Thymidine-5'- Diphosphate

Identification

Name
Thymidine-5'- Diphosphate
Accession Number
DB03103  (EXPT03136)
Type
Small Molecule
Groups
Experimental
Description
Not Available
Structure
Thumb
Synonyms
Not Available
Categories
Not Available
UNII
Not Available
CAS number
Not Available
Weight
Average: 402.1884
Monoisotopic: 402.022932388
Chemical Formula
C10H16N2O11P2
InChI Key
UJLXYODCHAELLY-XLPZGREQSA-N
InChI
InChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
IUPAC Name
{[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy}phosphonic acid
SMILES
CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)NC1=O

Pharmacology

Indication
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UNucleoside diphosphate kinase ANot 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
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

General References
Not Available
External Links
Human Metabolome Database
HMDB0001274
KEGG Compound
C00363
PubChem Compound
164628
PubChem Substance
46505634
ChemSpider
144320
ChEBI
18075
ChEMBL
CHEMBL259724
HET
TYD
PDB Entries
1cr4 / 1e2g / 1epz / 1gtv / 1h5t / 1h7l / 1h7q / 1ket / 1kew / 1lvw
show 67 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 Solubility6.94 mg/mLALOGPS
logP-0.87ALOGPS
logP-1.7ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area192.16 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity77.16 m3·mol-1ChemAxon
Polarizability32.13 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption-0.7735
Blood Brain Barrier+0.6582
Caco-2 permeable-0.7847
P-glycoprotein substrateNon-substrate0.6088
P-glycoprotein inhibitor INon-inhibitor0.7734
P-glycoprotein inhibitor IINon-inhibitor0.9613
Renal organic cation transporterNon-inhibitor0.9216
CYP450 2C9 substrateNon-substrate0.6086
CYP450 2D6 substrateNon-substrate0.8509
CYP450 3A4 substrateSubstrate0.5396
CYP450 1A2 substrateNon-inhibitor0.8866
CYP450 2C9 inhibitorNon-inhibitor0.8836
CYP450 2D6 inhibitorNon-inhibitor0.9093
CYP450 2C19 inhibitorNon-inhibitor0.8733
CYP450 3A4 inhibitorNon-inhibitor0.8648
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9163
Ames testNon AMES toxic0.6137
CarcinogenicityNon-carcinogens0.8145
BiodegradationNot ready biodegradable0.5842
Rat acute toxicity2.3754 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9443
hERG inhibition (predictor II)Non-inhibitor0.7581
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
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-0900000000-f02dc55e07c9935275d9
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-4901000000-bc16523808594ec9a806
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-5900000000-2199218952cf36a3e3a2
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0udi-2607900000-696f76b41235895dc296
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9801000000-9bc55b2280dfcf3aed1d
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9100000000-d33e29452de0777eaa0d
LC-MS/MS Spectrum - LC-ESI-QTOF , negativeLC-MS/MSsplash10-0kdi-9720700000-003f87d03143415a6bf9

Taxonomy

Description
This compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate 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 diphosphates
Alternative Parents
Organic pyrophosphates / Pyrimidones / Monoalkyl phosphates / Hydropyrimidines / Vinylogous amides / Heteroaromatic compounds / Tetrahydrofurans / Ureas / Secondary alcohols / Lactams
show 6 more
Substituents
Pyrimidine 2'-deoxyribonucleoside diphosphate / Organic pyrophosphate / Pyrimidone / Monoalkyl phosphate / Hydropyrimidine / Organic phosphoric acid derivative / Phosphoric acid ester / Pyrimidine / Alkyl phosphate / Heteroaromatic compound
show 17 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
pyrimidine 2'-deoxyribonucleoside 5'-diphosphate, thymidine phosphate (CHEBI:18075) / Deoxyribonucleotides (C00363)

Targets

Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Ribosomal small subunit binding
Specific Function
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-sit...
Gene Name
NME1
Uniprot ID
P15531
Uniprot Name
Nucleoside diphosphate kinase A
Molecular Weight
17148.635 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]

Drug created on June 13, 2005 07:24 / Updated on November 02, 2018 05:29