NAV

2'deoxy-Thymidine-5'-Diphospho-Alpha-D-Glucose

Identification

Generic Name
2'deoxy-Thymidine-5'-Diphospho-Alpha-D-Glucose
DrugBank Accession Number
DB03751
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 564.329
Monoisotopic: 564.075755818
Chemical Formula
C16H26N2O16P2
Synonyms
Not Available
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Pharmacology

Indication

Not Available

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Contraindications & Blackbox Warnings
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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UdTDP-glucose 4,6-dehydrataseNot AvailableSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
UDTDP-4-dehydrorhamnose 3,5-epimeraseNot AvailableStreptococcus suis
UdTDP-glucose 4,6-dehydrataseNot AvailableStreptococcus mutans serotype c (strain ATCC 700610 / UA159)
UGlucose-1-phosphate thymidylyltransferaseNot AvailablePseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
UdTDP-glucose 4,6-dehydrataseNot AvailableStreptomyces venezuelae
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 nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Pyrimidine nucleotides
Sub Class
Pyrimidine nucleotide sugars
Direct Parent
Pyrimidine nucleotide sugars
Alternative Parents
Pyrimidine 2'-deoxyribonucleoside diphosphates / Pentose phosphates / Monosaccharide phosphates / Organic pyrophosphates / Monoalkyl phosphates / Pyrimidones / Oxanes / Hydropyrimidines / Tetrahydrofurans / Vinylogous amides
show 12 more
Substituents
Alcohol / Alkyl phosphate / Aromatic heteromonocyclic compound / Azacycle / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Lactam / Monoalkyl phosphate / Monosaccharide
show 24 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
dTDP-sugar (CHEBI:15700)
Affected organisms
Not Available

Chemical Identifiers

UNII
Q9XRK94HEF
CAS number
Not Available
InChI Key
YSYKRGRSMLTJNL-URARBOGNSA-N
InChI
InChI=1S/C16H26N2O16P2/c1-6-3-18(16(25)17-14(6)24)10-2-7(20)9(31-10)5-30-35(26,27)34-36(28,29)33-15-13(23)12(22)11(21)8(4-19)32-15/h3,7-13,15,19-23H,2,4-5H2,1H3,(H,26,27)(H,28,29)(H,17,24,25)/t7-,8+,9+,10+,11+,12-,13+,15+/m0/s1
IUPAC Name
{[hydroxy({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphoryl]oxy}({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid
SMILES
CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O

References

General References
Not Available
KEGG Compound
C00842
PubChem Compound
443210
PubChem Substance
46508412
ChemSpider
391476
ChEBI
15700
ChEMBL
CHEMBL412989
PDBe Ligand
DAU
PDB Entries
1g1l / 1h5t / 1ker / 1keu / 1nyw / 1r6d / 4ecm / 4ho5 / 4ly0 / 6b5e

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 Solubility11.2 mg/mLALOGPS
logP-1.2ALOGPS
logP-3.7Chemaxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.73Chemaxon
pKa (Strongest Basic)-3Chemaxon
Physiological Charge-2Chemaxon
Hydrogen Acceptor Count13Chemaxon
Hydrogen Donor Count8Chemaxon
Polar Surface Area271.31 Å2Chemaxon
Rotatable Bond Count9Chemaxon
Refractivity109.3 m3·mol-1Chemaxon
Polarizability46.66 Å3Chemaxon
Number of Rings3Chemaxon
Bioavailability0Chemaxon
Rule of FiveNoChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleYesChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.9194
Blood Brain Barrier-0.7502
Caco-2 permeable-0.7573
P-glycoprotein substrateNon-substrate0.5392
P-glycoprotein inhibitor INon-inhibitor0.7531
P-glycoprotein inhibitor IINon-inhibitor0.9864
Renal organic cation transporterNon-inhibitor0.9209
CYP450 2C9 substrateNon-substrate0.6285
CYP450 2D6 substrateNon-substrate0.8475
CYP450 3A4 substrateSubstrate0.558
CYP450 1A2 substrateNon-inhibitor0.8581
CYP450 2C9 inhibitorNon-inhibitor0.8345
CYP450 2D6 inhibitorNon-inhibitor0.8693
CYP450 2C19 inhibitorNon-inhibitor0.8101
CYP450 3A4 inhibitorInhibitor0.6489
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.7978
Ames testAMES toxic0.5319
CarcinogenicityNon-carcinogens0.7981
BiodegradationNot ready biodegradable0.6784
Rat acute toxicity2.4660 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9183
hERG inhibition (predictor II)Inhibitor0.5317
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 MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-016s-0220290000-117675103d2689351f2d
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-03di-0000190000-53ef1dde1de25d6b0c11
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-6690420000-9d296070dac428ce3e25
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-002f-4000930000-d8bcaea646dbc83ab50a
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-01t9-2920200000-f7e8ca1fce001638d704
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-052g-9817620000-b55197cc4ac1961710a3
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-245.754017
predicted
DarkChem Lite v0.1.0
[M-H]-187.58101
predicted
DeepCCS 1.0 (2019)
[M+H]+250.867417
predicted
DarkChem Lite v0.1.0
[M+H]+189.40414
predicted
DeepCCS 1.0 (2019)
[M+Na]+244.907717
predicted
DarkChem Lite v0.1.0
[M+Na]+195.01164
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. dTDP-glucose 4,6-dehydratase
Kind
Protein
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Pharmacological action
Unknown
General Function
Nadh binding
Specific Function
Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction.
Gene Name
rfbB
Uniprot ID
P26391
Uniprot Name
dTDP-glucose 4,6-dehydratase
Molecular Weight
40718.29 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]
Details2. DTDP-4-dehydrorhamnose 3,5-epimerase
Kind
Protein
Organism
Streptococcus suis
Pharmacological action
Unknown
General Function
Dtdp-4-dehydrorhamnose 3,5-epimerase activity
Specific Function
Not Available
Gene Name
rmlC
Uniprot ID
Q8GIQ0
Uniprot Name
dTDP-4-dehydrorhamnose 3,5-epimerase
Molecular Weight
22463.2 Da
Details3. dTDP-glucose 4,6-dehydratase
Kind
Protein
Organism
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
Pharmacological action
Unknown
General Function
Dtdp-glucose 4,6-dehydratase activity
Specific Function
Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction.
Gene Name
rmlB
Uniprot ID
P95780
Uniprot Name
dTDP-glucose 4,6-dehydratase
Molecular Weight
39280.625 Da
Details4. Glucose-1-phosphate thymidylyltransferase
Kind
Protein
Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pharmacological action
Unknown
General Function
Nucleotide binding
Specific Function
Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis.
Gene Name
rmlA
Uniprot ID
Q9HU22
Uniprot Name
Glucose-1-phosphate thymidylyltransferase
Molecular Weight
32456.65 Da
Details5. dTDP-glucose 4,6-dehydratase
Kind
Protein
Organism
Streptomyces venezuelae
Pharmacological action
Unknown
General Function
Oxidoreductase activity
Specific Function
Not Available
Gene Name
desIV
Uniprot ID
Q9ZGH3
Uniprot Name
dTDP-glucose 4,6-dehydratase
Molecular Weight
36456.53 Da

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