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

enzymes (8) Show 8 proteins

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

Adverse health effect

Genetic disorder

Inborn errors of metabolism

Dihydropyrimidinase deficiency (PMID: 17383919 )

Disposition

Biological location

Cellular substructure

Organelle

Nucleus

Green lentil

Other pulses

Peas

Lentils

Lentils

Onion-family vegetables

Herb and spice mixtures

Curry powder

Cereals and cereal products

Cereals

Cereal products

Doughs

Sourdough

Leavened breads

Flat breads

Other breads

Potato bread

Sweet breads

Raisin bread

Teas

Herbal tea

Herbal teas

Taco shell
Tostada shell

Nuts

Cocoa and cocoa products

Cocoa

Cocoa bean

Horse

Lagomorphs

Ovis

Sheep (Mutton, Lamb)

Caprae

Domestic goat

Coffee and coffee products

Coffee

Soy

Soy products

Soy bean

Baking goods

Wrappers

Wonton wrapper

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Pyrimidine metabolism

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

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

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - dUMP GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9410000000-3abd5b4815950ff662f5	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - dUMP GC-MS (1 TMS) - 70eV, Positive	splash10-01ow-9321000000-f216f77409b12a9c39d1	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - dUMP GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - dUMP GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP Quattro_QQQ 10V, N/A-QTOF (Annotated)	splash10-001i-9100000000-c9b7092bb72f342d372f	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP Quattro_QQQ 25V, N/A-QTOF (Annotated)	splash10-001i-9000000000-d2272878a49bc62c1955	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP Quattro_QQQ 40V, N/A-QTOF (Annotated)	splash10-001i-9000000000-69451d809e5517ef09cb	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative-QTOF	splash10-01ta-9803000000-f0e26cbfb75f3fb7b36e	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP LC-ESI-QTOF , negative-QTOF	splash10-01ta-9803000000-f0e26cbfb75f3fb7b36e	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP LC-ESI-QTOF 35V, positive-QTOF	splash10-001i-9000000000-e479009af7b70bba530d	2020-07-21	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP LC-ESI-QTOF 10V, positive-QTOF	splash10-001i-9120000000-68df7c9d0651f44d4ec7	2020-07-21	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP LC-ESI-QTOF 40V, positive-QTOF	splash10-0f89-9100000000-8d632914cc75f30e28a2	2020-07-21	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP LC-ESI-QTOF 20V, positive-QTOF	splash10-001i-9230000000-1e8624ca24971f32ad74	2020-07-21	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 40V, Positive-QTOF	splash10-001i-9000000000-e3761e9ef1ac38190893	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 10V, Positive-QTOF	splash10-001i-9000000000-489d2a85cc04ba0a5d6a	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 35V, Positive-QTOF	splash10-053r-9122000000-056f8bdc172db3cba93a	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 20V, Positive-QTOF	splash10-001i-9000000000-88bc2ad1e6aeada6888f	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 10V, Positive-QTOF	splash10-001i-9120000000-68df7c9d0651f44d4ec7	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 35V, Positive-QTOF	splash10-001i-9000000000-f9632ee285ee7f2901f7	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 40V, Positive-QTOF	splash10-0f89-9100000000-ed98a4451221d6d749f2	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 20V, Positive-QTOF	splash10-001i-9230000000-4990b01871cfbeec214d	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 20V, Positive-QTOF	splash10-001i-9000000000-b1e75c91dac815141295	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - dUMP 35V, Negative-QTOF	splash10-01ot-1900000000-fb8b7ffefbb81eb54969	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - dUMP 10V, Positive-QTOF	splash10-03di-1900000000-446c86aec7739d354d2c	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - dUMP 20V, Positive-QTOF	splash10-03di-5900000000-00b01a3db61a05d06fb7	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - dUMP 40V, Positive-QTOF	splash10-03di-7900000000-cc618ed7c89e1e816a5d	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - dUMP 10V, Negative-QTOF	splash10-06tf-9143000000-78a62ec1d8e492431f91	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - dUMP 20V, Negative-QTOF	splash10-004i-9100000000-5ad77843f75db170ab17	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - dUMP 40V, Negative-QTOF	splash10-004i-9000000000-06305d10841a2df94c23	2016-09-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum

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

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions