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Showing metabocard for dUMP (HMDB0001409)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (8) Show 8 proteinsXML
enzymes (8) Show 8 proteins
Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-03-17 18:49:29 UTC
HMDB IDHMDB0001409
Secondary Accession Numbers
  • HMDB01409
Metabolite Identification
Common NamedUMP
DescriptiondUMP, also known as deoxyuridylate or deoxy-UMP, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. dUMP is an extremely weak basic (essentially neutral) compound (based on its pKa). dUMP exists in all living species, ranging from bacteria to humans. Within humans, dUMP participates in a number of enzymatic reactions. In particular, dUMP can be biosynthesized from dCMP through its interaction with the enzyme deoxycytidylate deaminase. In addition, dUMP can be biosynthesized from deoxyuridine; which is mediated by the enzyme thymidine kinase, cytosolic. In humans, dUMP is involved in pyrimidine metabolism. A pyrimidine 2'-deoxyribonucleoside 5'-monophosphate having uracil as the nucleobase. Outside of the human body, dUMP has been detected, but not quantified in, several different foods, such as breadnut tree seeds, sea-buckthornberries, sour cherries, black walnuts, and common oregano. This could make dUMP a potential biomarker for the consumption of these foods.
Structure
Data?1584470969
MOLSDFPDBSMILESInChI
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'-monophosphateHMDB
2'-Deoxyuridylic acid, disodium saltHMDB
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
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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine deoxyribonucleotides
Direct ParentPyrimidine 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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9410000000-3abd5b4815950ff662f5Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-01ow-9321000000-f216f77409b12a9c39d1Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, N/A (Annotated)splash10-001i-9100000000-c9b7092bb72f342d372fSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, N/A (Annotated)splash10-001i-9000000000-d2272878a49bc62c1955Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, N/A (Annotated)splash10-001i-9000000000-69451d809e5517ef09cbSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-01ta-9803000000-f0e26cbfb75f3fb7b36eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-01ta-9803000000-f0e26cbfb75f3fb7b36eSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 35V, positivesplash10-001i-9000000000-e479009af7b70bba530dSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 10V, positivesplash10-001i-9120000000-68df7c9d0651f44d4ec7Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 40V, positivesplash10-0f89-9100000000-8d632914cc75f30e28a2Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 20V, positivesplash10-001i-9230000000-1e8624ca24971f32ad74Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-446c86aec7739d354d2cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-00b01a3db61a05d06fb7Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-7900000000-cc618ed7c89e1e816a5dSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-06tf-9143000000-78a62ec1d8e492431f91Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5ad77843f75db170ab17Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-06305d10841a2df94c23Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
Biological Properties
Cellular Locations
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03800
Phenol Explorer Compound IDNot Available
FooDB IDFDB022604
KNApSAcK IDC00019282
Chemspider ID58574
KEGG Compound IDC00365
BioCyc IDDUMP
BiGG ID34762
Wikipedia LinkDeoxyuridine_monophosphate
METLIN ID6225
PubChem Compound65063
PDB IDNot Available
ChEBI ID17622
Food Biomarker OntologyNot Available
VMH IDDUMP
MarkerDB ID
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

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 + Ammoniadetails
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 + dUDPdetails
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 + Pyrophosphatedetails
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 + Pyrophosphatedetails
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 + dUMPdetails
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 + dUMPdetails
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 aciddetails
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