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Identification
NameUridine-5'-Diphosphate
Accession NumberDB03435  (EXPT03172)
TypeSmall Molecule
GroupsExperimental
Description

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

Structure
Thumb
SynonymsNot Available
Prescription ProductsNot Available
Generic Prescription ProductsNot Available
Over the Counter ProductsNot Available
International BrandsNot Available
Brand mixturesNot Available
SaltsNot Available
CategoriesNot Available
CAS number58-98-0
WeightAverage: 404.1612
Monoisotopic: 404.002196946
Chemical FormulaC9H14N2O12P2
InChI KeyXCCTYIAWTASOJW-ZAKLUEHWSA-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+/m0/s1
IUPAC Name
[({[(2S,3R,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[C@@H]1[C@@H](O)[C@@H](O[C@H]1CO[P@](O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O
Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribobucleotides 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
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Monosaccharide
  • Hydropyrimidine
  • Saccharide
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Urea
  • Secondary alcohol
  • Lactam
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Pharmacology
IndicationNot Available
PharmacodynamicsNot Available
Mechanism of actionNot Available
AbsorptionNot Available
Volume of distributionNot Available
Protein bindingNot Available
MetabolismNot Available
Route of eliminationNot Available
Half lifeNot Available
ClearanceNot Available
ToxicityNot Available
Affected organismsNot Available
Pathways
PathwayCategorySMPDB ID
Morphine Metabolism PathwayDrug metabolismSMP00622
Ibuprofen Metabolism PathwayDrug metabolismSMP00590
Sorafenib Metabolism PathwayDrug metabolismSMP00648
Nevirapine Metabolism PathwayDrug metabolismSMP00642
Celecoxib Metabolism PathwayDrug metabolismSMP00644
Irinotecan Metabolism PathwayDrug metabolismSMP00600
Artemether Metabolism PathwayDrug metabolismSMP00651
Tamoxifen Action PathwayDrug actionSMP00471
Irinotecan Action PathwayDrug actionSMP00433
Tamoxifen Metabolism PathwayDrug metabolismSMP00606
Nicotine Metabolism PathwayDrug metabolismSMP00628
Acetaminophen Metabolism PathwayDrug metabolismSMP00640
Codeine Metabolism PathwayDrug metabolismSMP00621
Tramadol Metabolism PathwayDrug metabolismSMP00637
Lamivudine Metabolism PathwayDrug metabolismSMP00649
Morphine Action PathwayDrug actionSMP00406
Krabbe diseaseDiseaseSMP00526
Sucrase-isomaltase deficiencyDiseaseSMP00557
Etoposide Metabolism PathwayDrug metabolismSMP00601
Valproic Acid Metabolism PathwayDrug metabolismSMP00635
Mycophenolic Acid Metabolism PathwayDrug metabolismSMP00652
Glycogen synthetase deficiencyDiseaseSMP00552
Glycogenosis, Type IV. Amylopectinosis, Anderson diseaseDiseaseSMP00554
Sphingolipid MetabolismMetabolicSMP00034
Starch and Sucrose MetabolismMetabolicSMP00058
Gaucher DiseaseDiseaseSMP00349
Globoid Cell LeukodystrophyDiseaseSMP00348
Etoposide Action PathwayDrug actionSMP00442
Glycogenosis, Type III. Cori disease, Debrancher glycogenosisDiseaseSMP00553
Glycogenosis, Type VI. Hers diseaseDiseaseSMP00555
Metachromatic Leukodystrophy (MLD)DiseaseSMP00347
Phenytoin (Antiarrhythmic) Action PathwayDrug actionSMP00327
Fabry diseaseDiseaseSMP00525
Mucopolysaccharidosis VI. Sly syndromeDiseaseSMP00556
Androgen and Estrogen MetabolismMetabolicSMP00068
Porphyrin MetabolismMetabolicSMP00024
Hereditary Coproporphyria (HCP)DiseaseSMP00342
GalactosemiaDiseaseSMP00182
G(M2)-Gangliosidosis: Variant B, Tay-sachs diseaseDiseaseSMP00534
Aromatase deficiencyDiseaseSMP00565
Amino Sugar MetabolismMetabolicSMP00045
Sialuria or French Type SialuriaDiseaseSMP00216
Galactose MetabolismMetabolicSMP00043
17-Beta Hydroxysteroid Dehydrogenase III DeficiencyDiseaseSMP00356
Salla Disease/Infantile Sialic Acid Storage DiseaseDiseaseSMP00240
Ibuprofen Action PathwayDrug actionSMP00086
Acute Intermittent PorphyriaDiseaseSMP00344
Porphyria Variegata (PV)DiseaseSMP00346
Codeine Action PathwayDrug actionSMP00405
Nicotine Action PathwayDrug actionSMP00431
Congenital disorder of glycosylation CDG-IIdDiseaseSMP00579
Lactose SynthesisMetabolicSMP00444
Celecoxib Action PathwayDrug actionSMP00096
Congenital Erythropoietic Porphyria (CEP) or Gunther DiseaseDiseaseSMP00345
Tay-Sachs DiseaseDiseaseSMP00390
Sialuria or French Type SialuriaDiseaseSMP00217
GLUT-1 deficiency syndromeDiseaseSMP00580
Pyrimidine MetabolismMetabolicSMP00046
Dihydropyrimidinase DeficiencyDiseaseSMP00178
Beta Ureidopropionase DeficiencyDiseaseSMP00172
UMP Synthase Deiciency (Orotic Aciduria)DiseaseSMP00219
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)DiseaseSMP00202
SNP Mediated EffectsNot Available
SNP Mediated Adverse Drug ReactionsNot Available
ADMET
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 substrateNon-inhibitor0.9131
CYP450 2D6 substrateNon-inhibitor0.9021
CYP450 2C19 substrateNon-inhibitor0.8878
CYP450 3A4 substrateNon-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
Pharmacoeconomics
ManufacturersNot Available
PackagersNot Available
Dosage formsNot Available
PricesNot Available
PatentsNot Available
Properties
StateSolid
Experimental PropertiesNot 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
Polarizability30.95 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Mass Spec (NIST)Not Available
SpectraNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
External Links
ATC CodesNot Available
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSNot Available
Interactions
Drug InteractionsNot Available
Food InteractionsNot Available

