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Showing metabocard for Uridine 5'-diphosphate (BMDB0000295)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (12) Show 12 proteinsXML
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
MOLSDFPDBSMILESInChI
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
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
Chemical FormulaC9H14N2O12P2
Average Molecular Weight404.1612
Monoisotopic Molecular Weight404.002196946
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry Number58-98-0
SMILESNot Available
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 PropertiesNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
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 IDUDP
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

Enzyme Details
1. Nucleoside diphosphate kinase 7
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
Enzyme Details
2. Nucleoside diphosphate kinase B
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
Enzyme Details
3. GTP:AMP phosphotransferase AK3, mitochondrial
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
Enzyme Details
4. Beta-1,4-galactosyltransferase 1
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
Enzyme Details
5. UDP-glucuronosyltransferase 3A1
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
Enzyme Details
6. Glycogen [starch] synthase, muscle
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
Enzyme Details
7. UMP-CMP kinase
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
Enzyme Details
8. Alpha-lactalbumin
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
Enzyme Details
9. Glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase
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
Enzyme Details
10. Calcium activated nucleotidase 1
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
Enzyme Details
11. Cytidine/uridine monophosphate kinase 2
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
Enzyme Details
12. Ribonucleotide reductase regulatory subunit M2
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