Showing metabocard for dUMP (BMDB0001409)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (4) Show 4 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:45:31 UTC
Update Date2020-05-21 16:29:02 UTC
BMDB IDBMDB0001409
Secondary Accession Numbers
  • BMDB01409
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 cattle, dUMP participates in a number of enzymatic reactions. In particular, dUMP can be biosynthesized from dCMP through the action of the enzyme deoxycytidylate deaminase. In addition, dUMP can be biosynthesized from deoxyuridine through the action of the enzyme thymidine kinase, cytosolic. In cattle, dUMP is involved in the metabolic pathway called the pyrimidine metabolism pathway.
Structure
Thumb
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
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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 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
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 35V, positivesplash10-001i-9000000000-e479009af7b70bba530dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 10V, positivesplash10-001i-9120000000-68df7c9d0651f44d4ec7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 40V, positivesplash10-0f89-9100000000-8d632914cc75f30e28a2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 20V, positivesplash10-001i-9230000000-1e8624ca24971f32ad74View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-e3761e9ef1ac38190893View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9000000000-489d2a85cc04ba0a5d6aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-053r-9122000000-056f8bdc172db3cba93aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-88bc2ad1e6aeada6888fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9120000000-68df7c9d0651f44d4ec7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9000000000-f9632ee285ee7f2901f7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0f89-9100000000-ed98a4451221d6d749f2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9230000000-4990b01871cfbeec214dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-b1e75c91dac815141295View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-01ot-1900000000-fb8b7ffefbb81eb54969View 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 Spectrum (1D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001409
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
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Thymidylate synthase
General function:
Nucleotide transport and metabolism
Specific function:
Contributes to the de novo mitochondrial thymidylate biosynthesis pathway.
Gene Name:
TYMS
Uniprot ID:
Q2TA32
Molecular weight:
39785.0
Reactions
dUMP + 5,10-Methylene-THF → 5-Thymidylic acid + Dihydrofolic aciddetails
dUMP + Adenosine triphosphate → dUDP + ADPdetails
Enzyme Details
2. DCTD protein
General function:
Nucleotide transport and metabolism
Specific function:
Not Available
Gene Name:
DCTD
Uniprot ID:
A6QQC3
Molecular weight:
20039.0
Reactions
dCMP + Water → dUMP + Ammoniadetails
Enzyme Details
3. Deoxyuridine triphosphatase
General function:
Not Available
Specific function:
Not Available
Gene Name:
DUT
Uniprot ID:
Q2NKU1
Molecular weight:
20018.0
Reactions
Deoxyuridine triphosphate + Water → dUMP + Hydrogen phosphatedetails
Enzyme Details
4. Thymidine kinase, cytosolic
General function:
Not Available
Specific function:
Not Available
Gene Name:
TK1
Uniprot ID:
A5D7R8
Molecular weight:
26377.0
Reactions
Deoxyuridine + Adenosine triphosphate → dUMP + ADPdetails