Showing Compound Card for dUMP (CDB004913)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraProtein targetPathwaysConcentrationsLinksReferencesenzymes (8) Show 12 proteinsXML
Record Information
Version1.0
Created at2020-04-17 18:49:51 UTC
Updated at2020-11-18 16:38:59 UTC
CannabisDB IDCDB004913
Secondary Accession NumbersNot Available
Cannabis Compound 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. dUMP is expected to be in Cannabis as all living plants are known to produce and metabolize it.
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 Weight308.18
Monoisotopic Molecular Weight308.041
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:

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
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
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSdUMP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0002-9410000000-3abd5b4815950ff662f5Spectrum
Predicted GC-MSdUMP, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-01ow-9321000000-f216f77409b12a9c39d1Spectrum
Predicted GC-MSdUMP, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdUMP, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, N/A (Annotated)splash10-001i-9100000000-c9b7092bb72f342d372f2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, N/A (Annotated)splash10-001i-9000000000-d2272878a49bc62c19552012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, N/A (Annotated)splash10-001i-9000000000-69451d809e5517ef09cb2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-01ta-9803000000-f0e26cbfb75f3fb7b36e2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-01ta-9803000000-f0e26cbfb75f3fb7b36e2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 35V, positivesplash10-001i-9000000000-e479009af7b70bba530d2020-07-21View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 10V, positivesplash10-001i-9120000000-68df7c9d0651f44d4ec72020-07-21View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 40V, positivesplash10-0f89-9100000000-8d632914cc75f30e28a22020-07-21View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF 20V, positivesplash10-001i-9230000000-1e8624ca24971f32ad742020-07-21View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-e3761e9ef1ac381908932021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9000000000-489d2a85cc04ba0a5d6a2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-053r-9122000000-056f8bdc172db3cba93a2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-88bc2ad1e6aeada6888f2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9120000000-68df7c9d0651f44d4ec72021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9000000000-f9632ee285ee7f2901f72021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0f89-9100000000-ed98a4451221d6d749f22021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9230000000-4990b01871cfbeec214d2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-b1e75c91dac8151412952021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-01ot-1900000000-fb8b7ffefbb81eb549692021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-446c86aec7739d354d2c2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-00b01a3db61a05d06fb72016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-7900000000-cc618ed7c89e1e816a5d2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-06tf-9143000000-78a62ec1d8e492431f912016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5ad77843f75db170ab172016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-06305d10841a2df94c232016-09-12View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Spectrum
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
Deoxycytidylate deaminaseDCTD4q35.1P32321 details
Thymidylate kinaseDTYMK2q37.3P23919 details
Inosine triphosphate pyrophosphataseITPA20pQ9BY32 details
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrialDUT15q21.1P33316 details
Thymidine kinase, cytosolicTK117q23.2-q25.3P04183 details
Thymidine kinase 2, mitochondrialTK216q22-q23.1O00142 details
Thymidylate synthaseTYMS18p11.32P04818 details
Thymidine kinaseQ8IZR3 details
TransportersNot Available
Metal Bindings
Protein NameGene NameLocusUniprot IDDetails
Deoxycytidylate deaminaseDCTD4q35.1P32321 details
Inosine triphosphate pyrophosphataseITPA20pQ9BY32 details
Thymidine kinase, cytosolicTK117q23.2-q25.3P04183 details
ReceptorsNot Available
Transcriptional Factors
Protein NameGene NameLocusUniprot IDDetails
Thymidylate synthaseTYMS18p11.32P04818 details
Concentrations Data
Not Available
HMDB IDHMDB0001409
DrugBank IDDB03800
Phenol Explorer Compound IDNot Available
FoodDB 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
General ReferencesNot Available

Only showing the first 10 proteins. There are 12 proteins in total.

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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
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
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
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
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
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
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
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

Only showing the first 10 proteins. There are 12 proteins in total.

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