Targets

1. UDP-N-acetylglucosamine 2-epimerase

Kind: protein

Organism: Escherichia coli (strain K12)

Pharmacological action: unknown

Components

Name UniProt ID Details
UDP-N-acetylglucosamine 2-epimerase P27828 Details

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
  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

2. Histo-blood group ABO system transferase

Kind: protein

Organism: Human

Pharmacological action: unknown

Components

Name UniProt ID Details
Histo-blood group ABO system transferase P16442 Details

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
  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

3. Galactose-1-phosphate uridylyltransferase

Kind: protein

Organism: Escherichia coli (strain K12)

Pharmacological action: unknown

Components

Name UniProt ID Details
Galactose-1-phosphate uridylyltransferase P09148 Details

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
  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

4. Pol polyprotein

Kind: protein

Organism: FIV

Pharmacological action: unknown

Components

Name UniProt ID Details
Pol polyprotein P16088 Details

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
  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

5. Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1

Kind: protein

Organism: Human

Pharmacological action: unknown

Components

Name UniProt ID Details
Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 Q9P2W7 Details

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
  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

6. Alpha,alpha-trehalose-phosphate synthase [UDP-forming]

Kind: protein

Organism: Escherichia coli (strain K12)

Pharmacological action: unknown

Components

Name UniProt ID Details
Alpha,alpha-trehalose-phosphate synthase [UDP-forming] P31677 Details

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
  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

7. Exostosin-like 2

Kind: protein

Organism: Human

Pharmacological action: unknown

Components

Name UniProt ID Details
Exostosin-like 2 Q9UBQ6 Details

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
  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
  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

8. Glycosyltransferase 6 domain-containing protein 1

Kind: protein

Organism: Human

Pharmacological action: unknown

Components

Name UniProt ID Details
Glycosyltransferase 6 domain-containing protein 1 Q7Z4J2 Details

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
  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
  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

9. Spore coat polysaccharide biosynthesis protein SpsA

Kind: protein

Organism: Bacillus subtilis (strain 168)

Pharmacological action: unknown

Components

Name UniProt ID Details
Spore coat polysaccharide biosynthesis protein SpsA P39621 Details

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
  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

10. UMP-CMP kinase

Kind: protein

Organism: Human

Pharmacological action: unknown

Components

Name UniProt ID Details
UMP-CMP kinase P30085 Details

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
  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
  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

11. DNA beta-glucosyltransferase

Kind: protein

Organism: Enterobacteria phage T4

Pharmacological action: unknown

Components

Name UniProt ID Details
DNA beta-glucosyltransferase P04547 Details

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
  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

12. UDP-glucose 4-epimerase

Kind: protein

Organism: Escherichia coli (strain K12)

Pharmacological action: unknown

Components

Name UniProt ID Details
UDP-glucose 4-epimerase P09147 Details

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
  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

13. Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3

Kind: protein

Organism: Human

Pharmacological action: unknown

Components

Name UniProt ID Details
Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3 O94766 Details

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
  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

14. UDP-galactose 4-epimerase

Kind: protein

Organism: Trypanosoma brucei

Pharmacological action: unknown

Components

Name UniProt ID Details
UDP-galactose 4-epimerase Q8T8E9 Details

15. Glycogenin-1

Kind: protein

Organism: Human

Pharmacological action: unknown

Components

Name UniProt ID Details
Glycogenin-1 P46976 Details

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

Comments
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Drug created on June 13, 2005 07:24 / Updated on September 16, 2013 17:21