NAV

Thymidine-5'- Diphosphate

Identification

Generic Name
Thymidine-5'- Diphosphate
DrugBank Accession Number
DB03103
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 402.1884
Monoisotopic: 402.022932388
Chemical Formula
C10H16N2O11P2
Synonyms
Not Available
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Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UNucleoside diphosphate kinase ANot AvailableHumans
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
Not Available
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
Not Available
Chemical TaxonomyProvided by Classyfire
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
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Substituents
Alcohol / Alkyl phosphate / Aromatic heteromonocyclic compound / Azacycle / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Lactam / Monoalkyl phosphate / Organic nitrogen compound
show 17 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
pyrimidine 2'-deoxyribonucleoside 5'-diphosphate, thymidine phosphate (CHEBI:18075) / Deoxyribonucleotides (C00363)
Affected organisms
Not Available

Chemical Identifiers

UNII
QQ3K1P45DF
CAS number
Not Available
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

References

General References
Not Available
Human Metabolome Database
HMDB0001274
KEGG Compound
C00363
PubChem Compound
164628
PubChem Substance
46505634
ChemSpider
144320
ChEBI
18075
ChEMBL
CHEMBL259724
ZINC
ZINC000008215882
PDBe Ligand
TYD
PDB Entries
1cr4 / 1e2g / 1epz / 1gtv / 1h5t / 1h7l / 1h7q / 1ket / 1kew / 1lvw …
show 78 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 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-3Chemaxon
Hydrogen Acceptor Count9Chemaxon
Hydrogen Donor Count5Chemaxon
Polar Surface Area192.16 Å2Chemaxon
Rotatable Bond Count6Chemaxon
Refractivity77.16 m3·mol-1Chemaxon
Polarizability32.12 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-MSsplash10-004m-6922000000-78987adf8e4b2b4baa77
LC-MS/MS Spectrum - LC-ESI-QTOF , negativeLC-MS/MSsplash10-0kdi-9720700000-003f87d03143415a6bf9
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-0fb9-3692800000-64244ee05fe6d0c0b60c
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0udi-0204900000-cf1906e2c0e20abe9b82
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-4900000000-142c5f2eac7220a32326
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-00pl-8219100000-4cb9eeef35587b3adcbb
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-0911000000-4af28eb8968c80246d46
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9001000000-dc58e6862bddcc8b386f
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]-206.8199619
predicted
DarkChem Lite v0.1.0
[M-H]-197.6615619
predicted
DarkChem Lite v0.1.0
[M-H]-170.59372
predicted
DeepCCS 1.0 (2019)
[M+H]+210.3396619
predicted
DarkChem Lite v0.1.0
[M+H]+198.2048619
predicted
DarkChem Lite v0.1.0
[M+H]+172.95184
predicted
DeepCCS 1.0 (2019)
[M+Na]+205.3693619
predicted
DarkChem Lite v0.1.0
[M+Na]+196.0607619
predicted
DarkChem Lite v0.1.0
[M+Na]+179.22078
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. Nucleoside diphosphate kinase A
Kind
Protein
Organism
Humans
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. [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]

Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52