of phosphoric acid with the nucleoside cytidine. CMP consists of the phosphate group, the pentose sugar ribose, and the nucleobase cytosine. It is an unusual, but naturally occurring form of CMP, as the normal form is 5'-CMP. It is a substrate for 2',3'-cyclic-nucleotide 2'-phosphodiesterase.

Structure

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

HMDB0243501
     RDKit          3D
Cytosine arabinose-5'-phosphate
 35 36  0  0  0  0  0  0  0  0999 V2000
   -6.2577   -0.5789    0.0914 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9805   -0.3884    0.1922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4747    0.7936    0.6816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1017    0.9058    0.7524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2736   -0.0926    0.3621 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8647    0.1377    0.4815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0848   -0.8758   -0.0028 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0615   -0.3563   -0.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3004   -0.7663    0.2663 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3883   -0.1794   -0.3795 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8390   -0.5317    0.3839 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.8076   -0.1878    1.8547 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1598   -2.1794    0.1968 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0462    0.4232   -0.3222 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9850    1.1447   -0.4668 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5665    1.7833   -1.5431 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5198    1.3355   -0.4156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1014    1.1208   -1.6410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8015   -1.2452   -0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9366   -2.2586   -0.5115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1345   -1.3558   -0.1852 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9023    0.1851    0.3899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1450    1.5897    0.9927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6873    1.8366    1.1380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5634    0.4570    1.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2577   -0.7093   -1.5843 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4469   -1.8562    0.2221 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1378   -0.3790    1.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1384   -2.2528    0.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1560    1.2924    0.1343 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3726    1.5090    0.5149 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1965    2.4631   -1.1646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8118    2.2909    0.0578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0041    0.1494   -1.8608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2147   -3.2242   -0.2813 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  1  0
 19 21  2  0
 21  2  1  0
 17  6  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  6 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 13 29  1  0
 14 30  1  0
 15 31  1  0
 16 32  1  0
 17 33  1  0
 18 34  1  0
 20 35  1  0
M  END


  Mrv1652310061709502D          

 21 22  0  0  0  0            999 V2000
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3856   -0.3337    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559   -1.3733    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3460    0.1959    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8163   -0.8436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6010   -0.5887    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 11  9  2  0  0  0  0
 12  2  1  0  0  0  0
 12  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13  6  1  0  0  0  0
 14  7  1  0  0  0  0
 15  9  1  0  0  0  0
 19  3  1  0  0  0  0
 20  4  1  0  0  0  0
 20  8  1  0  0  0  0
 21 16  1  0  0  0  0
 21 17  1  0  0  0  0
 21 18  2  0  0  0  0
 21 19  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030008

> <DATABASE_NAME>
MIME

> <SMILES>
OC1C(O)C(OC1COP(O)(O)=O)N1C=CC(=N)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)

> <INCHI_KEY>
IERHLVCPSMICTF-UHFFFAOYSA-N

> <FORMULA>
C9H14N3O8P

> <MOLECULAR_WEIGHT>
323.1965

> <EXACT_MASS>
323.051850951

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
27.433986505371024

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.04

> <JCHEM_LOGP>
-3.008585562389507

> <ALOGPS_LOGS>
-1.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.690471222131144

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2066420956975517

> <JCHEM_PKA_STRONGEST_BASIC>
2.567695935530979

> <JCHEM_POLAR_SURFACE_AREA>
176.13

> <JCHEM_REFRACTIVITY>
76.83019999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0243501
     RDKit          3D
Cytosine arabinose-5'-phosphate
 35 36  0  0  0  0  0  0  0  0999 V2000
   -6.2577   -0.5789    0.0914 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9805   -0.3884    0.1922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4747    0.7936    0.6816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1017    0.9058    0.7524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2736   -0.0926    0.3621 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8647    0.1377    0.4815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0848   -0.8758   -0.0028 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0615   -0.3563   -0.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3004   -0.7663    0.2663 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3883   -0.1794   -0.3795 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8390   -0.5317    0.3839 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.8076   -0.1878    1.8547 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1598   -2.1794    0.1968 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0462    0.4232   -0.3222 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9850    1.1447   -0.4668 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5665    1.7833   -1.5431 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5198    1.3355   -0.4156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1014    1.1208   -1.6410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8015   -1.2452   -0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9366   -2.2586   -0.5115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1345   -1.3558   -0.1852 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9023    0.1851    0.3899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1450    1.5897    0.9927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6873    1.8366    1.1380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5634    0.4570    1.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2577   -0.7093   -1.5843 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4469   -1.8562    0.2221 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1378   -0.3790    1.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1384   -2.2528    0.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1560    1.2924    0.1343 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3726    1.5090    0.5149 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1965    2.4631   -1.1646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8118    2.2909    0.0578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0041    0.1494   -1.8608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2147   -3.2242   -0.2813 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  1  0
 19 21  2  0
 21  2  1  0
 17  6  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  6 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 13 29  1  0
 14 30  1  0
 15 31  1  0
 16 32  1  0
 17 33  1  0
 18 34  1  0
 20 35  1  0
M  END

