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Showing Compound Uridine diphosphate (FDB007509)

Record Information
Version1.0
Creation date2010-04-08 22:07:38 UTC
Update date2020-09-17 15:40:42 UTC
Primary IDFDB007509
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameUridine diphosphate
DescriptionUridine 5'-diphosphate, also known as 5'-UDP or uridine diphosphoric acid, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. Uridine 5'-diphosphate is an important extracellular pyrimidine signaling molecule that mediates diverse biological effects via P1 and P2 purinergic receptors, such as the uptake of thymidine and proliferation of gliomas. Uridine 5'-diphosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Uridine 5'-diphosphate exists in all living species, ranging from bacteria to humans. Within humans, uridine 5'-diphosphate participates in a number of enzymatic reactions. In particular, tamoxifen-N-glucuronide and uridine 5'-diphosphate can be biosynthesized from tamoxifen and uridine diphosphate glucuronic acid through the action of the enzyme UDP-glucuronosyltransferase 1-4. In addition, 4-hydroxytamoxifen-O-glucuronide and uridine 5'-diphosphate can be biosynthesized from 4-hydroxytamoxifen and uridine diphosphate glucuronic acid through the action of the enzyme UDP-glucuronosyltransferase 1-4. In humans, uridine 5'-diphosphate is involved in tamoxifen metabolism pathway. Outside of the human body, Uridine 5'-diphosphate has been detected, but not quantified in, several different foods, such as pineapples, pine nuts, potato, swiss chards, and lima beans. This could make uridine 5'-diphosphate a potential biomarker for the consumption of these foods.
CAS Number58-98-0
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
SynonymSource
Uridine diphosphateChEBI
Uridine diphosphoric acidGenerator
Uridine 5'-diphosphoric acidGenerator
5'-UDPHMDB
UDPHMDB
Uridine 5'-pyrophosphateHMDB
Uridine 5'-pyrophosphorateHMDB
Uridine 5'-pyrophosphoric acidHMDB
Uridine pyrophosphateHMDB
Pyrophosphate, uridineHMDB
Diphosphate, uridineHMDB
5’-UDPHMDB
Uridine 5'-(trihydrogen pyrophosphate)HMDB
Uridine 5'-diphosphateHMDB
Uridine 5’-(trihydrogen pyrophosphate)HMDB
Uridine 5’-diphosphateHMDB
Uridine 5’-diphosphoric acidHMDB
Uridine 5’-pyrophosphateHMDB
Uridine 5’-pyrophosphoric acidHMDB
Uridine 5'-(trihydrogen diphosphate) (9CI)biospider
Uridine 5'-(trihydrogen pyrophosphate) (8CI)biospider
Uridine 5'-diateChEBI
Uridine 5'-diic acidGenerator
Uridine 5'-diphosphic acidbiospider
Uridine 5'-pyroateHMDB
Uridine 5'-pyroorateHMDB
Uridine 5'-pyrooric acidHMDB
Uridine diateChEBI
Uridine diic acidGenerator
Uridine diphosphate (6CI)biospider
Uridine pyroateHMDB
Uridine pyrophosphate (7CI)biospider
URIDINE-5'-DIPHOSPHATEbiospider
Uridine, 5'-(trihydrogen diphosphate)biospider
Predicted Properties
PropertyValueSource
Water Solubility8.89 g/LALOGPS
logP-0.94ALOGPS
logP-3ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area212.39 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity74.31 m³·mol⁻¹ChemAxon
Polarizability30.43 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC9H14N2O12P2
IUPAC name[({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
InChI IdentifierInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChI KeyXCCTYIAWTASOJW-XVFCMESISA-N
Isomeric SMILESO[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O
Average Molecular Weight404.1612
Monoisotopic Molecular Weight404.002196946
Classification
Description Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Hydroxypyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
OntologyNo ontology term
Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSUridine diphosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-004i-4911000000-e0e7874495a5b5baf6b1Spectrum
Predicted GC-MSUridine diphosphate, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-00pi-3795210000-ef08b4deabe40209df75Spectrum
Predicted GC-MSUridine diphosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_1_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_6, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_7, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_8, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_9, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_10, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TMS_2_11, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TBDMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TBDMS_1_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine diphosphate, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0002-9000000000-7c065a8df0e08b8c365f2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0002-9000000000-73234233232c376d095c2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0002-9000000000-7c065a8df0e08b8c365f2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0pdi-6910600000-bf4136774851b6559f172012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0pdi-6910600000-bf4136774851b6559f172017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-0bvi-3912100000-a85c42f0aa8800737e6c2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0bvi-5911000000-9cf722992950c6d4d8132021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-0bvi-3912100000-9a84dfae5b45e17588392021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-0a6r-5911100000-836559f8456eab3c21f12021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9300000000-bccd47417032b18d32482021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0000900000-36505fd7325