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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-10-23 19:03:51 UTC
HMDB IDHMDB0001409
Secondary Accession Numbers
  • HMDB01409
Metabolite Identification
Common NamedUMP
DescriptiondUMP is formed by the reduction of ribonucleotides to deoxyribonucleotides by ribonucleoside diphosphate reductase [EC 1.17.4.1]. dUMP by the action of by thymidylate synthetase [EC 2.1.1.45] produces dTMP (5,10-Methylene-5,6,7,8-tetrahydrofolate is a cofactor for the reaction). The nuclear form of uracil-DNA glycosylase (UNG2), that its major role is to remove misincorporated dUMP residues (cells deficient in removal of misincorporated dUMP accumulate uracil residues). (PMID 11554311 ).
Structure
Thumb
Synonyms
ValueSource
2'-Deoxyuridine 5'-monophosphateChEBI
2'-Deoxyuridine 5'-phosphateChEBI
Deoxyuridine 5'-phosphateChEBI
Deoxyuridine monophosphateChEBI
DeoxyuridylateChEBI
Deoxyuridylic acidChEBI
2'-Deoxyuridine 5'-monophosphoric acidGenerator
2'-Deoxyuridine 5'-phosphoric acidGenerator
Deoxyuridine 5'-phosphoric acidGenerator
Deoxyuridine monophosphoric acidGenerator
2'-Deoxy-5'-uridylateHMDB
2'-Deoxy-5'-uridylic acidHMDB
2'-DeoxyuridylateHMDB
2'-Deoxyuridylic acidHMDB
Deoxy-UMPHMDB
Deoxyuridine 5'-monophosphateHMDB
2'-Deoxyuridine-5'-monophosphateMeSH
2'-Deoxyuridylic acid, disodium saltMeSH
Chemical FormulaC9H13N2O8P
Average Molecular Weight308.1819
Monoisotopic Molecular Weight308.040951914
IUPAC Name{[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional Name2'-deoxyuridylic acid
CAS Registry Number964-26-1
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 KeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities 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.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleotides
Direct ParentPyrimidine 2'-deoxyribonucleoside monophosphates
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside monophosphate
  • Hydroxypyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Oxolane
  • Heteroaromatic compound
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Biological Location:

  Subcellular:

Source:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Role

Industrial application:

  Pharmaceutical industry:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility7.97 g/LALOGPS
logP-1.4ALOGPS
logP-1.6ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area145.63 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity61.93 m³·mol⁻¹ChemAxon
Polarizability25.86 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9410000000-3abd5b4815950ff662f5View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-01ow-9321000000-f216f77409b12a9c39d1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, N/A (Annotated)splash10-001i-9100000000-c9b7092bb72f342d372fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, N/A (Annotated)splash10-001i-9000000000-d2272878a49bc62c1955View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, N/A (Annotated)splash10-001i-9000000000-69451d809e5517ef09cbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-01ta-9803000000-f0e26cbfb75f3fb7b36eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-01ta-9803000000-f0e26cbfb75f3fb7b36eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-446c86aec7739d354d2cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-00b01a3db61a05d06fb7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-7900000000-cc618ed7c89e1e816a5dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-06tf-9143000000-78a62ec1d8e492431f91View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5ad77843f75db170ab17View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-06305d10841a2df94c23View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Mitochondria
  • Nucleus
Biofluid LocationsNot Available
Tissue LocationNot Available
Pathways
NameSMPDB/PathwhizKEGG
Beta Ureidopropionase DeficiencyPw000187Pw000187 greyscalePw000187 simpleNot Available
Dihydropyrimidinase DeficiencyPw000189Pw000189 greyscalePw000189 simpleNot Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)Pw000190Pw000190 greyscalePw000190 simpleNot Available
Pyrimidine MetabolismPw000160Pw000160 greyscalePw000160 simpleMap00240
UMP Synthase Deficiency (Orotic Aciduria)Pw000188Pw000188 greyscalePw000188 simpleNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022604
KNApSAcK IDNot Available
Chemspider ID58574
KEGG Compound IDC00365
BioCyc IDDUMP
BiGG ID34762
Wikipedia LinkdUMP
METLIN ID6225
PubChem Compound65063
PDB IDDU
ChEBI ID17622
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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 ]
  2. 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

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 + Ammoniadetails
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 + dUDPdetails
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 + Pyrophosphatedetails
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 + Pyrophosphatedetails
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 + dUMPdetails
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 + dUMPdetails
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 aciddetails
General function:
Involved in ATP binding
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q8IZR3
Molecular weight:
35439.6