HEADER    PROTEIN                                 06-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-OCT-17         0                                  
HETATM    1  C   UNK     0       3.182  -6.383   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.087  -5.138   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.846  -0.544   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.650  -6.222   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.929  -3.570   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.745  -7.468   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       1.024  -4.816   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       3.460  -3.731   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       5.136   1.425   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.425  -0.544   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.302  -2.163   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      11.920  -0.623   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      10.931  -2.564   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       9.979   0.366   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       8.990  -1.575   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.906  -2.485   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0      10.455  -1.099   0.000  0.00  0.00           P+0
CONECT    1    2    5                                                       
CONECT    2    1   12                                                       
CONECT    3    4   19                                                       
CONECT    4    3    6   20                                                  
CONECT    5    1   10   11                                                  
CONECT    6    4    7   13                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7   12   20                                                  
CONECT    9   11   12   15                                                  
CONECT   10    5                                                            
CONECT   11    5    9                                                       
CONECT   12    2    8    9                                                  
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    9                                                            
CONECT   16   21                                                            
CONECT   17   21                                                            
CONECT   18   21                                                            
CONECT   19    3   21                                                       
CONECT   20    4    8                                                       
CONECT   21   16   17   18   19                                             
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

COMPND    HMDB0243501
HETATM    1  N1  UNL     1      -6.258  -0.579   0.091  1.00  0.00           N  
HETATM    2  C1  UNL     1      -4.981  -0.388   0.192  1.00  0.00           C  
HETATM    3  C2  UNL     1      -4.475   0.794   0.682  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.102   0.906   0.752  1.00  0.00           C  
HETATM    5  N2  UNL     1      -2.274  -0.093   0.362  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.865   0.138   0.481  1.00  0.00           C  
HETATM    7  O1  UNL     1      -0.085  -0.876  -0.003  1.00  0.00           O  
HETATM    8  C5  UNL     1       1.061  -0.356  -0.542  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.300  -0.766   0.266  1.00  0.00           C  
HETATM   10  O2  UNL     1       3.388  -0.179  -0.379  1.00  0.00           O  
HETATM   11  P1  UNL     1       4.839  -0.532   0.384  1.00  0.00           P  
HETATM   12  O3  UNL     1       4.808  -0.188   1.855  1.00  0.00           O  
HETATM   13  O4  UNL     1       5.160  -2.179   0.197  1.00  0.00           O  
HETATM   14  O5  UNL     1       6.046   0.423  -0.322  1.00  0.00           O  
HETATM   15  C7  UNL     1       0.985   1.145  -0.467  1.00  0.00           C  
HETATM   16  O6  UNL     1       1.567   1.783  -1.543  1.00  0.00           O  
HETATM   17  C8  UNL     1      -0.520   1.336  -0.416  1.00  0.00           C  
HETATM   18  O7  UNL     1      -1.101   1.121  -1.641  1.00  0.00           O  
HETATM   19  C9  UNL     1      -2.801  -1.245  -0.116  1.00  0.00           C  
HETATM   20  O8  UNL     1      -1.937  -2.259  -0.511  1.00  0.00           O  
HETATM   21  N3  UNL     1      -4.134  -1.356  -0.185  1.00  0.00           N  
HETATM   22  H1  UNL     1      -6.902   0.185   0.390  1.00  0.00           H  
HETATM   23  H2  UNL     1      -5.145   1.590   0.993  1.00  0.00           H  
HETATM   24  H3  UNL     1      -2.687   1.837   1.138  1.00  0.00           H  
HETATM   25  H4  UNL     1      -0.563   0.457   1.518  1.00  0.00           H  
HETATM   26  H5  UNL     1       1.258  -0.709  -1.584  1.00  0.00           H  
HETATM   27  H6  UNL     1       2.447  -1.856   0.222  1.00  0.00           H  
HETATM   28  H7  UNL     1       2.138  -0.379   1.284  1.00  0.00           H  
HETATM   29  H8  UNL     1       6.138  -2.253   0.016  1.00  0.00           H  
HETATM   30  H9  UNL     1       6.156   1.292   0.134  1.00  0.00           H  
HETATM   31  H10 UNL     1       1.373   1.509   0.515  1.00  0.00           H  
HETATM   32  H11 UNL     1       2.196   2.463  -1.165  1.00  0.00           H  
HETATM   33  H12 UNL     1      -0.812   2.291   0.058  1.00  0.00           H  
HETATM   34  H13 UNL     1      -1.004   0.149  -1.861  1.00  0.00           H  
HETATM   35  H14 UNL     1      -2.215  -3.224  -0.281  1.00  0.00           H  
CONECT    1    2    2   22
CONECT    2    3   21
CONECT    3    4    4   23
CONECT    4    5   24
CONECT    5    6   19
CONECT    6    7   17   25
CONECT    7    8
CONECT    8    9   15   26
CONECT    9   10   27   28
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   29
CONECT   14   30
CONECT   15   16   17   31
CONECT   16   32
CONECT   17   18   33
CONECT   18   34
CONECT   19   20   21   21
CONECT   20   35
END

