NAV

5-O-phosphono-alpha-D-ribofuranosyl diphosphate

Identification

Generic Name
5-O-phosphono-alpha-D-ribofuranosyl diphosphate
DrugBank Accession Number
DB01632
Background

The key substance in the biosynthesis of histidine, tryptophan, and purine and pyrimidine nucleotides.

Type
Small Molecule
Groups
Approved, Experimental, Investigational
Structure
3D
Similar Structures
Weight
Average: 390.0696
Monoisotopic: 389.95181466
Chemical Formula
C5H13O14P3
Synonyms
  • 5-O-phosphono-α-D-ribofuranosyl diphosphate
  • 5-Phospho-alpha-D-ribose 1-diphosphate
  • 5-Phosphoribosyl 1-pyrophosphate
  • 5-Phosphoribosyl diphosphate
  • Phosphoribosyl pyrophosphate
  • Phosphoribosylpyrophosphate
  • PRib-PP
  • PRPP
  • α-D-ribofuranose 5-(dihydrogen phosphate) 1-(trihydrogen diphosphate)
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Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UHypoxanthine-guanine phosphoribosyltransferaseNot AvailableHumans
UOrotate phosphoribosyltransferase
substrate
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
UUridine-cytidine kinase-like 1Not AvailableHumans
UHypoxanthine-guanine phosphoribosyltransferaseNot AvailableTrypanosoma cruzi
UAdenine phosphoribosyltransferaseNot AvailableHumans
UAnthranilate phosphoribosyltransferaseNot AvailableErwinia carotovora
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

Adverse Effects
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Toxicity

Not Available

Pathways
PathwayCategory
Adenylosuccinate Lyase DeficiencyDisease
Xanthine Dehydrogenase Deficiency (Xanthinuria)Disease
HomocarnosinosisDisease
Xanthinuria Type IDisease
Glucose-6-phosphate Dehydrogenase DeficiencyDisease
Mitochondrial DNA Depletion SyndromeDisease
Myoadenylate Deaminase DeficiencyDisease
Pentose Phosphate PathwayMetabolic
Pyrimidine MetabolismMetabolic
Purine MetabolismMetabolic
Glutamate MetabolismMetabolic
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)Disease
Purine Nucleoside Phosphorylase DeficiencyDisease
Hyperinsulinism-Hyperammonemia SyndromeDisease
Lesch-Nyhan Syndrome (LNS)Disease
Gout or Kelley-Seegmiller SyndromeDisease
Mercaptopurine Action PathwayDrug action
Ribose-5-phosphate Isomerase DeficiencyDisease
Adenine Phosphoribosyltransferase Deficiency (APRT)Disease
Nicotinate and Nicotinamide MetabolismMetabolic
2-Hydroxyglutric Aciduria (D and L Form)Disease
Adenosine Deaminase DeficiencyDisease
AICA-RibosiduriaDisease
beta-Ureidopropionase DeficiencyDisease
Dihydropyrimidinase DeficiencyDisease
Molybdenum Cofactor DeficiencyDisease
UMP Synthase Deficiency (Orotic Aciduria)Disease
4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase DeficiencyDisease
Azathioprine Action PathwayDrug action
Thioguanine Action PathwayDrug action
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
Not Available
Food Interactions
Not Available

Categories

Drug Categories
Chemical TaxonomyProvided by Classyfire
Description
This compound belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
Kingdom
Organic compounds
Super Class
Organic oxygen compounds
Class
Organooxygen compounds
Sub Class
Carbohydrates and carbohydrate conjugates
Direct Parent
Pentose phosphates
Alternative Parents
Organic pyrophosphates / Monosaccharide phosphates / Monoalkyl phosphates / Tetrahydrofurans / Secondary alcohols / 1,2-diols / Oxacyclic compounds / Organic oxides / Hydrocarbon derivatives
Substituents
1,2-diol / Alcohol / Aliphatic heteromonocyclic compound / Alkyl phosphate / Hydrocarbon derivative / Monoalkyl phosphate / Monosaccharide phosphate / Organic oxide / Organic phosphoric acid derivative / Organic pyrophosphate
Molecular Framework
Aliphatic heteromonocyclic compounds
External Descriptors
5-O-phosphono-D-ribofuranosyl diphosphate (CHEBI:17111)
Affected organisms
Not Available

