Uridine-5'-Diphosphate

Identification

Name
Uridine-5'-Diphosphate
Accession Number
DB03435  (EXPT03172)
Type
Small Molecule
Groups
Experimental
Description

A uracil nucleotide containing a pyrophosphate group esterified to C5 of the sugar moiety. [PubChem]

Structure
Thumb
Synonyms
Not Available
Categories
Not Available
UNII
5G0F599A1Y
CAS number
58-98-0
Weight
Average: 404.1612
Monoisotopic: 404.002196946
Chemical Formula
C9H14N2O12P2
InChI Key
XCCTYIAWTASOJW-XVFCMESISA-N
InChI
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
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
SMILES
O[[email protected]]1[[email protected]@H](O)[[email protected]@H](O[[email protected]@H]1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O

Pharmacology

Indication
Not Available
Structured Indications
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UUDP-N-acetylglucosamine 2-epimeraseNot AvailableEscherichia coli (strain K12)
UHisto-blood group ABO system transferaseNot AvailableHuman
UGalactose-1-phosphate uridylyltransferaseNot AvailableEscherichia coli (strain K12)
UPol polyproteinNot AvailableFIV
UGalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1Not AvailableHuman
UAlpha,alpha-trehalose-phosphate synthase [UDP-forming]Not AvailableEscherichia coli (strain K12)
UExostosin-like 2Not AvailableHuman
UGlycosyltransferase 6 domain-containing protein 1Not AvailableHuman
USpore coat polysaccharide biosynthesis protein SpsANot AvailableBacillus subtilis (strain 168)
UUMP-CMP kinaseNot AvailableHuman
UDNA beta-glucosyltransferaseNot AvailableEnterobacteria phage T4
UUDP-glucose 4-epimeraseNot AvailableEscherichia coli (strain K12)
UGalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3Not AvailableHuman
UUDP-galactose 4-epimeraseNot AvailableTrypanosoma brucei
UGlycogenin-1Not AvailableHuman
Absorption
Not Available
Volume of distribution
Not Available
Protein binding
Not Available
Metabolism
Not Available
Route of elimination
Not Available
Half life
Not Available
Clearance
Not Available
Toxicity
Not Available
Affected organisms
Not Available
Pathways
PathwayCategory
GalactosemiaDisease
Sialuria or French Type SialuriaDisease
Congenital Erythropoietic Porphyria (CEP) or Gunther DiseaseDisease
Porphyria Variegata (PV)Disease
Gaucher DiseaseDisease
17-Beta Hydroxysteroid Dehydrogenase III DeficiencyDisease
Sucrase-isomaltase deficiencyDisease
Celecoxib Metabolism PathwayDrug metabolism
Mycophenolic Acid Metabolism PathwayDrug metabolism
Androstenedione MetabolismMetabolic
Porphyrin MetabolismMetabolic
Ibuprofen Action PathwayDrug action
Acute Intermittent PorphyriaDisease
Nicotine Action PathwayDrug action
Fabry diseaseDisease
Glycogenosis, Type VI. Hers diseaseDisease
GLUT-1 deficiency syndromeDisease
Irinotecan Metabolism PathwayDrug metabolism
Etoposide Metabolism PathwayDrug metabolism
Tramadol Metabolism PathwayDrug metabolism
Estrone MetabolismMetabolic
Sphingolipid MetabolismMetabolic
Amino Sugar MetabolismMetabolic
Starch and Sucrose MetabolismMetabolic
Beta Ureidopropionase DeficiencyDisease
Dihydropyrimidinase DeficiencyDisease
UMP Synthase Deficiency (Orotic Aciduria)Disease
Tay-Sachs DiseaseDisease
Lactose SynthesisMetabolic
Glycogenosis, Type IV. Amylopectinosis, Anderson diseaseDisease
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

General References
Not Available
External Links
Human Metabolome Database
HMDB00295
KEGG Compound
C00015
PubChem Compound
6031
PubChem Substance
46505736
ChemSpider
5809
BindingDB
50403871
ChEBI
17659
ChEMBL
CHEMBL130266
HET
UDP
PDB Entries
1bgu / 1c3j / 1f6d / 1f7p / 1f7r / 1fgg / 1gwv / 1gww / 1gx0 / 1gx4
show 358 more

