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Record Information
Version1.0
Creation Date2016-09-30 22:27:59 UTC
Update Date2020-05-21 16:29:27 UTC
BMDB IDBMDB0000295
Secondary Accession Numbers
  • BMDB00295
Metabolite Identification
Common NameUridine 5'-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 extremely weak basic (essentially neutral) compound (based on its pKa). Uridine 5'-diphosphate exists in all living species, ranging from bacteria to humans.
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, uridineHMDB
Diphosphate, uridineHMDB
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
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
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Endoplasmic reticulum
  • Golgi
  • Lysosome
  • 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-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
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
  • Endoplasmic reticulum
  • Golgi
  • Lysosome
  • Mitochondria
  • Nucleus
Biospecimen Locations
  • Placenta
  • Prostate Tissue
  • Thyroid Gland
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
PlacentaExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Prostate TissueExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Thyroid GlandExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Abnormal Concentrations
Not Available
HMDB IDHMDB0000295
DrugBank IDDB03435
Phenol Explorer Compound IDNot Available
FooDB IDFDB031236
KNApSAcK IDC00007313
Chemspider ID5809
KEGG Compound IDC00015
BioCyc IDNot Available
BiGG ID33518
Wikipedia LinkUridine_Diphosphate
METLIN IDNot Available
PubChem Compound6031
PDB IDNot Available
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)Not Available
General ReferencesNot Available

Enzymes

General function:
Nucleotide transport and metabolism
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 (By similarity).
Gene Name:
NME7
Uniprot ID:
Q5E9Y9
Molecular weight:
42599.0
Reactions
Uridine triphosphate + ADP → Uridine 5'-diphosphate + Adenosine triphosphatedetails
General function:
Nucleotide transport and metabolism
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 (By similarity). Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically. Binds to both single-stranded guanine- and cytosine-rich strands within the nuclease hypersensitive element (NHE) III(1) region of the MYC gene promoter. Does not bind to duplex NHE III(1). Has G-quadruplex (G4) DNA-binding activity, which is independent of its nucleotide-binding and kinase activity. Binds both folded and unfolded G4 with similar low nanomolar affinities. Stabilizes folded G4s regardless of whether they are prefolded or not (By similarity). Exhibits histidine protein kinase activity (PubMed:12486123).
Gene Name:
NME2
Uniprot ID:
Q3T0Q4
Molecular weight:
17316.0
Reactions
Adenosine triphosphate + Uridine 5'-diphosphate → ADP + Uridine triphosphatedetails
General function:
Nucleotide transport and metabolism
Specific function:
Involved in maintaining the homeostasis of cellular nucleotides by catalyzing the interconversion of nucleoside phosphates. Has GTP:AMP phosphotransferase and ITP:AMP phosphotransferase activities.
Gene Name:
AK3
Uniprot ID:
P08760
Molecular weight:
25671.0
Reactions
Uridine 5'-diphosphate + ADP → Uridine triphosphate + 3'-AMPdetails
General function:
Involved in alpha-tubulin binding
Specific function:
The Golgi complex form catalyzes the production of lactose in the lactating mammary gland and could also be responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids.
Gene Name:
B4GALT1
Uniprot ID:
P08037
Molecular weight:
44843.0
Reactions
Uridine diphosphategalactose + D-Glucose → Uridine 5'-diphosphate + Alpha-Lactosedetails
D-Glucose + Uridine diphosphategalactose → Uridine 5'-diphosphate + Alpha-Lactosedetails
General function:
Carbohydrate transport and metabolism
Specific function:
UDP-glucuronosyltransferases catalyze phase II biotransformation reactions in which lipophilic substrates are conjugated with glucuronic acid to increase water solubility and enhance excretion. They are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds (By similarity).
Gene Name:
UGT3A1
Uniprot ID:
Q1LZI1
Molecular weight:
59682.0
Reactions
Uridine diphosphate glucuronic acid → Isovalerylglucuronide + Uridine 5'-diphosphatedetails
General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Transfers the glycosyl residue from UDP-Glc to the non-reducing end of alpha-1,4-glucan.
Gene Name:
GYS1
Uniprot ID:
A7MB78
Molecular weight:
83814.0
Reactions
Uridine diphosphate glucose → Amylose + Uridine 5'-diphosphatedetails
General function:
Nucleotide transport and metabolism
Specific function:
Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and CMP as phosphate acceptors. Also displays broad nucleoside diphosphate kinase activity.
Gene Name:
CMPK1
Uniprot ID:
Q2KIW9
Molecular weight:
22279.0
Reactions
Adenosine triphosphate + Uridine 5'-monophosphate → ADP + Uridine 5'-diphosphatedetails
General function:
Involved in calcium ion binding
Specific function:
Regulatory subunit of lactose synthase, changes the substrate specificity of galactosyltransferase in the mammary gland making glucose a good acceptor substrate for this enzyme. This enables LS to synthesize lactose, the major carbohydrate component of milk. In other tissues, galactosyltransferase transfers galactose onto the N-acetylglucosamine of the oligosaccharide chains in glycoproteins.
Gene Name:
LALBA
Uniprot ID:
P00711
Molecular weight:
16247.0
Reactions
D-Glucose + Uridine diphosphategalactose → Uridine 5'-diphosphate + Alpha-Lactosedetails
General function:
Not Available
Specific function:
Not Available
Gene Name:
GNE
Uniprot ID:
F1MIL9
Molecular weight:
79390.0
Reactions
Uridine diphosphate-N-acetylglucosamine + Water → N-Acetyl-D-mannosamine + Uridine 5'-diphosphatedetails
General function:
Not Available
Specific function:
Not Available
Gene Name:
CANT1
Uniprot ID:
E1BGL5
Molecular weight:
44706.0
Reactions
Uridine 5'-diphosphate + Water → Uridine 5'-monophosphate + Hydrogen phosphatedetails
Uridine triphosphate + Water → Uridine 5'-diphosphate + Hydrogen phosphatedetails
General function:
Not Available
Specific function:
Not Available
Gene Name:
CMPK2
Uniprot ID:
F1N2W6
Molecular weight:
64396.0
Reactions
Uridine 5'-monophosphate + Adenosine triphosphate → Uridine 5'-diphosphate + ADPdetails
General function:
Not Available
Specific function:
Not Available
Gene Name:
RRM2
Uniprot ID:
E1BI58
Molecular weight:
44821.0
Reactions
Uridine 5'-diphosphate + Thioredoxin disulfide + Water → dUDP + Thioredoxindetails