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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (8) Show 8 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:40:09 UTC

HMDB ID

HMDB0001409

Secondary Accession Numbers

HMDB01409

Metabolite Identification

Common Name

dUMP

Description

Deoxyuridine monophosphate (dUMP), also known as deoxyuridylic acid or deoxyuridylate in its conjugate acid and conjugate base forms, respectively, is a deoxynucleotide. It 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 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.

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>
HMDB0001409

> <DATABASE_NAME>
hmdb

> <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

View in JSmol View NMR Assignments View Stereo Labels

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

Chemical Formula

C₉H₁₃N₂O₈P

Average Molecular Weight

308.1819

Monoisotopic Molecular Weight

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

964-26-1

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 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cytoplasm (HMDB: HMDB0001409)

Cellular substructure

Organelle

Mitochondria

Mitochondria (HMDB: HMDB0001409)

Mitochondria (HMDB: HMDB0001409)
Nucleus (HMDB: HMDB0001409)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0001409)

Source

Endogenous

Endogenous (HMDB: HMDB0001409)

Plant

Animal

Animal (HMDB: HMDB0001409)

Exogenous

Food

Food (HMDB: HMDB0001409)

Herbs and Spices (FooDB: FOOD00866)

Herb and spice mixture

Curry powder (FooDB: FOOD00678)

Fruit

Berry

Gooseberry (FooDB: FOOD00157)
Grape (FooDB: FOOD00369)
Lingonberry (FooDB: FOOD00194)
Loganberry (FooDB: FOOD00400)
Strawberry (FooDB: FOOD00083)
Boysenberry (FooDB: FOOD00542)
Common grape (FooDB: FOOD00204)
American cranberry (FooDB: FOOD00192)
Strawberry guava (FooDB: FOOD00482)
Black mulberry (FooDB: FOOD00117)
Red raspberry (FooDB: FOOD00162)
Muscadine grape (FooDB: FOOD00203)
Salmonberry (FooDB: FOOD00456)
Alaska blueberry (FooDB: FOOD00380)
Sea-buckthornberry (FooDB: FOOD00087)
Black elderberry (FooDB: FOOD00166)
Black crowberry (FooDB: FOOD00075)
Black huckleberry (FooDB: FOOD00084)
Mulberry (FooDB: FOOD00116)
Black chokeberry (FooDB: FOOD00136)
Cloudberry (FooDB: FOOD00161)
Black raspberry (FooDB: FOOD00163)
Arctic blackberry (FooDB: FOOD00207)
Rowanberry (FooDB: FOOD00176)
Lowbush blueberry (FooDB: FOOD00189)
Sparkleberry (FooDB: FOOD00190)
Highbush blueberry (FooDB: FOOD00191)
Elliott's blueberry (FooDB: FOOD00210)
Bayberry (FooDB: FOOD00209)
Bog bilberry (FooDB: FOOD00212)
Canada blueberry (FooDB: FOOD00211)
Buffalo currant (FooDB: FOOD00213)
European cranberry (FooDB: FOOD00217)
Deerberry (FooDB: FOOD00218)
Cascade huckleberry (FooDB: FOOD00220)
Oval-leaf huckleberry (FooDB: FOOD00221)
Evergreen huckleberry (FooDB: FOOD00222)
Red huckleberry (FooDB: FOOD00223)
Summer grape (FooDB: FOOD00227)
Fox grape (FooDB: FOOD00228)
Half-highbush blueberry (FooDB: FOOD00248)
Jostaberry (FooDB: FOOD00257)
Skunk currant (FooDB: FOOD00267)
Sweet rowanberry (FooDB: FOOD00265)
Squashberry (FooDB: FOOD00344)
Ohelo berry (FooDB: FOOD00419)
Chinese bayberry (FooDB: FOOD00852)
Nanking cherry (FooDB: FOOD00885)
Saskatoon berry (FooDB: FOOD00884)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Bilberry (FooDB: FOOD00193)
Elderberry (FooDB: FOOD00358)
Rabbiteye blueberry (FooDB: FOOD00898)
Blackberry (FooDB: FOOD00906)
Partridge berry (FooDB: FOOD00931)
Green grape (FooDB: FOOD00964)
Black raisin (FooDB: FOOD00968)
Red grape (FooDB: FOOD00965)
Black plum (FooDB: FOOD00966)
Monk fruit (FooDB: FOOD00983)
Chinese plum (FooDB: FOOD00978)
Green plum (FooDB: FOOD00979)
Wampee (FooDB: FOOD00980)
Goji (FooDB: FOOD00982)
Hawthorn (FooDB: FOOD00985)
Lantern fruit (FooDB: FOOD00986)
Cape gooseberry (FooDB: FOOD00988)
Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)