Clinical Trials

Clinical Trials
Not Available

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
Not Available
Predicted Properties
PropertyValueSource
Water Solubility8.89 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity74.31 m3·mol-1ChemAxon
Polarizability30.41 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption-0.9556
Blood Brain Barrier+0.7546
Caco-2 permeable-0.8073
P-glycoprotein substrateNon-substrate0.7589
P-glycoprotein inhibitor INon-inhibitor0.8744
P-glycoprotein inhibitor IINon-inhibitor0.9663
Renal organic cation transporterNon-inhibitor0.9495
CYP450 2C9 substrateNon-substrate0.6515
CYP450 2D6 substrateNon-substrate0.853
CYP450 3A4 substrateNon-substrate0.5684
CYP450 1A2 substrateNon-inhibitor0.8879
CYP450 2C9 inhibitorNon-inhibitor0.9131
CYP450 2D6 inhibitorNon-inhibitor0.9021
CYP450 2C19 inhibitorNon-inhibitor0.8878
CYP450 3A4 inhibitorNon-inhibitor0.9193
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9549
Ames testNon AMES toxic0.897
CarcinogenicityNon-carcinogens0.9069
BiodegradationReady biodegradable0.5964
Rat acute toxicity2.1803 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9708
hERG inhibition (predictor II)Non-inhibitor0.7504
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSNot Available
MS/MS Spectrum - Quattro_QQQ 10V, PositiveLC-MS/MSsplash10-0002-9000000000-7c065a8df0e08b8c365f
MS/MS Spectrum - Quattro_QQQ 25V, PositiveLC-MS/MSsplash10-0002-9000000000-73234233232c376d095c
MS/MS Spectrum - Quattro_QQQ 40V, PositiveLC-MS/MSsplash10-0002-9000000000-7c065a8df0e08b8c365f
LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , NegativeLC-MS/MSsplash10-0pdi-6910600000-bf4136774851b6559f17
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSNot Available
LC-MS/MS Spectrum - LC-ESI-QTOF , negativeLC-MS/MSsplash10-0pdi-6910600000-bf4136774851b6559f17
1H NMR Spectrum1D NMRNot Applicable
1H NMR Spectrum1D NMRNot Applicable
13C NMR Spectrum1D NMRNot Applicable
[1H,13C] 2D NMR Spectrum2D NMRNot Applicable

Taxonomy

Description
This 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.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Pyrimidine nucleotides
Sub Class
Pyrimidine ribonucleotides
Direct Parent
Pyrimidine ribonucleoside diphosphates
Alternative Parents
Pentose phosphates / Glycosylamines / Organic pyrophosphates / Monosaccharide phosphates / Pyrimidones / Monoalkyl phosphates / Hydroxypyrimidines / Hydropyrimidines / Tetrahydrofurans / Heteroaromatic compounds
show 8 more
Substituents
Pyrimidine ribonucleoside diphosphate / Pentose phosphate / Pentose-5-phosphate / Glycosyl compound / N-glycosyl compound / Monosaccharide phosphate / Organic pyrophosphate / Hydroxypyrimidine / Pyrimidone / Monoalkyl phosphate
show 22 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
pyrimidine ribonucleoside 5'-diphosphate, uridine 5'-phosphate (CHEBI:17659) / Ribonucleotides (C00015)

