2'-deoxyuridylic acid

Identification

Name
2'-deoxyuridylic acid
Accession Number
DB03800  (EXPT03187)
Type
Small Molecule
Groups
Experimental
Description
Not Available
Structure
Thumb
Synonyms
  • dUMP
Categories
UNII
Not Available
CAS number
Not Available
Weight
Average: 308.1819
Monoisotopic: 308.040951914
Chemical Formula
C9H13N2O8P
InChI Key
JSRLJPSBLDHEIO-SHYZEUOFSA-N
InChI
InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
IUPAC Name
{[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid
SMILES
O[C@H]1C[C@@H](O[C@@H]1COP(O)(O)=O)N1C=CC(=O)NC1=O

Pharmacology

Indication
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UThymidylate synthaseNot AvailablePneumocystis carinii
UDeoxyuridine 5'-triphosphate nucleotidohydrolaseNot AvailableEscherichia coli (strain K12)
UThymidylate synthaseNot AvailableLactobacillus casei
UThymidylate synthaseNot AvailableEscherichia coli (strain K12)
UThymidylate synthaseNot AvailableHuman
UThymidylate synthase ThyXNot AvailableThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
UPol polyproteinNot AvailableFIV
UDeoxyuridine 5'-triphosphate nucleotidohydrolaseNot AvailableMycobacterium tuberculosis
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
Dihydropyrimidinase DeficiencyDisease
beta-Ureidopropionase DeficiencyDisease
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)Disease
One Carbon Pool by Folate I Metabolic
Pyrimidine Deoxyribonucleosides SalvageMetabolic
Pyrimidine MetabolismMetabolic
Pyrimidine MetabolismMetabolic
Pyrimidine MetabolismMetabolic
One Carbon Pool by Folate IMetabolic
UMP Synthase Deficiency (Orotic Aciduria)Disease
Salvage Pathways of Pyrimidine DeoxyribonucleotidesMetabolic
Pyrimidine Metabolism Metabolic
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

General References
Not Available
External Links
Human Metabolome Database
HMDB0001409
KEGG Compound
C00365
PubChem Compound
65063
PubChem Substance
46506977
ChemSpider
58574
BindingDB
50028108
ChEBI
17622
ChEMBL
CHEMBL211312
HET
UMP
PDB Entries
1aiq / 1axw / 1bid / 1bp0 / 1bp6 / 1bpj / 1bq1 / 1ci7 / 1dna / 1f28
show 170 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 Solubility7.97 mg/mLALOGPS
logP-1.4ALOGPS
logP-1.6ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area145.63 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity61.93 m3·mol-1ChemAxon
Polarizability25.86 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption-0.736
Blood Brain Barrier+0.8502
Caco-2 permeable-0.7964
P-glycoprotein substrateNon-substrate0.6961
P-glycoprotein inhibitor INon-inhibitor0.7951
P-glycoprotein inhibitor IINon-inhibitor0.9467
Renal organic cation transporterNon-inhibitor0.903
CYP450 2C9 substrateNon-substrate0.715
CYP450 2D6 substrateNon-substrate0.8507
CYP450 3A4 substrateNon-substrate0.5
CYP450 1A2 substrateNon-inhibitor0.8951
CYP450 2C9 inhibitorNon-inhibitor0.8857
CYP450 2D6 inhibitorNon-inhibitor0.9161
CYP450 2C19 inhibitorNon-inhibitor0.8741
CYP450 3A4 inhibitorNon-inhibitor0.8089
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9289
Ames testNon AMES toxic0.5863
CarcinogenicityNon-carcinogens0.8247
BiodegradationNot ready biodegradable0.5481
Rat acute toxicity2.2793 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9497
hERG inhibition (predictor II)Non-inhibitor0.8131
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, N/ALC-MS/MSsplash10-001i-9100000000-c9b7092bb72f342d372f
MS/MS Spectrum - Quattro_QQQ 25V, N/ALC-MS/MSsplash10-001i-9000000000-d2272878a49bc62c1955
MS/MS Spectrum - Quattro_QQQ 40V, N/ALC-MS/MSsplash10-001i-9000000000-69451d809e5517ef09cb
LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , NegativeLC-MS/MSsplash10-01ta-9803000000-f0e26cbfb75f3fb7b36e
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/MSsplash10-01ta-9803000000-f0e26cbfb75f3fb7b36e
1H 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 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Pyrimidine nucleotides
Sub Class
Pyrimidine deoxyribonucleotides
Direct Parent
Pyrimidine 2'-deoxyribonucleoside monophosphates
Alternative Parents
Pyrimidones / Monoalkyl phosphates / Hydroxypyrimidines / Hydropyrimidines / Tetrahydrofurans / Heteroaromatic compounds / Secondary alcohols / Oxacyclic compounds / Azacyclic compounds / Organopnictogen compounds
show 3 more
Substituents
Pyrimidine 2'-deoxyribonucleoside monophosphate / Pyrimidone / Monoalkyl phosphate / Hydroxypyrimidine / Hydropyrimidine / Organic phosphoric acid derivative / Phosphoric acid ester / Pyrimidine / Alkyl phosphate / Tetrahydrofuran
show 14 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
pyrimidine 2'-deoxyribonucleoside 5'-monophosphate, deoxyuridine phosphate (CHEBI:17622) / Deoxyribonucleotides (C00365)

Targets

Kind
Protein
Organism
Pneumocystis carinii
Pharmacological action
Unknown
General Function
Thymidylate synthase activity
Specific Function
Not Available
Gene Name
THYA
Uniprot ID
P13100
Uniprot Name
Thymidylate synthase
Molecular Weight
34361.99 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
Magnesium ion binding
Specific Function
This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot b...
Gene Name
dut
Uniprot ID
P06968
Uniprot Name
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Molecular Weight
16155.34 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
Lactobacillus casei
Pharmacological action
Unknown
General Function
Thymidylate synthase activity
Specific Function
Provides the sole de novo source of dTMP for DNA biosynthesis.
Gene Name
thyA
Uniprot ID
P00469
Uniprot Name
Thymidylate synthase
Molecular Weight
36579.235 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
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Thymidylate synthase activity
Specific Function
Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.
Gene Name
thyA
Uniprot ID
P0A884
Uniprot Name
Thymidylate synthase
Molecular Weight
30479.475 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
Thymidylate synthase activity
Specific Function
Contributes to the de novo mitochondrial thymidylate biosynthesis pathway.
Gene Name
TYMS
Uniprot ID
P04818
Uniprot Name
Thymidylate synthase
Molecular Weight
35715.65 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
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Pharmacological action
Unknown
General Function
Thymidylate synthase (fad) activity
Specific Function
Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate.
Gene Name
thyX
Uniprot ID
Q9WYT0
Uniprot Name
Thymidylate synthase ThyX
Molecular Weight
26003.785 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
Mycobacterium tuberculosis
Pharmacological action
Unknown
General Function
This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.
Specific Function
Dutp diphosphatase activity
Gene Name
dut
Uniprot ID
P9WNS5
Uniprot Name
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Molecular Weight
15802.815 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]

Drug created on June 13, 2005 07:24 / Updated on October 01, 2018 13:40