Citrus

Grapefruit (FooDB: FOOD00256)
Lemon (FooDB: FOOD00054)
Lime (FooDB: FOOD00053)
Sweet orange (FooDB: FOOD00057)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Persian lime (FooDB: FOOD00543)
Pummelo (FooDB: FOOD00055)
Grapefruit/Pummelo hybrid (FooDB: FOOD00255)
Citrus (FooDB: FOOD00859)
Sour orange (FooDB: FOOD00918)
Mikan (FooDB: FOOD00932)
Clementine (FooDB: FOOD00959)

Tropical fruit

Drupe

Nectarine (FooDB: FOOD00229)
Peach (FooDB: FOOD00149)
European plum (FooDB: FOOD00147)
Sour cherry (FooDB: FOOD00146)
Sweet cherry (FooDB: FOOD00145)
Common chokecherry (FooDB: FOOD00562)
Peach (var.) (FooDB: FOOD00230)
Prunus (Cherry, Plum) (FooDB: FOOD00143)
Apricot (FooDB: FOOD00144)

Pome

Other fruit

Jujube (FooDB: FOOD00388)
Fig (FooDB: FOOD00081)
Date (FooDB: FOOD00135)

Fruits (FooDB: FOOD00871)

Onion-family vegetable

Leek (FooDB: FOOD00007)
Allium (FooDB: FOOD00005)
Wild leek (FooDB: FOOD00396)
Shallot (FooDB: FOOD00243)
Garden onion (FooDB: FOOD00006)
Garden onion (var.) (FooDB: FOOD00226)
Onion-family vegetables (FooDB: FOOD00855)
Red onion (FooDB: FOOD00962)
Green onion (FooDB: FOOD00963)

Mushroom

Other vegetable

Okra (FooDB: FOOD00420)
Sacred lotus (FooDB: FOOD00402)
Horseradish tree (FooDB: FOOD00379)
Chinese water chestnut (FooDB: FOOD00332)
Tree fern (FooDB: FOOD00797)
Nopal (FooDB: FOOD00416)
Carob (FooDB: FOOD00321)
Agave (FooDB: FOOD00563)
Narrowleaf cattail (FooDB: FOOD00564)
Giant butterbur (FooDB: FOOD00314)
Sesbania flower (FooDB: FOOD00469)
Heart of palm (FooDB: FOOD00718)

Fruit vegetable

Olive (FooDB: FOOD00121)
Pepper (FooDB: FOOD00040)
Garden tomato (FooDB: FOOD00171)
Mexican groundcherry (FooDB: FOOD00491)
Red bell pepper (FooDB: FOOD00880)
Green bell pepper (FooDB: FOOD00877)
Yellow bell pepper (FooDB: FOOD00878)
Italian sweet red pepper (FooDB: FOOD00881)
Garden tomato (var.) (FooDB: FOOD00173)
Cherry tomato (FooDB: FOOD00172)
Pepper (C. baccatum) (FooDB: FOOD00231)
Pepper (C. chinense) (FooDB: FOOD00232)
Pepper (Capsicum) (FooDB: FOOD00233)
Pepper (C. frutescens) (FooDB: FOOD00428)
Pepper (C. pubescens) (FooDB: FOOD00849)
Orange bell pepper (FooDB: FOOD00879)
Avocado (FooDB: FOOD00130)
Eggplant (FooDB: FOOD00174)
Groundcherry (FooDB: FOOD00371)
Jalapeno pepper (FooDB: FOOD00955)
Cubanelle pepper (FooDB: FOOD00971)