Targets

Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Udp-n-acetylglucosamine 2-epimerase activity
Specific Function
Catalyzes the reversible epimerization at C-2 of UDP-N-acetylglucosamine (UDP-GlcNAc) and thereby provides bacteria with UDP-N-acetylmannosamine (UDP-ManNAc), the activated donor of ManNAc residues...
Gene Name
wecB
Uniprot ID
P27828
Uniprot Name
UDP-N-acetylglucosamine 2-epimerase
Molecular Weight
42244.235 Da
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]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Metal ion binding
Specific Function
This protein is the basis of the ABO blood group system. The histo-blood group ABO involves three carbohydrate antigens: A, B, and H. A, B, and AB individuals express a glycosyltransferase activity...
Gene Name
ABO
Uniprot ID
P16442
Uniprot Name
Histo-blood group ABO system transferase
Molecular Weight
40933.555 Da
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]
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Zinc ion binding
Specific Function
Not Available
Gene Name
galT
Uniprot ID
P09148
Uniprot Name
Galactose-1-phosphate uridylyltransferase
Molecular Weight
39645.395 Da
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]
Kind
Protein
Organism
FIV
Pharmacological action
Unknown
General Function
Zinc ion binding
Specific Function
During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse tra...
Gene Name
pol
Uniprot ID
P16088
Uniprot Name
Pol polyprotein
Molecular Weight
127493.025 Da
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]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Udp-galactose:beta-n-acetylglucosamine beta-1,3-galactosyltransferase activity
Specific Function
Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on glycoproteins. Can also play a role in glycosaminoglycan biosynthesis. Substrates include asialo-orosomucoid (ASOR), asialo-fetuin, ...
Gene Name
B3GAT1
Uniprot ID
Q9P2W7
Uniprot Name
Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1
Molecular Weight
38255.675 Da
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]
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Alpha,alpha-trehalose-phosphate synthase (udp-forming) activity
Specific Function
Catalyzes the transfer of glucose from UDP-glucose to glucose-6-phosphate to form alpha,alpha-1,1 trehalose-6-phosphate. Acts with retention of the anomeric configuration of the UDP-sugar donor. Es...
Gene Name
otsA
Uniprot ID
P31677
Uniprot Name
Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
Molecular Weight
53610.655 Da
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]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Metal ion binding
Specific Function
Glycosyltransferase required for the biosynthesis of heparan-sulfate and responsible for the alternating addition of beta-1-4-linked glucuronic acid (GlcA) and alpha-1-4-linked N-acetylglucosamine ...
Gene Name
EXTL2
Uniprot ID
Q9UBQ6
Uniprot Name
Exostosin-like 2
Molecular Weight
37465.365 Da
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]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Transferase activity, transferring hexosyl groups
Specific Function
Not Available
Gene Name
GLT6D1
Uniprot ID
Q7Z4J2
Uniprot Name
Glycosyltransferase 6 domain-containing protein 1
Molecular Weight
36273.575 Da
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]
Kind
Protein
Organism
Bacillus subtilis (strain 168)
Pharmacological action
Unknown
General Function
Transferase activity, transferring glycosyl groups
Specific Function
Glycosyltransferase implicated in the synthesis of the spore coat.
Gene Name
spsA
Uniprot ID
P39621
Uniprot Name
Spore coat polysaccharide biosynthesis protein SpsA
Molecular Weight
30183.855 Da
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]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Uridylate kinase activity
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...
Gene Name
CMPK1
Uniprot ID
P30085
Uniprot Name
UMP-CMP kinase
Molecular Weight
22222.175 Da
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]
Kind
Protein
Organism
Enterobacteria phage T4
Pharmacological action
Unknown
General Function
Dna beta-glucosyltransferase activity
Specific Function
Catalyzes the transfer of glucose (Glc) from uridine diphosphoglucose (UDP-Glc) to 5-hydroxymethylcytosine (5-HMC) in double-stranded DNA. Is involved in a DNA modification process to protect the p...
Gene Name
bgt
Uniprot ID
P04547
Uniprot Name
DNA beta-glucosyltransferase
Molecular Weight
40665.6 Da
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]
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Udp-glucose 4-epimerase activity
Specific Function
Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD. It is only active...
Gene Name
galE
Uniprot ID
P09147
Uniprot Name
UDP-glucose 4-epimerase
Molecular Weight
37264.875 Da
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]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Protein phosphatase activator activity
Specific Function
Glycosaminoglycans biosynthesis. Involved in forming the linkage tetrasaccharide present in heparan sulfate and chondroitin sulfate. Transfers a glucuronic acid moiety from the uridine diphosphate-...
Gene Name
B3GAT3
Uniprot ID
O94766
Uniprot Name
Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3
Molecular Weight
37121.52 Da
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]
Kind
Protein
Organism
Trypanosoma brucei
Pharmacological action
Unknown
General Function
Udp-glucose 4-epimerase activity
Specific Function
Not Available
Gene Name
galE
Uniprot ID
Q8T8E9
Uniprot Name
UDP-galactose 4-epimerase
Molecular Weight
43519.96 Da
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Metal ion binding
Specific Function
Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.
Gene Name
GYG1
Uniprot ID
P46976
Uniprot Name
Glycogenin-1
Molecular Weight
39383.425 Da
References
  1. 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]

Drug created on June 13, 2005 07:24 / Updated on November 09, 2017 03:28