2'-Deoxyuridine

Identification

Name
2'-Deoxyuridine
Accession Number
DB02256  (EXPT01300)
Type
Small Molecule
Groups
Experimental
Description

2'-Deoxyuridine. An antimetabolite that is converted to deoxyuridine triphosphate during DNA synthesis. Laboratory suppression of deoxyuridine is used to diagnose megaloblastic anemias due to vitamin B12 and folate deficiencies. [PubChem]

Structure
Thumb
Synonyms
Not Available
Categories
Not Available
UNII
W78I7AY22C
CAS number
951-78-0
Weight
Average: 228.202
Monoisotopic: 228.074621504
Chemical Formula
C9H12N2O5
InChI Key
MXHRCPNRJAMMIM-SHYZEUOFSA-N
InChI
InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1
IUPAC Name
1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
SMILES
OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O

Pharmacology

Indication
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UUridine phosphorylaseNot AvailableEscherichia coli (strain K12)
UThymidylate synthaseNot AvailableEscherichia coli (strain K12)
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
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

Synthesis Reference

Kenzo Watanabe, Yoshinori Kato, Masahiko Saito, Takeo Oba, Hisashi Fukushima, Takeshi Hara, "5-fluoro-2'-deoxyuridine derivatives and a process for the preparation thereof." U.S. Patent US4605645, issued May, 1984.

US4605645
General References
Not Available
External Links
Human Metabolome Database
HMDB0000012
KEGG Compound
C00526
PubChem Compound
13712
PubChem Substance
46506680
ChemSpider
13118
ChEBI
16450
ChEMBL
CHEMBL353955
HET
DUR
PDB Entries
1bdu / 1oe5 / 1rxs / 1tdu / 2c53 / 2i7d / 2yb0 / 3kuk / 4aoo / 4aoz
show 6 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
PropertyValueSource
melting point (°C)163 °CPhysProp
logP-1.51BALZARINI,JM ET AL. (1989)
Predicted Properties
PropertyValueSource
Water Solubility90.6 mg/mLALOGPS
logP-1.5ALOGPS
logP-1.5ChemAxon
logS-0.4ALOGPS
pKa (Strongest Acidic)9.71ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area99.1 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity51.05 m3·mol-1ChemAxon
Polarizability21.06 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption+0.9512
Blood Brain Barrier+0.7655
Caco-2 permeable-0.8937
P-glycoprotein substrateNon-substrate0.7208
P-glycoprotein inhibitor INon-inhibitor0.8877
P-glycoprotein inhibitor IINon-inhibitor0.8561
Renal organic cation transporterNon-inhibitor0.8954
CYP450 2C9 substrateNon-substrate0.7602
CYP450 2D6 substrateNon-substrate0.8792
CYP450 3A4 substrateNon-substrate0.5493
CYP450 1A2 substrateNon-inhibitor0.9479
CYP450 2C9 inhibitorNon-inhibitor0.9459
CYP450 2D6 inhibitorNon-inhibitor0.9491
CYP450 2C19 inhibitorNon-inhibitor0.9499
CYP450 3A4 inhibitorNon-inhibitor0.9249
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.949
Ames testNon AMES toxic0.8635
CarcinogenicityNon-carcinogens0.8101
BiodegradationReady biodegradable0.5723
Rat acute toxicity1.8101 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9411
hERG inhibition (predictor II)Non-inhibitor0.8765
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
GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)GC-MSsplash10-0udi-0900000000-c680f47a48626bc1de41
GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)GC-MSsplash10-0udi-0900000000-13135426d5efdf47090c
GC-MS Spectrum - GC-MS (3 TMS)GC-MSsplash10-0v4i-2910000000-b0c82cef369c86d585bc
GC-MS Spectrum - GC-MS (3 TMS)GC-MSsplash10-0udi-2900000000-c2cdba9e46defe05a225
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSNot Available
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-0udi-0900000000-c680f47a48626bc1de41
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-0udi-0900000000-13135426d5efdf47090c
GC-MS Spectrum - GC-MSGC-MSsplash10-0v4i-2910000000-b0c82cef369c86d585bc
GC-MS Spectrum - GC-MSGC-MSsplash10-0udi-2900000000-c2cdba9e46defe05a225
MS/MS Spectrum - Quattro_QQQ 10V, PositiveLC-MS/MSsplash10-03di-1900000000-6610506190427bbb3b6c
MS/MS Spectrum - Quattro_QQQ 25V, PositiveLC-MS/MSsplash10-03di-9800000000-af237f79161aa13a5893
MS/MS Spectrum - Quattro_QQQ 40V, PositiveLC-MS/MSsplash10-022d-9100000000-a06cdd7ea870d049c8a9
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
MS/MS Spectrum - Linear Ion Trap , negativeLC-MS/MSsplash10-001r-0900000000-87d0da98372c9c5a167a
MS/MS Spectrum - Linear Ion Trap , negativeLC-MS/MSsplash10-001r-0900000000-795c89de7cd09998501c
MS/MS Spectrum - Linear Ion Trap , negativeLC-MS/MSsplash10-03di-0910000000-0f40c1aaec53591fe03d
MS/MS Spectrum - Linear Ion Trap , negativeLC-MS/MSsplash10-03di-0900000000-35312c7170aff90afa68
MS/MS Spectrum - Linear Ion Trap , negativeLC-MS/MSsplash10-004i-0090000000-dd791cff5aab8928952f
MS/MS Spectrum - Linear Ion Trap , negativeLC-MS/MSsplash10-004i-0090000000-e5c282f6027560386d07
MS/MS Spectrum - , negativeLC-MS/MSsplash10-001l-5900000000-4660ec5181499087824f
MS/MS Spectrum - Linear Ion Trap , positiveLC-MS/MSsplash10-001i-0910000000-8cef8299b80deeefe1ae
MS/MS Spectrum - Linear Ion Trap , positiveLC-MS/MSsplash10-001i-0900000000-043d88b7ac473889f319
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'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Pyrimidine nucleosides
Sub Class
Pyrimidine 2'-deoxyribonucleosides
Direct Parent
Pyrimidine 2'-deoxyribonucleosides
Alternative Parents
Pyrimidones / Hydropyrimidines / Vinylogous amides / Tetrahydrofurans / Heteroaromatic compounds / Ureas / Secondary alcohols / Lactams / Oxacyclic compounds / Azacyclic compounds
show 5 more
Substituents
Pyrimidine 2'-deoxyribonucleoside / Pyrimidone / Hydropyrimidine / Pyrimidine / Heteroaromatic compound / Tetrahydrofuran / Vinylogous amide / Lactam / Secondary alcohol / Urea
show 13 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
pyrimidine 2'-deoxyribonucleoside (CHEBI:16450) / Deoxyribonucleosides (C00526)

Targets

Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Uridine phosphorylase activity
Specific Function
Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources ...
Gene Name
udp
Uniprot ID
P12758
Uniprot Name
Uridine phosphorylase
Molecular Weight
27158.88 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]

Drug created on June 13, 2005 07:24 / Updated on November 02, 2018 05:14