HMDB0243501
     RDKit          3D
Cytosine arabinose-5'-phosphate
 35 36  0  0  0  0  0  0  0  0999 V2000
   -6.2577   -0.5789    0.0914 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9805   -0.3884    0.1922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4747    0.7936    0.6816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1017    0.9058    0.7524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2736   -0.0926    0.3621 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8647    0.1377    0.4815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0848   -0.8758   -0.0028 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0615   -0.3563   -0.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3004   -0.7663    0.2663 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3883   -0.1794   -0.3795 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8390   -0.5317    0.3839 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.8076   -0.1878    1.8547 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1598   -2.1794    0.1968 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0462    0.4232   -0.3222 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9850    1.1447   -0.4668 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5665    1.7833   -1.5431 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5198    1.3355   -0.4156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1014    1.1208   -1.6410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8015   -1.2452   -0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9366   -2.2586   -0.5115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1345   -1.3558   -0.1852 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9023    0.1851    0.3899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1450    1.5897    0.9927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6873    1.8366    1.1380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5634    0.4570    1.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2577   -0.7093   -1.5843 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4469   -1.8562    0.2221 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1378   -0.3790    1.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1384   -2.2528    0.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1560    1.2924    0.1343 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3726    1.5090    0.5149 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1965    2.4631   -1.1646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8118    2.2909    0.0578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0041    0.1494   -1.8608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2147   -3.2242   -0.2813 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  1  0
 19 21  2  0
 21  2  1  0
 17  6  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
  6 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 13 29  1  0
 14 30  1  0
 15 31  1  0
 16 32  1  0
 17 33  1  0
 18 34  1  0
 20 35  1  0
M  END

Synonyms

Value	Source
Cytosine arabinose-5'-phosphoric acid	Generator
Cytidine 5'-(dihydrogen phosphoric acid)	HMDB
Acids, polycytidylic	HMDB
Cytosine polynucleotides	HMDB
Poly C	HMDB
Polynucleotides, cytosine	HMDB
C, Poly	HMDB
Polycytidylic acids	HMDB

Molecular Formula

C₉H₁₄N₃O₈P

Average Mass

323.1965

Monoisotopic Mass

323.051850951

IUPAC Name

{[3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid

Traditional Name

[3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

63-37-6

SMILES

OC1C(O)C(OC1COP(O)(O)=O)N1C=CC(=N)N=C1O

InChI Identifier

InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)

InChI Key

IERHLVCPSMICTF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate 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 monophosphates

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	4.89 g/L	ALOGPS
logP	-2	ALOGPS
logP	-3	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	1.21	ChemAxon
pKa (Strongest Basic)	2.57	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	176.13 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	76.83 m³·mol⁻¹	ChemAxon
Polarizability	27.43 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9510000000-e2c5fb35ca9de806fdd1	2018-04-09	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_6) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2021-11-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0901000000-74cc09b6afe230ac2f3b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-3900000000-e684c62be0364b92eb98	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-7900000000-9ea3f20b72c079b85fbf	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0200-9848000000-90dcc7853f9127be7cd1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9200000000-65f0668e20ac68ad2da4	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-b0126a942406e80ca008	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-024i-0988000000-8c6e5b45eb57bb0b4ba2	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0920000000-aeff826b66dc61a2eb7c	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dj-7900000000-930ba7f66dc58ef04d3a	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-3409000000-52a220c57d7ec5346f82	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9300000000-51863ddac1b6d47b88f8	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-5fcfbdf7a01dd3366a68	2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 22.53 MHz, D₂O, experimental)		2016-09-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-12	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Placenta

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
MMDBr0014748	3'-CMP	Cytidine	5'/3'-nucleotidase SurE	Hydrolysis of nucleotide	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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference
Animal	Milk	Bos taurus	FooDB	31437929
Animal	Milk	Bos taurus	FooDB	31437929

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Blood	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	31557052
Human Placenta	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597

External Links

HMDB ID

HMDB0243501

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB011882

KNApSAcK ID

Not Available

Chemspider ID

308

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

314

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 3'-CMP (MMDBc0030008)

MOL for #<Metabolite:0x00007fe2744b1370>

3D MOL for #<Metabolite:0x00007fe2744b1370>

3D SDF for #<Metabolite:0x00007fe2744b1370>

3D-SDF for #<Metabolite:0x00007fe2744b1370>

PDB for #<Metabolite:0x00007fe2744b1370>

3D PDB for #<Metabolite:0x00007fe2744b1370>

SMILES for #<Metabolite:0x00007fe2744b1370>

INCHI for #<Metabolite:0x00007fe2744b1370>

Structure for #<Metabolite:0x00007fe2744b1370>

3D Structure for #<Metabolite:0x00007fe2744b1370>