e7a1183ed2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0bvi-3923300000-00c8815d00c3062c179c2021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1901000000-4c9ba16543da8ee18c742016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4901000000-1ff9973ec00da457d4532016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-7900000000-f88f01d934d46a57fefb2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ik9-3904300000-454bc02fb8862a1d0fac2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-057l-9801000000-5aabcad933dc7e5003a82016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-7a6d480c699f409f2f362016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0zfr-0301900000-5982e30a90f44090f97e2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9310100000-5890642f8c3624f36d552021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-7bb49a1f0cfcf1695e1e2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0bt9-0630900000-ff34650c58a8429ecb3c2021-09-25View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03fr-2960000000-62a0e10267c1a34669572021-09-25View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-6900000000-7237951ebe305f184b3e2021-09-25View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Spectrum
1D NMR1H NMR Spectrum (1D, D2O, experimental)Spectrum
1D NMR13C NMR Spectrum (1D, D2O, experimental)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Spectrum
ChemSpider ID5809
ChEMBL IDCHEMBL130266
KEGG Compound IDC00015
Pubchem Compound ID6031
Pubchem Substance IDNot Available
ChEBI ID17659
Phenol-Explorer IDNot Available
DrugBank IDDB03435
HMDB IDHMDB00295
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDURIDINE-DIPHOSPHATE
BIGG ID33518
KNApSAcK IDC00007313
HET IDUDP
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDUridine_diphosphate
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
Enzymes
NameGene NameUniProt ID
UDP-glucuronosyltransferase 2B28UGT2B28Q9BY64
UDP-glucuronosyltransferase 2B4UGT2B4P06133
UDP-glucuronosyltransferase 1-4UGT1A4P22310
UDP-glucuronosyltransferase 2B10UGT2B10P36537
UDP-glucuronosyltransferase 2B7UGT2B7P16662
UDP-glucuronosyltransferase 2B15UGT2B15P54855
UDP-glucuronosyltransferase 2A1UGT2A1Q9Y4X1
UDP-glucuronosyltransferase 1-1UGT1A1P22309
UDP-glucuronosyltransferase 1-9UGT1A9O60656
UDP-glucuronosyltransferase 1-8UGT1A8Q9HAW9
UDP-glucuronosyltransferase 1-3UGT1A3P35503
UDP-glucuronosyltransferase 1-10UGT1A10Q9HAW8
UDP-glucuronosyltransferase 2B17UGT2B17O75795
UDP-glucuronosyltransferase 1-6UGT1A6P19224
UDP-glucuronosyltransferase 1-5UGT1A5P35504
UDP-glucuronosyltransferase 2B11UGT2B11O75310
UDP-glucuronosyltransferase 1-7UGT1A7Q9HAW7
UDP-glucuronosyltransferase 2A3UGT2A3Q6UWM9
Glycogen [starch] synthase, liverGYS2P54840
Glycogen [starch] synthase, muscleGYS1P13807
Alpha-lactalbuminLALBAP00709
Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinaseGNEQ9Y223
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunitOGTO15294
Polypeptide N-acetylgalactosaminyltransferase 13GALNT13Q68VI8
Pp-GalNAc-transferase 20GALNT20Q2L4S5
Chondroitin sulfate N-acetylgalactosaminyltransferase 2CSGALNACT2Q8N6G5
Beta-1,3-N-acetylglucosaminyltransferase bGnT-2bGnT-2Q9NY97
Ceramide glucosyltransferaseUGCGQ16739
Phosphatidylinositol N-acetylglucosaminyltransferase subunit QPIGQQ9BRB3
Phosphatidylinositol N-acetylglucosaminyltransferase subunit APIGAP37287
Phosphatidylinositol N-acetylglucosaminyltransferase subunit HPIGHQ14442
Phosphatidylinositol N-acetylglucosaminyltransferase subunit PPIGPP57054
Phosphatidylinositol N-acetylglucosaminyltransferase subunit CPIGCQ92535
2-hydroxyacylsphingosine 1-beta-galactosyltransferaseUGT8Q16880
Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferaseB3GNT5Q9BYG0
Uridine-cytidine kinase-like 1UCKL1Q9NWZ5
ENTPD4 proteinENTPD4Q8NE73
UMP-CMP kinase 2, mitochondrialCMPK2Q5EBM0
Ribonucleoside-diphosphate reductase large subunitRRM1P23921
Chondroitin sulfate N-acetylgalactosaminyltransferase 1CSGALNACT1Q8TDX6
GTP:AMP phosphotransferase, mitochondrialAK3Q9UIJ7
Beta-1,4 N-acetylgalactosaminyltransferase 1B4GALNT1Q00973
Lactosylceramide 4-alpha-galactosyltransferaseA4GALTQ9NPC4
Dolichyl-phosphate beta-glucosyltransferaseALG5Q9Y673
Beta-1,3-galactosyltransferase 4B3GALT4O96024
Polyribonucleotide nucleotidyltransferase 1, mitochondrialPNPT1Q8TCS8
Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferaseMGAT2Q10469
Exostosin-1EXT1Q16394
Exostosin-like 3EXTL3O43909
Exostosin-2EXT2Q93063
Exostosin-like 1EXTL1Q92935
N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferaseB3GNT1O43505
Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase AMGAT5Q09328
Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferaseMGAT3Q09327
N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase, isoform BGCNT2Q06430
Chondroitin sulfate glucuronyltransferaseCHPF2Q9P2E5
Exostosin-like 2EXTL2Q9UBQ6
Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase AMGAT4AQ9UM21
Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase BMGAT4BQ9UQ53
Beta-1,4-N-acetylgalactosaminyltransferase 3B4GALNT3Q6L9W6
N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase 1B4GALNT4Q76KP1
UDP-N-acetylglucosamine transferase subunit ALG13 homologALG13Q9NP73
Pathways
NameSMPDB LinkKEGG Link
Lactose SynthesisSMP00444 Not Available
Pyrimidine MetabolismSMP00046 map00240
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference— Duke, James. 'Dr. Duke's Phytochemical and Ethnobotanical Databases. United States Department of Agriculture.' Agricultural Research Service, Accessed April 27 (2004).