Stalk vegetable

Leaf vegetable

Spinach (FooDB: FOOD00178)
Common beet (FooDB: FOOD00025)
Garland chrysanthemum (FooDB: FOOD00333)
Jute (FooDB: FOOD00389)
Lambsquarters (FooDB: FOOD00394)
New Zealand spinach (FooDB: FOOD00415)
Swamp cabbage (FooDB: FOOD00091)
Rocket salad (ssp.) (FooDB: FOOD00077)
Yautia (FooDB: FOOD00510)
Romaine lettuce (FooDB: FOOD00888)
Rocket salad (FooDB: FOOD00244)
Chicory leaves (FooDB: FOOD00250)
Corn salad (FooDB: FOOD00340)
Malabar spinach (FooDB: FOOD00404)
Ostrich fern (FooDB: FOOD00556)
Green vegetables (FooDB: FOOD00872)
Endive (FooDB: FOOD00048)
Lettuce (FooDB: FOOD00095)
Garden cress (FooDB: FOOD00099)
Swiss chard (FooDB: FOOD00237)
Iceberg lettuce (FooDB: FOOD00973)
Pea shoots (FooDB: FOOD00975)
Yau choy (FooDB: FOOD00976)
Water spinach (FooDB: FOOD00977)

Shoot vegetable

Brassica

Brassicas (FooDB: FOOD00857)

Castanospermum australe (FooDB: FOOD00893)
Gentiana lutea (FooDB: FOOD00894)
Juniperus communis (FooDB: FOOD00895)
Albizia gummifera (FooDB: FOOD00896)

Pulse

Lentil

Lentils (FooDB: FOOD00098)

Pea

Bean

Other pulse

White lupine (FooDB: FOOD00403)
Lupine (FooDB: FOOD00104)

Pulses (FooDB: FOOD00867)
Green lentil (FooDB: FOOD00970)

Cereal and cereal product

Cereal product

Cereal

Dough

Sourdough (FooDB: FOOD00275)

Cereals and cereal products (FooDB: FOOD00858)

Leavened bread

Flat bread

Other bread

Potato bread (FooDB: FOOD00811)
Other bread (FooDB: FOOD00269)

Sweet bread

Raisin bread (FooDB: FOOD00817)

Gourd

Muskmelon (FooDB: FOOD00064)
Cucurbita (FooDB: FOOD00066)
Watermelon (FooDB: FOOD00052)
Bitter gourd (FooDB: FOOD00115)
Calabash (FooDB: FOOD00318)
Towel gourd (FooDB: FOOD00492)
Winter squash (FooDB: FOOD00283)
Butternut squash (FooDB: FOOD00317)
Wax gourd (FooDB: FOOD00499)
Green zucchini (FooDB: FOOD00875)
Yellow zucchini (FooDB: FOOD00876)
Japanese pumpkin (FooDB: FOOD00886)
Sunburst squash (pattypan squash) (FooDB: FOOD00874)
Tinda (FooDB: FOOD00559)
Horned melon (FooDB: FOOD00761)
Cucumber (FooDB: FOOD00065)
Chayote (FooDB: FOOD00325)
Acorn squash (FooDB: FOOD00972)
Cantaloupe melon (FooDB: FOOD00984)

