NAV

Thymidine-5'-diphospho-beta-D-xylose

Identification

Generic Name
Thymidine-5'-diphospho-beta-D-xylose
DrugBank Accession Number
DB03161
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 534.303
Monoisotopic: 534.065191132
Chemical Formula
C15H24N2O15P2
Synonyms
Not Available
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Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UdTDP-glucose 4,6-dehydrataseNot AvailableStreptococcus mutans serotype c (strain ATCC 700610 / UA159)
UDTDP-4-dehydrorhamnose 3,5-epimeraseNot AvailableStreptococcus suis
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
Pentose phosphates / Monosaccharide phosphates / Organic pyrophosphates / Monoalkyl phosphates / Pyrimidones / Oxanes / Hydropyrimidines / Tetrahydrofurans / Vinylogous amides / Heteroaromatic compounds
show 10 more
Substituents
Alcohol / Alkyl phosphate / Aromatic heteromonocyclic compound / Azacycle / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Lactam / Monoalkyl phosphate / Monosaccharide
show 22 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
Not Available
Affected organisms
Not Available

Chemical Identifiers

UNII
Not Available
CAS number
Not Available
InChI Key
AJUADKZRQSBUAK-KDGZBOQCSA-N
InChI
InChI=1S/C15H24N2O15P2/c1-6-3-17(15(23)16-13(6)22)10-2-7(18)9(30-10)5-29-33(24,25)32-34(26,27)31-14-12(21)11(20)8(19)4-28-14/h3,7-12,14,18-21H,2,4-5H2,1H3,(H,24,25)(H,26,27)(H,16,22,23)/t7-,8+,9+,10+,11-,12+,14+/m0/s1
IUPAC Name
{[hydroxy({[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-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
[H]N1C(=O)N(C=C(C)C1=O)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2O)O1

References

General References
Not Available
PubChem Compound
447462
PubChem Substance
46505396
ChemSpider
394560
ZINC
ZINC000015634247
PDBe Ligand
TDX
PDB Entries
1kep / 1nzc / 1oc2

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 Solubility11.3 mg/mLALOGPS
logP-1.3ALOGPS
logP-3.1Chemaxon
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
Refractivity103.34 m3·mol-1Chemaxon
Polarizability44.46 Å3Chemaxon
Number of Rings3Chemaxon
Bioavailability0Chemaxon
Rule of FiveNoChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleYesChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.9443
Blood Brain Barrier-0.7737
Caco-2 permeable-0.7649
P-glycoprotein substrateNon-substrate0.5169
P-glycoprotein inhibitor INon-inhibitor0.7079
P-glycoprotein inhibitor IINon-inhibitor0.9841
Renal organic cation transporterNon-inhibitor0.9136
CYP450 2C9 substrateNon-substrate0.6457
CYP450 2D6 substrateNon-substrate0.8496
CYP450 3A4 substrateSubstrate0.5788
CYP450 1A2 substrateNon-inhibitor0.8624
CYP450 2C9 inhibitorNon-inhibitor0.839
CYP450 2D6 inhibitorNon-inhibitor0.8778
CYP450 2C19 inhibitorNon-inhibitor0.8025
CYP450 3A4 inhibitorInhibitor0.5808
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.7921
Ames testNon AMES toxic0.5357
CarcinogenicityNon-carcinogens0.8343
BiodegradationNot ready biodegradable0.7632
Rat acute toxicity2.4709 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9285
hERG inhibition (predictor II)Inhibitor0.5127
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, Negative (Annotated)Predicted LC-MS/MSsplash10-001i-0000190000-c477c69898bb7a3a4749
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-002r-0320690000-eec83dd71fa7574597ec
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-08iv-6324930000-7021d4d3134603e81cf5
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-1590000000-814f73959a87dda99c82
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-0920000000-9fd974dfda3baee48c64
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-0arv-9715830000-e3de132ebb99701e86ed
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-173.0067
predicted
DeepCCS 1.0 (2019)
[M+H]+174.83711
predicted
DeepCCS 1.0 (2019)
[M+Na]+180.77043
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. 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
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

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