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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2018-05-19 21:35:39 UTC
HMDB IDHMDB0000295
Secondary Accession Numbers
  • HMDB00295
Metabolite Identification
Common NameUridine 5'-diphosphate
DescriptionUridine 5'-diphosphate is a uracil nucleotide containing a pyrophosphate group esterified to C5 of the sugar moiety. UDP 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. (PMID: 14558596 ). UDP induces intracellular Ca(2+) responses and oscillations in HeLa cells, due to the activation of P2Ys (G-protein coupled ATP receptors). (PMID: 1257952 ).
Structure
Thumb
Synonyms
ValueSource
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, uridineMeSH
Diphosphate, uridineMeSH
Chemical FormulaC9H14N2O12P2
Average Molecular Weight404.1612
Monoisotopic Molecular Weight404.002196946
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
Traditional NameUDP
CAS Registry Number58-98-0
SMILES
O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O
InChI Identifier
InChI=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
Chemical Taxonomy
DescriptionThis compound 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
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

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
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
Polarizability30.41 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
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, Positivesplash10-004i-4911000000-e0e7874495a5b5baf6b1View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00pi-3795210000-ef08b4deabe40209df75View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0002-9000000000-7c065a8df0e08b8c365fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0002-9000000000-73234233232c376d095cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0002-9000000000-7c065a8df0e08b8c365fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0pdi-6910600000-bf4136774851b6559f17View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0pdi-6910600000-bf4136774851b6559f17View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1901000000-4c9ba16543da8ee18c74View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4901000000-1ff9973ec00da457d453View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-7900000000-f88f01d934d46a57fefbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ik9-3904300000-454bc02fb8862a1d0facView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-057l-9801000000-5aabcad933dc7e5003a8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-7a6d480c699f409f2f36View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
  • Endoplasmic reticulum
  • Golgi apparatus
Biospecimen Locations
  • Blood
Tissue Locations
  • Placenta
  • Prostate
  • Thyroid Gland
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified41.0 +/- 12.0 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB007509
KNApSAcK IDC00007313
Chemspider ID5809
KEGG Compound IDC00015
BioCyc IDUDP
BiGG ID33518
Wikipedia LinkUridine_Diphosphate
METLIN IDNot Available
PubChem Compound6031
PDB IDUDP
ChEBI ID17659
References
Synthesis ReferenceZeng, Bin; Rao, Linfan; Li, Gaowo. Method for manufacturing uridine diphosphate. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 14pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Brouwer A, Morse DC, Lans MC, Schuur AG, Murk AJ, Klasson-Wehler E, Bergman A, Visser TJ: Interactions of persistent environmental organohalogens with the thyroid hormone system: mechanisms and possible consequences for animal and human health. Toxicol Ind Health. 1998 Jan-Apr;14(1-2):59-84. [PubMed:9460170 ]
  3. Kamisako T, Kobayashi Y, Takeuchi K, Ishihara T, Higuchi K, Tanaka Y, Gabazza EC, Adachi Y: Recent advances in bilirubin metabolism research: the molecular mechanism of hepatocyte bilirubin transport and its clinical relevance. J Gastroenterol. 2000;35(9):659-64. [PubMed:11023036 ]
  4. Syme MR, Paxton JW, Keelan JA: Drug transfer and metabolism by the human placenta. Clin Pharmacokinet. 2004;43(8):487-514. [PubMed:15170365 ]
  5. Collier AC, Tingle MD, Paxton JW, Mitchell MD, Keelan JA: Metabolizing enzyme localization and activities in the first trimester human placenta: the effect of maternal and gestational age, smoking and alcohol consumption. Hum Reprod. 2002 Oct;17(10):2564-72. [PubMed:12351530 ]
  6. Morrone FB, Jacques-Silva MC, Horn AP, Bernardi A, Schwartsmann G, Rodnight R, Lenz G: Extracellular nucleotides and nucleosides induce proliferation and increase nucleoside transport in human glioma cell lines. J Neurooncol. 2003 Sep;64(3):211-8. [PubMed:14558596 ]
  7. Rise A: [Drugs and the fetus]. Tidsskr Nor Laegeforen. 1976 Jan 10;96(1):41-2. [PubMed:1257952 ]

Only showing the first 10 proteins. There are 149 proteins in total.

Enzymes

General function:
Involved in ATP binding
Specific function:
Catalyzes specific phosphoryl transfer from ATP to UMP and CMP.
Gene Name:
CMPK1
Uniprot ID:
P30085
Molecular weight:
20180.12
Reactions
Adenosine triphosphate + Uridine 5'-monophosphate → ADP + Uridine 5'-diphosphatedetails
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]
General function:
Involved in hydrolase activity
Specific function:
In the nervous system, could hydrolyze ATP and other nucleotides to regulate purinergic neurotransmission. Could also be implicated in the prevention of platelet aggregation by hydrolyzing platelet-activating ADP to AMP. Hydrolyzes ATP and ADP equally well.
Gene Name:
ENTPD1
Uniprot ID:
P49961
Molecular weight:
58706.0
Reactions
Uridine 5'-diphosphate + Water → Uridine 5'-monophosphate + Phosphoric aciddetails
Uridine triphosphate + Water → Uridine 5'-diphosphate + Phosphoric aciddetails
General function:
Involved in calcium ion binding
Specific function:
Calcium-dependent nucleotidase with a preference for UDP. The order of activity with different substrates is UDP > GDP > UTP > GTP. Has very low activity towards ADP and even lower activity towards ATP. Does not hydrolyze AMP and GMP. Involved in proteoglycan synthesis.
Gene Name:
CANT1
Uniprot ID:
Q8WVQ1
Molecular weight:
44839.24
Reactions
Uridine 5'-diphosphate + Water → Uridine 5'-monophosphate + Phosphoric aciddetails
General function:
Involved in hydrolase activity
Specific function:
Has a threefold preference for the hydrolysis of ATP over ADP.
Gene Name:
ENTPD3
Uniprot ID:
O75355
Molecular weight:
59104.76
Reactions
Uridine 5'-diphosphate + Water → Uridine 5'-monophosphate + Phosphoric aciddetails
Uridine triphosphate + Water → Uridine 5'-diphosphate + Phosphoric aciddetails
General function:
Involved in ATP binding
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:
UCK1
Uniprot ID:
Q9HA47
Molecular weight:
22760.43
Reactions
Uridine triphosphate + Cytidine → Uridine 5'-diphosphate + Cytidine monophosphatedetails
Uridine triphosphate + Uridine → Uridine 5'-diphosphate + Uridine 5'-monophosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP (By similarity).
Gene Name:
NME4
Uniprot ID:
O00746
Molecular weight:
20658.45
Reactions
Adenosine triphosphate + Uridine 5'-diphosphate → ADP + Uridine triphosphatedetails
General function:
Involved in oxidation reduction
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.
Gene Name:
RRM1
Uniprot ID:
P23921
Molecular weight:
90069.375
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination.
Gene Name:
NME1
Uniprot ID:
P15531
Molecular weight:
17148.635
Reactions
Adenosine triphosphate + Uridine 5'-diphosphate → ADP + Uridine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.
Gene Name:
NME7
Uniprot ID:
Q9Y5B8
Molecular weight:
42491.365
Reactions
Adenosine triphosphate + Uridine 5'-diphosphate → ADP + Uridine triphosphatedetails
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. Inhibits Wnt signaling.
Gene Name:
RRM2
Uniprot ID:
P31350
Molecular weight:
44877.25

Only showing the first 10 proteins. There are 149 proteins in total.