Nut

Peanut (FooDB: FOOD00016)
Hazelnut (FooDB: FOOD00376)
Pecan nut (FooDB: FOOD00044)
Pine nut (FooDB: FOOD00138)
Pistachio (FooDB: FOOD00140)
Walnut (FooDB: FOOD00608)
Acorn (FooDB: FOOD00282)
Beech nut (FooDB: FOOD00299)
Chinese chestnut (FooDB: FOOD00331)
Butternut (FooDB: FOOD00316)
European chestnut (FooDB: FOOD00363)
Hickory nut (FooDB: FOOD00377)
Macadamia nut (FooDB: FOOD00525)
Mixed nuts (FooDB: FOOD00771)
Pili nut (FooDB: FOOD00432)
Colorado pinyon (FooDB: FOOD00433)
Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)
Japanese chestnut (FooDB: FOOD00385)
Common hazelnut (FooDB: FOOD00062)
Macadamia nut (M. tetraphylla) (FooDB: FOOD00225)
Japanese walnut (FooDB: FOOD00240)
Nuts (FooDB: FOOD00869)
Cashew nut (FooDB: FOOD00011)
Brazil nut (FooDB: FOOD00024)
Chestnut (FooDB: FOOD00045)
Almond (FooDB: FOOD00148)

Abalone (FooDB: FOOD00279)
Conch (FooDB: FOOD00611)

Tea

Herbal tea

Greenthread tea (FooDB: FOOD00820)
Hibiscus tea (FooDB: FOOD00723)

Soy

Soy product

Soy bean (FooDB: FOOD00085)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Animal origin

Lagomorph

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Greylag goose (FooDB: FOOD00368)
Emu (FooDB: FOOD00360)
Ostrich (FooDB: FOOD00422)
Guinea hen (FooDB: FOOD00373)
Velvet duck (FooDB: FOOD00427)

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Bovine

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Coffee and coffee product

Coffee

Robusta coffee (FooDB: FOOD00060)
Arabica coffee (FooDB: FOOD00059)

Dish

Other dish

Taco shell (FooDB: FOOD00991)
Tostada shell (FooDB: FOOD00992)

Baking good

Wrapper

Wonton wrapper (FooDB: FOOD00818)

Process

Role

Industrial application

Pharmaceutical industry

Pharmaceutical (HMDB: HMDB0001409)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Not Available	158.1	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000122

