3'-UMP (ECMDB20081) (M2MDB000930)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)Transporters (4)XML
Proteins (132)
Record Information
Version2.0
Creation Date2012-05-31 14:26:29 -0600
Update Date2015-06-03 17:19:16 -0600
Secondary Accession Numbers
  • ECMDB20081
Identification
Name:3'-UMP
Description3'-UMP or 3' uridylic acid is a member of the chemical class known as Pyrimidine Nucleosides and Analogues. These are compounds comprising a pyrimidine base attached to a sugar. It is an unusual, but naturally occurring form of UMP, as the normal form is 5'-UMP. It is a substrate for 2',3'-cyclic-nucleotide 2'-phosphodiesterase.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 3'-UMP
  • 3'-URIDINEMONOPHOSPHATE
  • 3'-URIDINEMONOphosphoric acid
  • 3'-Uridylate
  • 3'-Uridylic acid
  • 4rsk
  • Uridine 3'-(dihydrogen phosphate)
  • Uridine 3'-(dihydrogen phosphoric acid)
  • Uridine 3'-monophosphate
  • Uridine 3'-monophosphoric acid
  • Uridine 3'-phosphate
  • Uridine 3'-phosphoric acid
Chemical Formula:C9H13N2O9P
Weight:Average: 324.1813
Monoisotopic: 324.035866536
InChI Key:FOGRQMPFHUHIGU-XVFCMESISA-N
InChI:InChI=1S/C9H13N2O9P/c12-3-4-7(20-21(16,17)18)6(14)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
CAS number:35170-03-7
IUPAC Name:{[(2R,3S,4R,5R)-4-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)-2-(hydroxymethyl)oxolan-3-yl]oxy}phosphonic acid
Traditional IUPAC Name:disodium salt 3'-uridylic acid
SMILES:[H][C@]1(CO)O[C@@]([H])(N2C=CC(O)=NC2=O)[C@]([H])(O)[C@]1([H])OP(O)(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as ribonucleoside 3'-phosphates. These are ribonucleosides that contain a phosphate group attached to the C-3 carbon of the ribose or deoxyribose moiety. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassRibonucleoside 3'-phosphates
Sub ClassNot Available
Direct ParentRibonucleoside 3'-phosphates
Alternative Parents
Substituents
  • Ribonucleoside 3'-phosphate
  • Pentose phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Hydroxypyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Alcohol
  • Primary alcohol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility12.9 g/LALOGPS
logP-1.8ALOGPS
logP-2.2ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)0.87ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area169.35 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity63.76 m³·mol⁻¹ChemAxon
Polarizability26.56 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
2',3'-Cyclic UMP + Water > 3'-UMP + Hydrogen ion
3'-UMP + Water > Phosphate + Uridine
2',3'-Cyclic UMP + Water <> 3'-UMP
SMPDB Pathways:
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine ribonucleosides degradtionPW002024 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9700000000-234bd44f3d34906cbeceView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0002-9421320000-9c4cf530cc9624248dadView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1901000000-307223cc9d7e5ca2c6eeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4900000000-62b17f2d271511410cf4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-9800000000-50f9fd6d43d9e5e16311View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03mi-7944000000-2b222aece47b6e9a695cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01tc-9311000000-cca262c231169b234379View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-82620f8bebfb8aa3568dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03fr-0957000000-a7d0f49263bb2b8e1973View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5914000000-d2595f9fec12f45442c7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-4900000000-bf51097d1da03b19fd1cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-0009000000-a27b730787a7cecdb7c6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9010000000-031f5fae06b2768c7c4dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-08ff6e231aab99a21c75View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID28895
HMDB IDHMDB0060282
Pubchem Compound ID101543
Kegg IDC01368
ChemSpider ID91753
Wikipedia IDNot Available
BioCyc IDCPD-3724
EcoCyc IDCPD-3724
Ligand ExpoU3P

Enzymes

Protein Details
1. 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase
General function:
Involved in hydrolase activity
Specific function:
This bifunctional enzyme catalyzes two consecutive reactions during ribonucleic acid degradation. Converts a 2',3'- cyclic nucleotide to a 3'-nucleotide and then the 3'-nucleotide to the corresponding nucleoside and phosphate
Gene Name:
cpdB
Uniprot ID:
P08331
Molecular weight:
70832
Reactions
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.

Transporters

Protein Details
1. Outer membrane protein N
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
Protein Details
2. Outer membrane pore protein E
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
Protein Details
3. Outer membrane protein F
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
Protein Details
4. Outer membrane protein C
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