Chemical Identifiers

UNII
W5555R4ERG
CAS number
13270-65-0
InChI Key
PQGCEDQWHSBAJP-TXICZTDVSA-N
InChI
InChI=1S/C5H13O14P3/c6-3-2(1-16-20(8,9)10)17-5(4(3)7)18-22(14,15)19-21(11,12)13/h2-7H,1H2,(H,14,15)(H2,8,9,10)(H2,11,12,13)/t2-,3-,4-,5-/m1/s1
IUPAC Name
[({[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid
SMILES
O[C@H]1[C@@H](O)[C@@H](OP(O)(=O)OP(O)(O)=O)O[C@@H]1COP(O)(O)=O

References

General References
Not Available
Human Metabolome Database
HMDB0000280
KEGG Compound
C00119
PubChem Compound
7339
PubChem Substance
46506467
ChemSpider
7062
BindingDB
25315
ChEBI
17111
ZINC
ZINC000008215630
PDBe Ligand
PRP
PDB Entries
1d6n / 1fsg / 1i0i / 1i0l / 1i13 / 1i14 / 1jls / 1kgz / 1l1r / 1lh0 …
show 76 more

Clinical Trials

Clinical Trials
PhaseStatusPurposeConditionsCount

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 Solubility11.6 mg/mLALOGPS
logP-0.74ALOGPS
logP-3Chemaxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.09Chemaxon
pKa (Strongest Basic)-3.7Chemaxon
Physiological Charge-4Chemaxon
Hydrogen Acceptor Count11Chemaxon
Hydrogen Donor Count7Chemaxon
Polar Surface Area229.74 Å2Chemaxon
Rotatable Bond Count7Chemaxon
Refractivity62.58 m3·mol-1Chemaxon
Polarizability27.46 Å3Chemaxon
Number of Rings1Chemaxon
Bioavailability0Chemaxon
Rule of FiveNoChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.9864
Blood Brain Barrier+0.924
Caco-2 permeable-0.7323
P-glycoprotein substrateNon-substrate0.7206
P-glycoprotein inhibitor INon-inhibitor0.8258
P-glycoprotein inhibitor IINon-inhibitor0.9919
Renal organic cation transporterNon-inhibitor0.9101
CYP450 2C9 substrateNon-substrate0.8024
CYP450 2D6 substrateNon-substrate0.8346
CYP450 3A4 substrateNon-substrate0.5843
CYP450 1A2 substrateNon-inhibitor0.8892
CYP450 2C9 inhibitorNon-inhibitor0.886
CYP450 2D6 inhibitorNon-inhibitor0.9188
CYP450 2C19 inhibitorNon-inhibitor0.8792
CYP450 3A4 inhibitorNon-inhibitor0.9727
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9715
Ames testNon AMES toxic0.7781
CarcinogenicityNon-carcinogens0.9024
BiodegradationReady biodegradable0.7128
Rat acute toxicity2.0708 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.923
hERG inhibition (predictor II)Non-inhibitor0.8905
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-MSsplash10-004j-7902000000-513a0a03122b76d768d9
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-0006-0029000000-acd587de4ec071909c4f
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-004r-9007000000-d98fc8dad7e62a26c411
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-03fs-2493000000-bf4735857ab52f1a8885
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-0a6r-6900000000-751a79834591a3f0440f
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-0a6r-5900000000-b07eceaeae43ea43db71
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-03ea-3940000000-d455c8eb3572918ce6c6
Predicted 1H NMR Spectrum1D NMRNot Applicable
Predicted 13C NMR Spectrum1D NMRNot Applicable
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-189.6469556
predicted
DarkChem Lite v0.1.0
[M-H]-187.0930556
predicted
DarkChem Lite v0.1.0
[M-H]-159.03252
predicted
DeepCCS 1.0 (2019)
[M+H]+189.8896556
predicted
DarkChem Lite v0.1.0
[M+H]+188.5281556
predicted
DarkChem Lite v0.1.0
[M+H]+161.42815
predicted
DeepCCS 1.0 (2019)
[M+Na]+189.2115556
predicted
DarkChem Lite v0.1.0
[M+Na]+187.6882556
predicted
DarkChem Lite v0.1.0
[M+Na]+167.56247
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. Hypoxanthine-guanine phosphoribosyltransferase
Kind
Protein
Organism
Humans
Pharmacological action
Unknown
General Function
Protein homodimerization activity
Specific Function
Converts guanine to guanosine monophosphate, and hypoxanthine to inosine monophosphate. Transfers the 5-phosphoribosyl group from 5-phosphoribosylpyrophosphate onto the purine. Plays a central role...
Gene Name
HPRT1
Uniprot ID
P00492
Uniprot Name
Hypoxanthine-guanine phosphoribosyltransferase
Molecular Weight
24579.155 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. [Article]
  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. [Article]
  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. [Article]
Details2. Orotate phosphoribosyltransferase
Kind
Protein
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Pharmacological action
Unknown
Actions
Substrate
General Function
Orotate phosphoribosyltransferase activity
Specific Function
Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP).
Gene Name
pyrE
Uniprot ID
P08870
Uniprot Name
Orotate phosphoribosyltransferase
Molecular Weight
23561.74 Da
References
  1. Breda A, Rosado LA, Lorenzini DM, Basso LA, Santos DS: Molecular, kinetic and thermodynamic characterization of Mycobacterium tuberculosis orotate phosphoribosyltransferase. Mol Biosyst. 2012 Feb;8(2):572-86. doi: 10.1039/c1mb05402c. Epub 2011 Nov 11. [Article]
  2. Breda A, Machado P, Rosado LA, Souto AA, Santos DS, Basso LA: Pyrimidin-2(1H)-ones based inhibitors of Mycobacterium tuberculosis orotate phosphoribosyltransferase. Eur J Med Chem. 2012 Aug;54:113-22. doi: 10.1016/j.ejmech.2012.04.031. Epub 2012 Apr 30. [Article]
  3. McClard RW, Holets EA, MacKinnon AL, Witte JF: Half-of-sites binding of orotidine 5'-phosphate and alpha-D-5-phosphorylribose 1-diphosphate to orotate phosphoribosyltransferase from Saccharomyces cerevisiae supports a novel variant of the Theorell-Chance mechanism with alternating site catalysis. Biochemistry. 2006 Apr 25;45(16):5330-42. doi: 10.1021/bi051650o. [Article]
Details3. Uridine-cytidine kinase-like 1
Kind
Protein
Organism
Humans
Pharmacological action
Unknown
General Function
Uridine kinase activity
Specific Function
May contribute to UTP accumulation needed for blast transformation and proliferation.
Gene Name
UCKL1
Uniprot ID
Q9NWZ5
Uniprot Name
Uridine-cytidine kinase-like 1
Molecular Weight
61140.395 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. [Article]
  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. [Article]
  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. [Article]
Details4. Hypoxanthine-guanine phosphoribosyltransferase
Kind
Protein
Organism
Trypanosoma cruzi
Pharmacological action
Unknown
General Function
Hypoxanthine phosphoribosyltransferase activity
Specific Function
Not Available
Gene Name
HGPRTase
Uniprot ID
Q27796
Uniprot Name
Hypoxanthine-guanine phosphoribosyltransferase
Molecular Weight
25529.02 Da
Details5. Adenine phosphoribosyltransferase
Kind
Protein
Organism
Humans
Pharmacological action
Unknown
General Function
Amp binding
Specific Function
Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.
Gene Name
APRT
Uniprot ID
P07741
Uniprot Name
Adenine phosphoribosyltransferase
Molecular Weight
19607.535 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. [Article]
Details6. Anthranilate phosphoribosyltransferase
Kind
Protein
Organism
Erwinia carotovora
Pharmacological action
Unknown
General Function
Magnesium ion binding
Specific Function
Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA).
Gene Name
trpD
Uniprot ID
Q8VP84
Uniprot Name
Anthranilate phosphoribosyltransferase
Molecular Weight
37017.84 Da

Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:51