MiMeDB: Showing metabocard for Cytidine 3'-monophosphate (MMDBc0000720)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:53:29 UTC

Update Date

2022-08-31 06:11:35 UTC

Metabolite ID

MMDBc0000720

Metabolite Identification

Common Name

Cytidine 3'-monophosphate

Description

Cytidine 3'-monophosphate (3'-CMP), also known as 3'-cytidylic acid or 3'-cytidylate, belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. Cytidine 3'-monophosphate has been identified in the human placenta (PMID: 32033212 ).

Structure

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

HMDB0240312
     RDKit          3D
Cytidine 3'-monophosphate
 35 36  0  0  0  0  0  0  0  0999 V2000
    5.7459    1.6347    0.8510 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4905    1.0454    0.5661 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7686    0.4650    1.5983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5424   -0.1092    1.3137 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0245   -0.1252    0.0722 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7450   -0.7484   -0.1061 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1793   -0.4660   -1.3554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1053   -0.9737   -1.1661 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9956   -0.7436   -2.3552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1572    0.5847   -2.6584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5563   -0.1738    0.0471 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5805   -0.8243    0.7317 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9242    0.1436    0.9807 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.1040    0.4398    2.4619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2833   -0.7250    0.4276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7834    1.6273    0.1928 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2790   -0.1598    0.8677 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3969   -1.0391    1.9205 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7452    0.4427   -0.9011 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2722    0.4343   -2.0658 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9532    1.0170   -0.6631 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6118    1.0378    0.8783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8479    2.6554    1.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1530    0.4565    2.6205 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9911   -0.5618    2.1476 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7751   -1.8559   -0.0236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0470   -2.0166   -0.8559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4914   -1.2351   -3.2265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9456   -1.2922   -2.2165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3757    0.6401   -3.6364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8160    0.8706   -0.2106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1065   -1.6983    0.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6251    1.8202   -0.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0064    0.8676    1.1654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2793   -1.4347    2.0153 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
 11 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  2  0
 19 21  1  0
 21  2  2  0
 17  6  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  4 25  1  0
  6 26  1  1
  8 27  1  1
  9 28  1  0
  9 29  1  0
 10 30  1  0
 11 31  1  6
 15 32  1  0
 16 33  1  0
 17 34  1  1
 18 35  1  0
M  END


  Mrv1652310301916352D          

 21 22  0  0  0  0            999 V2000
 9999.542710001.5530    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.8068 9999.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.8068 9998.8826    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.321310000.9304    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.8911 9998.4569    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.0358 9999.6947    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.321410000.1071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.6068 9999.6946    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.6068 9998.8696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.3213 9998.4571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.0358 9998.8697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.4199 9999.6118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.752510000.0968    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.007410000.8814    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.832410000.8814    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.087310000.0968    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10002.558410002.2630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.145110001.5490    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10002.146110000.7239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.861010001.1367    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.317310001.5488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  6  7  1  0  0  0  0
 11  6  1  0  0  0  0
  7  4  2  0  0  0  0
  9  5  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 12 13  1  0  0  0  0
 12 16  1  0  0  0  0
 14  1  1  6  0  0  0
 13  6  1  1  0  0  0
 16  2  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 18 21  1  0  0  0  0
 15 21  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000720

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-6(14)7(4(3-13)19-8)20-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
UOOOPKANIPLQPU-XVFCMESISA-N

> <FORMULA>
C9H14N3O8P

> <MOLECULAR_WEIGHT>
323.1965

> <EXACT_MASS>
323.051850951

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
27.175500831379907

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.99

> <JCHEM_LOGP>
-3.213644082365966

> <ALOGPS_LOGS>
-1.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.906314798716843