Predicted Molecular 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	166.319	31661259
DarkChem	[M-H]-	163.722	31661259
AllCCS	[M+H]+	165.817	32859911
AllCCS	[M-H]-	161.757	32859911
DeepCCS	[M+H]+	160.937	30932474
DeepCCS	[M-H]-	158.578	30932474
DeepCCS	[M-2H]-	192.456	30932474
DeepCCS	[M+Na]+	167.52	30932474
AllCCS	[M+H]+	165.8	32859911
AllCCS	[M+H-H2O]+	162.6	32859911
AllCCS	[M+NH4]+	168.8	32859911
AllCCS	[M+Na]+	169.6	32859911
AllCCS	[M-H]-	161.8	32859911
AllCCS	[M+Na-2H]-	161.7	32859911
AllCCS	[M+HCOO]-	161.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
dUMP	O[C@H]1C[C@@H](O[C@@H]1COP(O)(O)=O)N1C=CC(=O)NC1=O	3652.9	Standard polar	33892256
dUMP	O[C@H]1C[C@@H](O[C@@H]1COP(O)(O)=O)N1C=CC(=O)NC1=O	2132.0	Standard non polar	33892256
dUMP	O[C@H]1C[C@@H](O[C@@H]1COP(O)(O)=O)N1C=CC(=O)NC1=O	2997.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
dUMP,1TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)O	2519.8	Semi standard non polar	33892256
dUMP,1TMS,isomer #2	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O	2681.8	Semi standard non polar	33892256
dUMP,1TMS,isomer #3	C[Si](C)(C)N1C(=O)C=CN([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)C1=O	2655.9	Semi standard non polar	33892256
dUMP,2TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C	2639.9	Semi standard non polar	33892256
dUMP,2TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C	2781.4	Standard non polar	33892256
dUMP,2TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C	3742.8	Standard polar	33892256
dUMP,2TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O	2608.7	Semi standard non polar	33892256
dUMP,2TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O	2864.6	Standard non polar	33892256
dUMP,2TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O	4142.2	Standard polar	33892256
dUMP,2TMS,isomer #3	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O)O[Si](C)(C)C	2689.4	Semi standard non polar	33892256
dUMP,2TMS,isomer #3	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O)O[Si](C)(C)C	2802.5	Standard non polar	33892256
dUMP,2TMS,isomer #3	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O)O[Si](C)(C)C	3471.7	Standard polar	33892256
dUMP,2TMS,isomer #4	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O	2731.8	Semi standard non polar	33892256
dUMP,2TMS,isomer #4	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O	2818.7	Standard non polar	33892256
dUMP,2TMS,isomer #4	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O	3760.5	Standard polar	33892256
dUMP,3TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2662.8	Semi standard non polar	33892256
dUMP,3TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2835.0	Standard non polar	33892256
dUMP,3TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	3266.6	Standard polar	33892256
dUMP,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C	2705.9	Semi standard non polar	33892256
dUMP,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C	2859.4	Standard non polar	33892256
dUMP,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C	3465.8	Standard polar	33892256
dUMP,3TMS,isomer #3	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O)O[Si](C)(C)C	2739.9	Semi standard non polar	33892256
dUMP,3TMS,isomer #3	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O)O[Si](C)(C)C	2869.0	Standard non polar	33892256
dUMP,3TMS,isomer #3	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O)O[Si](C)(C)C	3243.9	Standard polar	33892256
dUMP,4TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2743.4	Semi standard non polar	33892256
dUMP,4TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2886.0	Standard non polar	33892256
dUMP,4TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	3065.6	Standard polar	33892256
dUMP,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)O	2793.6	Semi standard non polar	33892256
dUMP,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O	2918.3	Semi standard non polar	33892256
dUMP,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C(=O)C=CN([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)C1=O	2876.1	Semi standard non polar	33892256
dUMP,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C(C)(C)C	3098.6	Semi standard non polar	33892256
dUMP,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C(C)(C)C	3241.8	Standard non polar	33892256
dUMP,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C(C)(C)C	3854.6	Standard polar	33892256
dUMP,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O	3080.0	Semi standard non polar	33892256
dUMP,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O	3314.8	Standard non polar	33892256
dUMP,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O	4085.5	Standard polar	33892256
dUMP,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O)O[Si](C)(C)C(C)(C)C	3118.9	Semi standard non polar	33892256
dUMP,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O)O[Si](C)(C)C(C)(C)C	3218.8	Standard non polar	33892256
dUMP,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O)O[Si](C)(C)C(C)(C)C	3660.3	Standard polar	33892256
dUMP,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O	3163.3	Semi standard non polar	33892256
dUMP,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O	3234.7	Standard non polar	33892256
dUMP,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O	3816.4	Standard polar	33892256
dUMP,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3294.0	Semi standard non polar	33892256
dUMP,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3447.9	Standard non polar	33892256
dUMP,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3526.2	Standard polar	33892256
dUMP,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C(C)(C)C	3372.3	Semi standard non polar	33892256
dUMP,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C(C)(C)C	3467.7	Standard non polar	33892256
dUMP,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C(C)(C)C	3605.9	Standard polar	33892256
dUMP,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O)O[Si](C)(C)C(C)(C)C	3392.5	Semi standard non polar	33892256
dUMP,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O)O[Si](C)(C)C(C)(C)C	3442.3	Standard non polar	33892256
dUMP,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O)O[Si](C)(C)C(C)(C)C	3473.3	Standard polar	33892256
dUMP,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3589.4	Semi standard non polar	33892256
dUMP,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3605.0	Standard non polar	33892256
dUMP,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3362.5	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Mitochondria
Nucleus

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Pyrimidine metabolism	Not Available
Beta Ureidopropionase Deficiency		Not Available
UMP Synthase Deficiency (Orotic Aciduria)		Not Available
Dihydropyrimidinase Deficiency		Not Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

