Record Information
Version2.0
Creation Date2012-05-31 13:52:00 -0600
Update Date2015-09-13 12:56:11 -0600
Secondary Accession Numbers
  • ECMDB01409
Identification
Name:dUMP
Description:dUMP 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:
  • 2'-Deoxy-5'-uridylate
  • 2'-Deoxy-5'-uridylic acid
  • 2'-Deoxyuridine 5'-monophosphate
  • 2'-Deoxyuridine 5'-monophosphoric acid
  • 2'-Deoxyuridine 5'-phosphate
  • 2'-Deoxyuridine 5'-phosphoric acid
  • 2'-Deoxyuridine-5'-phosphate
  • 2'-Deoxyuridine-5'-phosphoric acid
  • 2'-Deoxyuridine-5-monophosphate
  • 2'-Deoxyuridine-5-monophosphoric acid
  • 2'-Deoxyuridylate
  • 2'-Deoxyuridylic acid
  • Deoxy-UMP
  • Deoxyurdine-phosphate
  • Deoxyurdine-phosphoric acid
  • Deoxyuridine 5'-monophosphate
  • Deoxyuridine 5'-monophosphoric acid
  • Deoxyuridine 5'-phosphate
  • Deoxyuridine 5'-phosphoric acid
  • Deoxyuridine monophosphate
  • Deoxyuridine monophosphoric acid
  • Deoxyuridine-phosphate
  • Deoxyuridine-phosphoric acid
  • Deoxyuridylate
  • Deoxyuridylic acid
  • DUMP
  • U
Chemical Formula:C9H13N2O8P
Weight:Average: 308.1819
Monoisotopic: 308.040951914
InChI Key:JSRLJPSBLDHEIO-SHYZEUOFSA-N
InChI: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
CAS number:964-26-1
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 Name:2'-deoxyuridylic acid
SMILES:O[C@H]1C[C@@H](O[C@@H]1COP(O)(O)=O)N1C=CC(=O)NC1=O
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
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility7.97 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity61.93 m3·mol-1ChemAxon
Polarizability25.86 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
One Carbon Pool by Folate IPW001735 Pw001735Pw001735 greyscalePw001735 simple
One carbon pool by folatePW000773 Pw000773Pw000773 greyscalePw000773 simple
Pyrimidine metabolismPW000942 Pw000942Pw000942 greyscalePw000942 simple
salvage pathways of pyrimidine deoxyribonucleotidesPW002061 Pw002061Pw002061 greyscalePw002061 simple
KEGG Pathways:
EcoCyc Pathways:
  • formylTHF biosynthesis I 1CMET2-PWY
  • pyrimidine deoxyribonucleotides de novo biosynthesis I PWY0-166
  • salvage pathways of pyrimidine deoxyribonucleotides PWY0-181
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MSsplash10-0002-9410000000-3abd5b4815950ff662f5View in MoNA
GC-MSGC-MS Spectrum - GC-MS (1 TMS)splash10-01ow-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 Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Krokan, H. E., Otterlei, M., Nilsen, H., Kavli, B., Skorpen, F., Andersen, S., Skjelbred, C., Akbari, M., Aas, P. A., Slupphaug, G. (2001). "Properties and functions of human uracil-DNA glycosylase from the UNG gene." Prog Nucleic Acid Res Mol Biol 68:365-386. Pubmed: 11554311
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID17622
HMDB IDHMDB01409
Pubchem Compound ID65063
Kegg IDC00365
ChemSpider ID58574
WikipediadUMP
BioCyc IDDUMP
EcoCyc IDDUMP
Ligand ExpoUMP

Enzymes

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:
P06968
Molecular weight:
16155
Reactions
dUTP + H(2)O = dUMP + diphosphate.
General function:
Involved in hydrolase activity
Specific function:
Degradation of external UDP-glucose to uridine monophosphate and glucose-1-phosphate, which can then be used by the cell
Gene Name:
ushA
Uniprot ID:
P07024
Molecular weight:
60824
Reactions
UDP-sugar + H(2)O = UMP + alpha-D-aldose 1-phosphate.
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
General function:
Involved in thymidylate kinase activity
Specific function:
Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth
Gene Name:
tmk
Uniprot ID:
P0A720
Molecular weight:
23783
Reactions
ATP + dTMP = ADP + dTDP.
General function:
Involved in hydrolase activity
Specific function:
Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'- monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain- length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. Also plays a significant physiological role in stress-response and is required for the survival of E.coli in stationary growth phase
Gene Name:
surE
Uniprot ID:
P0A840
Molecular weight:
26900
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.
General function:
Involved in thymidylate synthase activity
Specific function:
Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation
Gene Name:
thyA
Uniprot ID:
P0A884
Molecular weight:
30480
Reactions
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP.
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows high phosphatase activity toward three nucleoside 5'-monophosphates, UMP, dUMP, and dTMP, and very low activity against TDP, IMP, UDP, GMP, dGMP, AMP, dAMP, and 6- phosphogluconate. Is strictly specific to substrates with 5'- phosphates and shows no activity against nucleoside 2'- or 3'- monophosphates. Might be involved in the pyrimidine nucleotide substrate cycles
Gene Name:
yjjG
Uniprot ID:
P0A8Y1
Molecular weight:
25300
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
General function:
Involved in acid phosphatase activity
Specific function:
Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:
aphA
Uniprot ID:
P0AE22
Molecular weight:
26103
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.
General function:
Involved in nucleoside-triphosphate diphosphatase activity
Specific function:
Specific function unknown
Gene Name:
mazG
Uniprot ID:
P0AEY3
Molecular weight:
30412
Reactions
ATP + H(2)O = AMP + diphosphate.
General function:
Involved in thymidine kinase activity
Specific function:
Phosphorylates both thymidine and deoxyuridine
Gene Name:
tdk
Uniprot ID:
P23331
Molecular weight:
23456
Reactions
ATP + thymidine = ADP + thymidine 5'-phosphate.
General function:
Involved in hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Specific function:
Catalyzes the hydrolysis of nucleoside triphosphates, with a preference for pyrimidine deoxynucleoside triphosphates (dUTP, dTTP and dCTP)
Gene Name:
nudI
Uniprot ID:
P52006
Molecular weight:
16371
Reactions
Nucleoside triphosphate + H(2)O = nucleoside monophosphate + diphosphate.
General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes O6 atom-containing purine bases deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to nucleotide monophosphate and pyrophosphate. Probably excludes non- standard purines from DNA precursor pool, preventing thus incorporation into DNA and avoiding chromosomal lesions
Gene Name:
rdgB
Uniprot ID:
P52061
Molecular weight:
21039
Reactions
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate.
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows strict specificity toward deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. Might be involved in the regulation of all dNTP pools in E.coli
Gene Name:
yfbR
Uniprot ID:
P76491
Molecular weight:
22708
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.

Transporters

General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368