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2'-Deoxy-thymidine-beta-L-rhamnose

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Data Packages
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Identification

Generic Name
2'-Deoxy-thymidine-beta-L-rhamnose
DrugBank Accession Number
DB03723
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 548.3296
Monoisotopic: 548.080841196
Chemical Formula
C16H26N2O15P2
Synonyms
  • dTDP-6-deoxy-L-mannose
  • dTDP-6-deoxy-β-L-mannose
  • dTDP-L-rhamnose
  • dTDP-β-L-rhamnose
  • Thymidine diphosphate-L-rhamnose
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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-4-dehydrorhamnose reductaseNot AvailableSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
UGlucose-1-phosphate thymidylyltransferaseNot AvailablePseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
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
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
Pentose phosphates / Monosaccharide phosphates / Organic pyrophosphates / Hydroxypyrimidines / Monoalkyl phosphates / Pyrimidones / Hydropyrimidines / Oxanes / Tetrahydrofurans / Heteroaromatic compounds
show 8 more
Substituents
Alcohol / Alkyl phosphate / Aromatic heteromonocyclic compound / Azacycle / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Hydroxypyrimidine / Monoalkyl phosphate / Monosaccharide
show 20 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
dTDP-L-rhamnose (CHEBI:15774)
Affected organisms
Not Available

Chemical Identifiers

UNII
Not Available
CAS number
2147-59-3
InChI Key
ZOSQFDVXNQFKBY-CGAXJHMRSA-N
InChI
InChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,11-,12+,13+,15+/m0/s1
IUPAC Name
{[hydroxy({[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-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
C[C@@H]1O[C@H](OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N2C=C(C)C(=O)NC2=O)[C@H](O)[C@H](O)[C@H]1O

References

General References
Not Available
KEGG Compound
C03319
PubChem Compound
121966
PubChem Substance
46505764
ChemSpider
108806
ChEBI
15774
ZINC
ZINC000008218444
PDBe Ligand
TRH
PDB Entries
1g3l / 1kc3 / 2ixc / 2ixh / 2ixl / 2x0f / 4j7g / 4j7h / 5ify / 5nv8 …
show 7 more

Clinical Trials

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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 Solubility11.6 mg/mLALOGPS
logP-1.1ALOGPS
logP-2.7Chemaxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.73Chemaxon
pKa (Strongest Basic)-3.2Chemaxon
Physiological Charge-2Chemaxon
Hydrogen Acceptor Count12Chemaxon
Hydrogen Donor Count7Chemaxon
Polar Surface Area251.08 Å2Chemaxon
Rotatable Bond Count8Chemaxon
Refractivity107.76 m3·mol-1Chemaxon
Polarizability46.34 Å3Chemaxon
Number of Rings3Chemaxon
Bioavailability0Chemaxon
Rule of FiveNoChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleYesChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.9389
Blood Brain Barrier-0.7863
Caco-2 permeable-0.7858
P-glycoprotein substrateNon-substrate0.5648
P-glycoprotein inhibitor INon-inhibitor0.7171
P-glycoprotein inhibitor IINon-inhibitor0.9759
Renal organic cation transporterNon-inhibitor0.9348
CYP450 2C9 substrateNon-substrate0.6844
CYP450 2D6 substrateNon-substrate0.8508
CYP450 3A4 substrateSubstrate0.6133
CYP450 1A2 substrateNon-inhibitor0.8691
CYP450 2C9 inhibitorNon-inhibitor0.8612
CYP450 2D6 inhibitorNon-inhibitor0.8918
CYP450 2C19 inhibitorNon-inhibitor0.828
CYP450 3A4 inhibitorNon-inhibitor0.5932
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.8431
Ames testNon AMES toxic0.6707
CarcinogenicityNon-carcinogens0.8211
BiodegradationNot ready biodegradable0.8357
Rat acute toxicity2.4742 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9589
hERG inhibition (predictor II)Non-inhibitor0.5772
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/MSsplash10-002b-0210190000-5f9ba921ddbda513d187
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-002b-0000190000-cea0081c28150f4f8fc1
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-3590010000-0d7b2d2c42274f8880b6
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-01td-3000920000-3f795627260171f77bae
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-056r-2911000000-1133c4dac503ae408592
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-054p-7715920000-1fb67fc7ba86bf9a0bd3
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-233.5439963
predicted
DarkChem Lite v0.1.0
[M-H]-190.46552
predicted
DeepCCS 1.0 (2019)
[M+H]+235.1563963
predicted
DarkChem Lite v0.1.0
[M+H]+192.46095
predicted
DeepCCS 1.0 (2019)
[M+Na]+232.9760963
predicted
DarkChem Lite v0.1.0
[M+Na]+198.21
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. dTDP-4-dehydrorhamnose reductase
Kind
Protein
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Pharmacological action
Unknown
General Function
Involved in the biosynthesis of the dTDP-L-rhamnose which is an important component of lipopolysaccharide (LPS). Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.
Specific Function
dTDP-4-dehydrorhamnose reductase activity
Gene Name
rfbD
Uniprot ID
P26392
Uniprot Name
dTDP-4-dehydrorhamnose reductase
Molecular Weight
32553.76 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. Glucose-1-phosphate thymidylyltransferase
Kind
Protein
Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pharmacological action
Unknown
General Function
Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis.
Specific Function
glucose-1-phosphate thymidylyltransferase activity
Gene Name
rmlA
Uniprot ID
Q9HU22
Uniprot Name
Glucose-1-phosphate thymidylyltransferase
Molecular Weight
32456.65 Da

Drug created at June 13, 2005 13:24 / Updated at December 11, 2021 01:26