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

VMH ID

DUMP

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Richards RG, Sowers LC, Laszlo J, Sedwick WD: The occurrence and consequences of deoxyuridine in DNA. Adv Enzyme Regul. 1984;22:157-85. [PubMed:6147963 ]
Krokan HE, Otterlei M, Nilsen H, Kavli B, Skorpen F, Andersen S, Skjelbred C, Akbari M, Aas PA, Slupphaug G: Properties and functions of human uracil-DNA glycosylase from the UNG gene. Prog Nucleic Acid Res Mol Biol. 2001;68:365-86. [PubMed:11554311 ]

Enzymes

Enzyme Details

1. Deoxycytidylate deaminase

General function:: Involved in zinc ion binding
Specific function:: Supplies the nucleotide substrate for thymidylate synthetase.
Gene Name:: DCTD
Uniprot ID:: P32321
Molecular weight:: 21013.96

Reactions

dCMP + Water → dUMP + Ammonia	details

Enzyme Details

2. Thymidylate kinase

General function:: Involved in thymidylate kinase activity
Specific function:: Catalyzes the conversion of dTMP to dTDP.
Gene Name:: DTYMK
Uniprot ID:: P23919
Molecular weight:: 23819.105

Reactions

Adenosine triphosphate + dUMP → ADP + dUDP	details

Enzyme Details

3. Inosine triphosphate pyrophosphatase

General function:: Involved in hydrolase activity
Specific function:: Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) and xanthosine 5'-triphosphate (XTP) to their respective monophosphate derivatives. The enzyme does not distinguish between the deoxy- and ribose forms. Probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.
Gene Name:: ITPA
Uniprot ID:: Q9BY32
Molecular weight:: 16833.23

Reactions

Deoxyuridine triphosphate + Water → dUMP + Pyrophosphate	details

Enzyme Details

4. Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial

General function:: Involved in hydrolase activity
Specific function:: This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.
Gene Name:: DUT
Uniprot ID:: P33316
Molecular weight:: 26562.975

Reactions

Deoxyuridine triphosphate + Water → dUMP + Pyrophosphate	details

Enzyme Details

5. Thymidine kinase, cytosolic

General function:: Nucleotide transport and metabolism
Specific function:: Not Available
Gene Name:: TK1
Uniprot ID:: P04183
Molecular weight:: 25468.455

Reactions

Adenosine triphosphate + Deoxyuridine → ADP + dUMP	details

Enzyme Details

6. Thymidine kinase 2, mitochondrial

General function:: Involved in ATP binding
Specific function:: Deoxyribonucleoside kinase that phosphorylates thymidine, deoxycytidine, and deoxyuridine. Also phosphorylates anti-viral and anti-cancer nucleoside analogs.
Gene Name:: TK2
Uniprot ID:: O00142
Molecular weight:: 27561.495

Reactions

Adenosine triphosphate + Deoxyuridine → ADP + dUMP	details

Enzyme Details

7. Thymidylate synthase

General function:: Involved in thymidylate synthase activity
Specific function:: Contributes to the de novo mitochondrial thymidylate biosynthesis pathway.
Gene Name:: TYMS
Uniprot ID:: P04818
Molecular weight:: 35715.65

Reactions

5,10-Methylene-THF + dUMP → Dihydrofolic acid + 5-Thymidylic acid	details

Enzyme Details

8. Thymidine kinase

General function:: Involved in ATP binding
Specific function:: Not Available
Gene Name:: Not Available
Uniprot ID:: Q8IZR3
Molecular weight:: 35439.6

Showing metabocard for dUMP (HMDB0001409)

MOL for HMDB0001409 (dUMP)

3D MOL for HMDB0001409 (dUMP)

3D SDF for HMDB0001409 (dUMP)

3D-SDF for HMDB0001409 (dUMP)

PDB for HMDB0001409 (dUMP)

3D PDB for HMDB0001409 (dUMP)

SMILES for HMDB0001409 (dUMP)

INCHI for HMDB0001409 (dUMP)

Structure for HMDB0001409 (dUMP)

3D Structure for HMDB0001409 (dUMP)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions