MiMeDB: Showing metabocard for 2'-Deoxyuridine 5'-phosphate (MMDBc0057146)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-11-09 19:15:03 UTC

Update Date

2022-12-15 22:52:22 UTC

Metabolite ID

MMDBc0057146

Metabolite Identification

Common Name

2'-Deoxyuridine 5'-phosphate

Description

dUMP, also known as deoxyuridylate or deoxy-UMP, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. dUMP is an extremely weak basic (essentially neutral) compound (based on its pKa). dUMP exists in all living species, ranging from bacteria to humans. Within humans, dUMP participates in a number of enzymatic reactions. In particular, dUMP can be biosynthesized from dCMP through its interaction with the enzyme deoxycytidylate deaminase. In addition, dUMP can be biosynthesized from deoxyuridine; which is mediated by the enzyme thymidine kinase, cytosolic. In humans, dUMP is involved in pyrimidine metabolism. A pyrimidine 2'-deoxyribonucleoside 5'-monophosphate having uracil as the nucleobase. Outside of the human body, dUMP has been detected, but not quantified in, several different foods, such as breadnut tree seeds, sea-buckthornberries, sour cherries, black walnuts, and common oregano. This could make dUMP a potential biomarker for the consumption of these foods.

Structure

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

HMDB0001409
     RDKit          3D
dUMP
 33 34  0  0  0  0  0  0  0  0999 V2000
   -5.8531   -0.1741   -1.8658 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7154    0.0248   -1.4073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5426    0.9915   -0.4444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2705    1.2303    0.0840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2010    0.5284   -0.3328 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9227    0.8390    0.2655 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9177    0.2753    1.6635 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3797   -0.5240    1.6712 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0197   -0.4703    2.8822 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1304    0.2127    0.5743 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3531   -0.5349    0.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8727    0.1119   -0.9858 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2564   -0.6331   -1.5907 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9835   -1.9654   -2.2078 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9329    0.4070   -2.7487 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4326   -0.8215   -0.3696 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1435    0.2674   -0.4091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3942   -0.4042   -1.2679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3750   -1.0562   -1.6490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6187   -0.6594   -1.8007 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3993    1.5581   -0.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2131    2.0056    0.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8283    1.9489    0.2538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8231    1.1505    2.3624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7890   -0.3503    1.8905 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1331   -1.5525    1.3376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4343   -1.3643    3.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3642    1.2203    0.9831 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022   -0.4669    0.9370 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0835   -1.5827   -0.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5090    1.1068   -2.3152 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4911    0.0706    0.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7582   -1.3893   -2.5298 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  1  0
 17  6  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  1
  7 24  1  0
  7 25  1  0
  8 26  1  6
  9 27  1  0
 10 28  1  1
 11 29  1  0
 11 30  1  0
 15 31  1  0
 16 32  1  0
 20 33  1  0
M  END


  Mrv1652309042000222D          

 20 21  0  0  1  0            999 V2000
    1.3191    0.3126    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5285    0.0513    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9379   -0.2373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4911    1.1168    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1141    0.5256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2879   -0.7563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7250    0.0204    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7728   -1.0452    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2712    1.3816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7844    0.0307    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5369   -0.7563    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8935    0.8316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5716    0.2850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0284   -1.4164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6772    1.0859    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1524   -0.2889    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9774   -0.2889    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9809   -1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7989   -0.2889    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9809    0.5359    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  2  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
 10 13  1  1  0  0  0
 11 14  1  6  0  0  0
 12 15  2  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 17 20  2  0  0  0  0
  9 12  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057146

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@H]1C[C@@H](O[C@@H]1COP(O)(O)=O)N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

> <INCHI_KEY>
JSRLJPSBLDHEIO-SHYZEUOFSA-N

> <FORMULA>
C9H13N2O8P

> <MOLECULAR_WEIGHT>
308.1819

> <EXACT_MASS>
308.040951914

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.855873865751356

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-1.42

> <JCHEM_LOGP>
-1.6381701099999995

> <ALOGPS_LOGS>
-1.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.258419473521287

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.232757608087275

> <JCHEM_PKA_STRONGEST_BASIC>
-3.240343942911336

> <JCHEM_POLAR_SURFACE_AREA>
145.63

> <JCHEM_REFRACTIVITY>
61.927800000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.97e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2'-deoxyuridylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001409
     RDKit          3D
dUMP
 33 34  0  0  0  0  0  0  0  0999 V2000
   -5.8531   -0.1741   -1.8658 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7154    0.0248   -1.4073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5426    0.9915   -0.4444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2705    1.2303    0.0840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2010    0.5284   -0.3328 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9227    0.8390    0.2655 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9177    0.2753    1.6635 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3797   -0.5240    1.6712 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0197   -0.4703    2.8822 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1304    0.2127    0.5743 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3531   -0.5349    0.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8727    0.1119   -0.9858 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2564   -0.6331   -1.5907 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9835   -1.9654   -2.2078 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9329    0.4070   -2.7487 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4326   -0.8215   -0.3696 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1435    0.2674   -0.4091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3942   -0.4042   -1.2679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3750   -1.0562   -1.6490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6187   -0.6594   -1.8007 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3993    1.5581   -0.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2131    2.0056    0.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8283    1.9489    0.2538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8231    1.1505    2.3624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7890   -0.3503    1.8905 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1331   -1.5525    1.3376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4343   -1.3643    3.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3642    1.2203    0.9831 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022   -0.4669    0.9370 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0835   -1.5827   -0.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5090    1.1068   -2.3152 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4911    0.0706    0.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7582   -1.3893   -2.5298 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  1  0
 17  6  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  1
  7 24  1  0
  7 25  1  0
  8 26  1  6
  9 27  1  0
 10 28  1  1
 11 29  1  0
 11 30  1  0
 15 31  1  0
 16 32  1  0
 20 33  1  0
M  END

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       2.462   0.584   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.987   0.096   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.617  -0.443   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.783   2.085   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.213   0.981   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.537  -1.412   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       5.087   0.038   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       3.309  -1.951   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.240   2.579   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.464   0.057   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.002  -1.412   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.401   1.552   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.934   0.532   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.920  -2.644   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       6.864   2.027   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -4.018  -0.539   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0      -5.558  -0.539   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      -5.564  -2.073   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -7.091  -0.539   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -5.564   1.000   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10                                                       
CONECT    6    2   11                                                       
CONECT    7    3   12                                                       
CONECT    8    3                                                            
CONECT    9    4   12                                                       
CONECT   10    5   13   11                                                  
CONECT   11    6   14   10                                                  
CONECT   12    7   15    9                                                  
CONECT   13   10   16                                                       
CONECT   14   11                                                            
CONECT   15   12                                                            
CONECT   16   13   17                                                       
CONECT   17   16   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

COMPND    HMDB0001409
HETATM    1  O1  UNL     1      -5.853  -0.174  -1.866  1.00  0.00           O  
HETATM    2  C1  UNL     1      -4.715   0.025  -1.407  1.00  0.00           C  
HETATM    3  C2  UNL     1      -4.543   0.991  -0.444  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.270   1.230   0.084  1.00  0.00           C  
HETATM    5  N1  UNL     1      -2.201   0.528  -0.333  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.923   0.839   0.266  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.918   0.275   1.664  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.380  -0.524   1.671  1.00  0.00           C  
HETATM    9  O2  UNL     1       1.020  -0.470   2.882  1.00  0.00           O  
HETATM   10  C7  UNL     1       1.130   0.213   0.574  1.00  0.00           C  
HETATM   11  C8  UNL     1       2.353  -0.535   0.125  1.00  0.00           C  
HETATM   12  O3  UNL     1       2.873   0.112  -0.986  1.00  0.00           O  
HETATM   13  P1  UNL     1       4.256  -0.633  -1.591  1.00  0.00           P  
HETATM   14  O4  UNL     1       3.984  -1.965  -2.208  1.00  0.00           O  
HETATM   15  O5  UNL     1       4.933   0.407  -2.749  1.00  0.00           O  
HETATM   16  O6  UNL     1       5.433  -0.822  -0.370  1.00  0.00           O  
HETATM   17  O7  UNL     1       0.144   0.267  -0.409  1.00  0.00           O  
HETATM   18  C9  UNL     1      -2.394  -0.404  -1.268  1.00  0.00           C  
HETATM   19  O8  UNL     1      -1.375  -1.056  -1.649  1.00  0.00           O  
HETATM   20  N2  UNL     1      -3.619  -0.659  -1.801  1.00  0.00           N  
HETATM   21  H1  UNL     1      -5.399   1.558  -0.106  1.00  0.00           H  
HETATM   22  H2  UNL     1      -3.213   2.006   0.837  1.00  0.00           H  
HETATM   23  H3  UNL     1      -0.828   1.949   0.254  1.00  0.00           H  
HETATM   24  H4  UNL     1      -0.823   1.150   2.362  1.00  0.00           H  
HETATM   25  H5  UNL     1      -1.789  -0.350   1.891  1.00  0.00           H  
HETATM   26  H6  UNL     1       0.133  -1.553   1.338  1.00  0.00           H  
HETATM   27  H7  UNL     1       1.434  -1.364   3.044  1.00  0.00           H  
HETATM   28  H8  UNL     1       1.364   1.220   0.983  1.00  0.00           H  
HETATM   29  H9  UNL     1       3.102  -0.467   0.937  1.00  0.00           H  
HETATM   30  H10 UNL     1       2.084  -1.583  -0.049  1.00  0.00           H  
HETATM   31  H11 UNL     1       5.509   1.107  -2.315  1.00  0.00           H  
HETATM   32  H12 UNL     1       5.491   0.071   0.085  1.00  0.00           H  
HETATM   33  H13 UNL     1      -3.758  -1.389  -2.530  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   20
CONECT    3    4    4   21
CONECT    4    5   22
CONECT    5    6   18
CONECT    6    7   17   23
CONECT    7    8   24   25
CONECT    8    9   10   26
CONECT    9   27
CONECT   10   11   17   28
CONECT   11   12   29   30
CONECT   12   13
CONECT   13   14   14   15   16
CONECT   15   31
CONECT   16   32
CONECT   18   19   19   20
CONECT   20   33
END

HMDB0001409
     RDKit          3D
dUMP
 33 34  0  0  0  0  0  0  0  0999 V2000
   -5.8531   -0.1741   -1.8658 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7154    0.0248   -1.4073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5426    0.9915   -0.4444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2705    1.2303    0.0840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2010    0.5284   -0.3328 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9227    0.8390    0.2655 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9177    0.2753    1.6635 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3797   -0.5240    1.6712 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0197   -0.4703    2.8822 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1304    0.2127    0.5743 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3531   -0.5349    0.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8727    0.1119   -0.9858 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2564   -0.6331   -1.5907 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9835   -1.9654   -2.2078 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9329    0.4070   -2.7487 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4326   -0.8215   -0.3696 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1435    0.2674   -0.4091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3942   -0.4042   -1.2679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3750   -1.0562   -1.6490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6187   -0.6594   -1.8007 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3993    1.5581   -0.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2131    2.0056    0.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8283    1.9489    0.2538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8231    1.1505    2.3624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7890   -0.3503    1.8905 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1331   -1.5525    1.3376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4343   -1.3643    3.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3642    1.2203    0.9831 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022   -0.4669    0.9370 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0835   -1.5827   -0.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5090    1.1068   -2.3152 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4911    0.0706    0.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7582   -1.3893   -2.5298 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 10 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  1  0
 17  6  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  1
  7 24  1  0
  7 25  1  0
  8 26  1  6
  9 27  1  0
 10 28  1  1
 11 29  1  0
 11 30  1  0
 15 31  1  0
 16 32  1  0
 20 33  1  0
M  END

Synonyms

Value	Source
2'-Deoxyuridine 5'-monophosphate	ChEBI
2'-Deoxyuridine 5'-phosphate	ChEBI
Deoxyuridine 5'-phosphate	ChEBI
Deoxyuridine monophosphate	ChEBI
Deoxyuridylate	ChEBI
Deoxyuridylic acid	ChEBI
2'-Deoxyuridine 5'-monophosphoric acid	Generator
2'-Deoxyuridine 5'-phosphoric acid	Generator
Deoxyuridine 5'-phosphoric acid	Generator
Deoxyuridine monophosphoric acid	Generator
2'-Deoxy-5'-uridylate	HMDB
2'-Deoxy-5'-uridylic acid	HMDB
2'-Deoxyuridylate	HMDB
2'-Deoxyuridylic acid	HMDB
Deoxy-UMP	HMDB
Deoxyuridine 5'-monophosphate	HMDB
2'-Deoxyuridine-5'-monophosphate	HMDB
2'-Deoxyuridylic acid, disodium salt	HMDB

Molecular Formula

C₉H₁₃N₂O₈P

Average Mass

308.1819

Monoisotopic Mass

308.040951914

IUPAC Name

{[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

2'-deoxyuridylic acid

CAS Registry Number

Not Available

SMILES

O[C@H]1C[C@@H](O[C@@H]1COP(O)(O)=O)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

InChI Key

JSRLJPSBLDHEIO-SHYZEUOFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine deoxyribonucleotides

Direct Parent

Pyrimidine 2'-deoxyribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside monophosphate
Pyrimidone
Monoalkyl phosphate
Hydroxypyrimidine
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organopnictogen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside 5'-monophosphate (CHEBI:17622 )
deoxyuridine phosphate (CHEBI:17622 )
Deoxyribonucleotides (C00365 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	7.97 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-1.6	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	145.63 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	61.93 m³·mol⁻¹	ChemAxon
Polarizability	25.86 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	splash10-0002-9410000000-3abd5b4815950ff662f5	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-01ow-9321000000-f216f77409b12a9c39d1	2017-10-06	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 (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, N/A (Annotated)	splash10-001i-9100000000-c9b7092bb72f342d372f	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, N/A (Annotated)	splash10-001i-9000000000-d2272878a49bc62c1955	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, N/A (Annotated)	splash10-001i-9000000000-69451d809e5517ef09cb	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-01ta-9803000000-f0e26cbfb75f3fb7b36e	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-01ta-9803000000-f0e26cbfb75f3fb7b36e	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, positive	splash10-001i-9000000000-e479009af7b70bba530d	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 10V, positive	splash10-001i-9120000000-68df7c9d0651f44d4ec7	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 40V, positive	splash10-0f89-9100000000-8d632914cc75f30e28a2	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 20V, positive	splash10-001i-9230000000-1e8624ca24971f32ad74	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9000000000-e3761e9ef1ac38190893	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9000000000-489d2a85cc04ba0a5d6a	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-053r-9122000000-056f8bdc172db3cba93a	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-88bc2ad1e6aeada6888f	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9120000000-68df7c9d0651f44d4ec7	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-001i-9000000000-f9632ee285ee7f2901f7	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0f89-9100000000-ed98a4451221d6d749f2	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9230000000-4990b01871cfbeec214d	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-b1e75c91dac815141295	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-01ot-1900000000-fb8b7ffefbb81eb54969	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-446c86aec7739d354d2c	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5900000000-00b01a3db61a05d06fb7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-7900000000-cc618ed7c89e1e816a5d	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-06tf-9143000000-78a62ec1d8e492431f91	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-5ad77843f75db170ab17	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-06305d10841a2df94c23	2016-09-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Mitochondria
Nucleus

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0001409

DrugBank ID

DB03800

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Deoxyuridine_monophosphate

METLIN ID

6225

PubChem Compound

65063

PDB ID

Not Available

ChEBI ID

17622

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 2'-Deoxyuridine 5'-phosphate (MMDBc0057146)

MOL for #<Metabolite:0x00007fece00201a0>

3D MOL for #<Metabolite:0x00007fece00201a0>

3D SDF for #<Metabolite:0x00007fece00201a0>

3D-SDF for #<Metabolite:0x00007fece00201a0>

PDB for #<Metabolite:0x00007fece00201a0>

3D PDB for #<Metabolite:0x00007fece00201a0>

SMILES for #<Metabolite:0x00007fece00201a0>

INCHI for #<Metabolite:0x00007fece00201a0>

Structure for #<Metabolite:0x00007fece00201a0>

3D Structure for #<Metabolite:0x00007fece00201a0>