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.9227119253827052

> <JCHEM_PKA_STRONGEST_BASIC>
-0.17866294869486177

> <JCHEM_POLAR_SURFACE_AREA>
175.13999999999996

> <JCHEM_REFRACTIVITY>
65.4177

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.76e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0240312
     RDKit          3D
Cytidine 3'-monophosphate
 35 36  0  0  0  0  0  0  0  0999 V2000
    5.7459    1.6347    0.8510 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4905    1.0454    0.5661 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7686    0.4650    1.5983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5424   -0.1092    1.3137 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0245   -0.1252    0.0722 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7450   -0.7484   -0.1061 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1793   -0.4660   -1.3554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1053   -0.9737   -1.1661 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9956   -0.7436   -2.3552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1572    0.5847   -2.6584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5563   -0.1738    0.0471 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5805   -0.8243    0.7317 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9242    0.1436    0.9807 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.1040    0.4398    2.4619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2833   -0.7250    0.4276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7834    1.6273    0.1928 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2790   -0.1598    0.8677 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3969   -1.0391    1.9205 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7452    0.4427   -0.9011 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2722    0.4343   -2.0658 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9532    1.0170   -0.6631 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6118    1.0378    0.8783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8479    2.6554    1.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1530    0.4565    2.6205 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9911   -0.5618    2.1476 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7751   -1.8559   -0.0236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0470   -2.0166   -0.8559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4914   -1.2351   -3.2265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9456   -1.2922   -2.2165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3757    0.6401   -3.6364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8160    0.8706   -0.2106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1065   -1.6983    0.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6251    1.8202   -0.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0064    0.8676    1.1654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2793   -1.4347    2.0153 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
 11 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  2  0
 19 21  1  0
 21  2  2  0
 17  6  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  4 25  1  0
  6 26  1  1
  8 27  1  1
  9 28  1  0
  9 29  1  0
 10 30  1  0
 11 31  1  6
 15 32  1  0
 16 33  1  0
 17 34  1  1
 18 35  1  0
M  END

HEADER    PROTEIN                                 30-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-OCT-19         0                                  
HETATM    1  O   UNK     0    8665.8138669.566   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0    8670.0398666.120   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8670.0398664.581   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8663.5338668.403   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0    8660.8638663.786   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0    8664.8678666.097   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8663.5338666.867   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0    8662.1998666.097   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0    8662.1998664.557   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8663.5338663.787   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8664.8678664.557   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0    8667.4508665.942   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0    8666.2058666.847   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8666.6808668.312   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8668.2208668.312   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8668.6968666.847   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0    8671.4428670.891   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0    8670.6718669.558   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0    8670.6738668.018   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0    8672.0078668.789   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0    8669.1268669.558   0.000  0.00  0.00           O+0
CONECT    1   14                                                            
CONECT    2    3   16                                                       
CONECT    3    2                                                            
CONECT    4    7                                                            
CONECT    5    9                                                            
CONECT    6    7   11   13                                                  
CONECT    7    8    6    4                                                  
CONECT    8    7    9                                                       
CONECT    9   10    8    5                                                  
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12   13   16                                                       
CONECT   13   14   12    6                                                  
CONECT   14   13   15    1                                                  
CONECT   15   14   16   21                                                  
CONECT   16   15   12    2                                                  
CONECT   17   18                                                            
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18   15                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

COMPND    HMDB0240312
HETATM    1  N1  UNL     1       5.746   1.635   0.851  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.490   1.045   0.566  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.769   0.465   1.598  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.542  -0.109   1.314  1.00  0.00           C  
HETATM    5  N2  UNL     1       2.025  -0.125   0.072  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.745  -0.748  -0.106  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.179  -0.466  -1.355  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.105  -0.974  -1.166  1.00  0.00           C  
HETATM    9  C6  UNL     1      -1.996  -0.744  -2.355  1.00  0.00           C  
HETATM   10  O2  UNL     1      -2.157   0.585  -2.658  1.00  0.00           O  
HETATM   11  C7  UNL     1      -1.556  -0.174   0.047  1.00  0.00           C  
HETATM   12  O3  UNL     1      -2.581  -0.824   0.732  1.00  0.00           O  
HETATM   13  P1  UNL     1      -3.924   0.144   0.981  1.00  0.00           P  
HETATM   14  O4  UNL     1      -4.104   0.440   2.462  1.00  0.00           O  
HETATM   15  O5  UNL     1      -5.283  -0.725   0.428  1.00  0.00           O  
HETATM   16  O6  UNL     1      -3.783   1.627   0.193  1.00  0.00           O  
HETATM   17  C8  UNL     1      -0.279  -0.160   0.868  1.00  0.00           C  
HETATM   18  O7  UNL     1      -0.397  -1.039   1.920  1.00  0.00           O  
HETATM   19  C9  UNL     1       2.745   0.443  -0.901  1.00  0.00           C  
HETATM   20  O8  UNL     1       2.272   0.434  -2.066  1.00  0.00           O  
HETATM   21  N3  UNL     1       3.953   1.017  -0.663  1.00  0.00           N  
HETATM   22  H1  UNL     1       6.612   1.038   0.878  1.00  0.00           H  
HETATM   23  H2  UNL     1       5.848   2.655   1.038  1.00  0.00           H  
HETATM   24  H3  UNL     1       4.153   0.457   2.621  1.00  0.00           H  
HETATM   25  H4  UNL     1       1.991  -0.562   2.148  1.00  0.00           H  
HETATM   26  H5  UNL     1       0.775  -1.856  -0.024  1.00  0.00           H  
HETATM   27  H6  UNL     1      -1.047  -2.017  -0.856  1.00  0.00           H  
HETATM   28  H7  UNL     1      -1.491  -1.235  -3.227  1.00  0.00           H  
HETATM   29  H8  UNL     1      -2.946  -1.292  -2.217  1.00  0.00           H  
HETATM   30  H9  UNL     1      -2.376   0.640  -3.636  1.00  0.00           H  
HETATM   31  H10 UNL     1      -1.816   0.871  -0.211  1.00  0.00           H  
HETATM   32  H11 UNL     1      -5.107  -1.698   0.599  1.00  0.00           H  
HETATM   33  H12 UNL     1      -4.625   1.820  -0.281  1.00  0.00           H  
HETATM   34  H13 UNL     1       0.006   0.868   1.165  1.00  0.00           H  
HETATM   35  H14 UNL     1      -1.279  -1.435   2.015  1.00  0.00           H  
CONECT    1    2   22   23
CONECT    2    3   21   21
CONECT    3    4    4   24
CONECT    4    5   25
CONECT    5    6   19
CONECT    6    7   17   26
CONECT    7    8
CONECT    8    9   11   27
CONECT    9   10   28   29
CONECT   10   30
CONECT   11   12   17   31
CONECT   12   13
CONECT   13   14   14   15   16
CONECT   15   32
CONECT   16   33
CONECT   17   18   34
CONECT   18   35
CONECT   19   20   20   21
END

HMDB0240312
     RDKit          3D
Cytidine 3'-monophosphate
 35 36  0  0  0  0  0  0  0  0999 V2000
    5.7459    1.6347    0.8510 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4905    1.0454    0.5661 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7686    0.4650    1.5983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5424   -0.1092    1.3137 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0245   -0.1252    0.0722 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7450   -0.7484   -0.1061 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1793   -0.4660   -1.3554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1053   -0.9737   -1.1661 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9956   -0.7436   -2.3552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1572    0.5847   -2.6584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5563   -0.1738    0.0471 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5805   -0.8243    0.7317 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9242    0.1436    0.9807 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.1040    0.4398    2.4619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2833   -0.7250    0.4276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7834    1.6273    0.1928 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2790   -0.1598    0.8677 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3969   -1.0391    1.9205 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7452    0.4427   -0.9011 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2722    0.4343   -2.0658 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9532    1.0170   -0.6631 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6118    1.0378    0.8783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8479    2.6554    1.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1530    0.4565    2.6205 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9911   -0.5618    2.1476 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7751   -1.8559   -0.0236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0470   -2.0166   -0.8559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4914   -1.2351   -3.2265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9456   -1.2922   -2.2165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3757    0.6401   -3.6364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8160    0.8706   -0.2106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1065   -1.6983    0.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6251    1.8202   -0.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0064    0.8676    1.1654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2793   -1.4347    2.0153 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
 11 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  2  0
 19 21  1  0
 21  2  2  0
 17  6  1  0
  1 22  1  0
  1 23  1  0
  3 24  1  0
  4 25  1  0
  6 26  1  1
  8 27  1  1
  9 28  1  0
  9 29  1  0
 10 30  1  0
 11 31  1  6
 15 32  1  0
 16 33  1  0
 17 34  1  1
 18 35  1  0
M  END

