dUMP (YMDB00221)

Identification
YMDB IDYMDB00221
NamedUMP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
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.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2'-Deoxy-5'-uridylate
  • 2'-Deoxy-5'-uridylic acid
  • 2'-Deoxyuridine 5'-monophosphate
  • 2'-Deoxyuridine 5'-phosphate
  • 2'-Deoxyuridylate
  • 2'-Deoxyuridylic acid
  • Deoxy-UMP
  • Deoxyuridine 5'-monophosphate
  • Deoxyuridine 5'-phosphate
  • Deoxyuridine monophosphate
  • Deoxyuridylate
  • Deoxyuridylic acid
  • 2'-Deoxyuridine 5'-monophosphoric acid
  • 2'-Deoxyuridine 5'-phosphoric acid
  • Deoxyuridine 5'-phosphoric acid
  • Deoxyuridine monophosphoric acid
  • 2'-Deoxyuridine-5'-monophosphate
  • 2'-Deoxyuridylic acid, disodium salt
CAS number964-26-1
WeightAverage: 308.1819
Monoisotopic: 308.040951914
InChI KeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
InChIInChI=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
IUPAC Name{[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name2'-deoxyuridylic acid
Chemical FormulaC9H13N2O8P
SMILES[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(=O)(O[H])O[H])N1C([H])=C([H])C(=O)N([H])C1=O
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
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
Biological Properties
Cellular Locations
  • nucleus
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
One Carbon Pool by Folate IPW002468 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB Reactions
Dihydrofolic acid + 5-Thymidylic acid → 5,10-Methylene-THF + dUMP
dUMP + 5,10-methenyltetrahydrofolate mono-L-glutamate → Dihydrofolic acid + 5-Thymidylic acid
Deoxyuridine triphosphate + water → phosphate + hydron + dUMP
KEGG Reactions
dUMP + water → phosphate + 2'-Deoxyuridine
water + hydron + dCMP ↔ dUMP + Ammonium
Adenosine triphosphate + 2'-Deoxyuridine → dUMP + hydron + ADP
Deoxyuridine triphosphate + water → Pyrophosphate + dUMP + hydron
dUMP + 5,10-Methylene-THF → 5-Thymidylic acid + Dihydrofolic acid
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9410000000-3abd5b4815950ff662f5JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-01ow-9321000000-f216f77409b12a9c39d1JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, N/A (Annotated)splash10-001i-9100000000-c9b7092bb72f342d372fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, N/A (Annotated)splash10-001i-9000000000-d2272878a49bc62c1955JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, N/A (Annotated)splash10-001i-9000000000-69451d809e5517ef09cbJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-01ta-9803000000-f0e26cbfb75f3fb7b36eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-01ta-9803000000-f0e26cbfb75f3fb7b36eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 35V, positivesplash10-001i-9000000000-e479009af7b70bba530dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 10V, positivesplash10-001i-9120000000-68df7c9d0651f44d4ec7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 40V, positivesplash10-0f89-9100000000-8d632914cc75f30e28a2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 20V, positivesplash10-001i-9230000000-1e8624ca24971f32ad74JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-e3761e9ef1ac38190893JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9000000000-489d2a85cc04ba0a5d6aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-053r-9122000000-056f8bdc172db3cba93aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-88bc2ad1e6aeada6888fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9120000000-68df7c9d0651f44d4ec7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9000000000-f9632ee285ee7f2901f7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0f89-9100000000-ed98a4451221d6d749f2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9230000000-4990b01871cfbeec214dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-b1e75c91dac815141295JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-01ot-1900000000-fb8b7ffefbb81eb54969JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-446c86aec7739d354d2cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-00b01a3db61a05d06fb7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-7900000000-cc618ed7c89e1e816a5dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-06tf-9143000000-78a62ec1d8e492431f91JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5ad77843f75db170ab17JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-06305d10841a2df94c23JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID17622
HMDB IDHMDB01409
Pubchem Compound ID65063
Kegg IDC00365
ChemSpider ID58574
FOODB IDFDB022604
WikipediaDeoxyuridine_monophosphate
BioCyc IDDUMP

Enzymes

Protein Details
1. Uridylate kinase
General function:
Involved in ATP binding
Specific function:
Furnishes the cell with pyrimidines. Accepts UMP, and dUMP as phosphate acceptors with high activity; to a lesser extent, it can also use IMP, GMP, dGMP, 5-iodo-dUMP, XMP, and dTMP as substrates. ATP and dATP are the best phosphate donors; can use GTP, dGTP, dCTP, and dTTP to some degree (30-50%)
Gene Name:
URA6
Uniprot ID:
P15700
Molecular weight:
22933.0
Reactions
ATP + UMP → ADP + UDP.
Protein Details
2. Thymidylate synthase
General function:
Involved in thymidylate synthase activity
Specific function:
Required for both nuclear and mitochondrial DNA synthesis
Gene Name:
TMP1
Uniprot ID:
P06785
Molecular weight:
35046.89844
Reactions
5,10-methylenetetrahydrofolate + dUMP → dihydrofolate + dTMP.
Protein Details
3. Deoxycytidylate deaminase
General function:
Involved in zinc ion binding
Specific function:
Supplies the nucleotide substrate for thymidylate synthetase
Gene Name:
DCD1
Uniprot ID:
P06773
Molecular weight:
35645.69922
Reactions
dCMP + H(2)O → dUMP + NH(3).
Protein Details
4. Deoxyuridine 5'-triphosphate nucleotidohydrolase
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:
DUT1
Uniprot ID:
P33317
Molecular weight:
15307.2002
Reactions
dUTP + H(2)O → dUMP + diphosphate.