Synonyms

Value	Source
3'-Cytidylic acid	ChEBI
Cytidine 3'-phosphate	ChEBI
CYTIDINE-3'-monophosphATE	ChEBI
3'-Cytidylate	Generator
Cytidine 3'-phosphoric acid	Generator
CYTIDINE-3'-monophosphoric acid	Generator
Cytidine 3'-monophosphoric acid	Generator
CMP	HMDB
monoPhosphate, cytidine	HMDB
Acid, cytidylic	HMDB
Cytidylic acid	HMDB
3' CMP	HMDB
Cytidine monophosphate	HMDB
3'-CMP	HMDB
3'-Cytidinephosphoric acid	HMDB
3'-Cytosylic acid	HMDB
3’-CMP	HMDB
3’-cytidinephosphoric acid	HMDB
3’-cytosylic acid	HMDB
Cytidine 3’-monophosphate	HMDB
Ribocytidine 3'-monophosphate	HMDB
Ribocytidine 3’-monophosphate	HMDB
Cytidine 3'-monophosphate	ChEBI

Molecular Formula

C₉H₁₄N₃O₈P

Average Mass

323.1965

Monoisotopic Mass

323.051850951

IUPAC Name

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

Traditional Name

[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-6(14)7(4(3-13)19-8)20-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChI Key

UOOOPKANIPLQPU-XVFCMESISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Hydroxypyrimidine
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Primary alcohol
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

cytidine 3'-phosphate (CHEBI:53013 )
pyrimidine ribonucleoside 3'-monophosphate (CHEBI:53013 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	17.6 g/L	ALOGPS
logP	-2	ALOGPS
logP	-3.2	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	0.92	ChemAxon
pKa (Strongest Basic)	-0.18	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	175.14 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	65.42 m³·mol⁻¹	ChemAxon
Polarizability	27.18 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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	splash10-0002-9500000000-319902c312a7464558d0	2017-08-28	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-01t9-9053000000-98586caa88a9542b6869	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-03fr-9160000000-696e9f36a6aa3034e301	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1900000000-e529ab704ca5aed9e776	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-c1fba7357ab0717b9f74	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-03di-6900000000-bc76466e48292f7ef6ea	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0900000000-5999e32b216386dd66f6	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-004j-9100000000-ceb03193b07d5eafd4db	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-00di-4009000000-ba4e64a96034baf4bdf5	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-ce80c9f6d840ae7aefa9	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3900000000-5fbbc53670e9ed9d8044	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-47fcb86baa2fc7ec1cd1	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1901000000-20dd9d897851bcd8f3ec	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-8fe08c0bed5ca9823340	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-8900000000-7fdbd98da9404cc83da2	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-024i-6958000000-3178bcca26585a8da251	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9320000000-4dd1569ad0c95ea3ee55	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-04c2b671e84e242cc8e3	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0903000000-7785db50e484fec59c87	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1911000000-a76bf9ec5ab99f179011	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-4900000000-ea205c9339be61eb8d9a	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0009000000-1d6b5138ee78b0f547d4	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00b9-9486000000-3181c8ec1395f6ce61ca	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004l-9120000000-a99ff2c1f6649cee7c01	2021-09-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0026010	Cytidine 3'-monophosphate	Cytidine	5'/3'-nucleotidase SurE	Hydrolysis of nucleotide	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	Bacteroidetes	1	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Firmicutes	1	Human stool; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen

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
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

HMDB0240312

DrugBank ID

DB01961

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

59906

KEGG Compound ID

C05822

BioCyc ID

CPD-3711

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

66535

PDB ID

Not Available

ChEBI ID

53013

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 3'-monophosphate (MMDBc0000720)

MOL for #<Metabolite:0x00007fe2880296b8>

3D MOL for #<Metabolite:0x00007fe2880296b8>

3D SDF for #<Metabolite:0x00007fe2880296b8>

3D-SDF for #<Metabolite:0x00007fe2880296b8>

PDB for #<Metabolite:0x00007fe2880296b8>

3D PDB for #<Metabolite:0x00007fe2880296b8>

SMILES for #<Metabolite:0x00007fe2880296b8>

INCHI for #<Metabolite:0x00007fe2880296b8>

Structure for #<Metabolite:0x00007fe2880296b8>

3D Structure for #<Metabolite:0x00007fe2880296b8>