NAV

Cytidine-5'-diphospho-beta-D-xylose

Identification

Generic Name
Cytidine-5'-diphospho-beta-D-xylose
DrugBank Accession Number
DB03069
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 535.291
Monoisotopic: 535.060440105
Chemical Formula
C14H23N3O15P2
Synonyms
Not Available
Poor quality drug data slowing you down?
Unlock 38% more drug discovery time and eliminate decision-making doubts with this one-stop guide to quality drug data.
Download eBook
Poor quality drug data slowing you down?
Download eBook

Pharmacology

Indication

Not Available

Reduce drug development failure rates
Build, train, & validate machine-learning models
with evidence-based and structured datasets.
See how
Build, train, & validate predictive machine-learning models with structured datasets.
See how
Contraindications & Blackbox Warnings
Prevent Adverse Drug Events Today
Tap into our Clinical API for life-saving information on contraindications & blackbox warnings, population restrictions, harmful risks, & more.
Learn more
Avoid life-threatening adverse drug events with our Clinical API
Learn more
Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UCDP-glucose 4,6-dehydrataseNot AvailableSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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
Improve decision support & research outcomes
With structured adverse effects data, including: blackbox warnings, adverse reactions, warning & precautions, & incidence rates. View sample adverse effects data in our new Data Library!
See the data
Improve decision support & research outcomes with our structured adverse effects data.
See a data sample
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 ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Pyrimidine nucleotides
Sub Class
Pyrimidine ribonucleotides
Direct Parent
Pyrimidine ribonucleoside diphosphates
Alternative Parents
Pentose phosphates / Glycosylamines / Monosaccharide phosphates / Organic pyrophosphates / Aminopyrimidines and derivatives / Pyrimidones / Monoalkyl phosphates / Hydropyrimidines / Imidolactams / Oxanes
show 10 more
Substituents
Alcohol / Alkyl phosphate / Amine / Aminopyrimidine / Aromatic heteromonocyclic compound / Azacycle / Glycosyl compound / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine
show 26 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
NWSKPSPTJOAICE-OCIMBMBZSA-N
InChI
InChI=1S/C14H23N3O15P2/c15-7-1-2-17(14(23)16-7)12-10(21)9(20)6(30-12)4-29-33(24,25)32-34(26,27)31-13-11(22)8(19)5(18)3-28-13/h1-2,5-6,8-13,18-22H,3-4H2,(H,24,25)(H,26,27)(H2,15,16,23)/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1
IUPAC Name
{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[hydroxy({[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy})phosphoryl]oxy})phosphinic acid
SMILES
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2O)[C@@H](O)[C@H]1O

References

General References
Not Available
PubChem Compound
449144
PubChem Substance
46506620
ChemSpider
395758
ZINC
ZINC000016051634
PDBe Ligand
CXY
PDB Entries
1wvg

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 Solubility22.3 mg/mLALOGPS
logP-1.2ALOGPS
logP-4.9Chemaxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1.7Chemaxon
pKa (Strongest Basic)4.33Chemaxon
Physiological Charge-2Chemaxon
Hydrogen Acceptor Count14Chemaxon
Hydrogen Donor Count8Chemaxon
Polar Surface Area280.59 Å2Chemaxon
Rotatable Bond Count8Chemaxon
Refractivity102.47 m3·mol-1Chemaxon
Polarizability43.92 Å3Chemaxon
Number of Rings3Chemaxon
Bioavailability0Chemaxon
Rule of FiveNoChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleYesChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.9374
Blood Brain Barrier+0.6795
Caco-2 permeable-0.7578
P-glycoprotein substrateNon-substrate0.6814
P-glycoprotein inhibitor INon-inhibitor0.8616
P-glycoprotein inhibitor IINon-inhibitor0.9689
Renal organic cation transporterNon-inhibitor0.9574
CYP450 2C9 substrateNon-substrate0.7604
CYP450 2D6 substrateNon-substrate0.8464
CYP450 3A4 substrateNon-substrate0.56
CYP450 1A2 substrateNon-inhibitor0.8905
CYP450 2C9 inhibitorNon-inhibitor0.8798
CYP450 2D6 inhibitorNon-inhibitor0.8727
CYP450 2C19 inhibitorNon-inhibitor0.8446
CYP450 3A4 inhibitorNon-inhibitor0.6914
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.8874
Ames testNon AMES toxic0.8401
CarcinogenicityNon-carcinogens0.8933
BiodegradationNot ready biodegradable0.8839
Rat acute toxicity2.4358 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9825
hERG inhibition (predictor II)Non-inhibitor0.6291
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/MSsplash10-000i-0200190000-335fcb0e72723bc9acce
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-001i-0000190000-693d6b7091627cfb86cb
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-03di-0942210000-642164c2f2cdf41abbca
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-052f-1611920000-2ce12d9eddfe57279fde
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-03e9-0932000000-32bc72e50104761ad8e1
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-0a59-3928040000-45d1200c6e24b4d6c728
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-184.2427
predicted
DeepCCS 1.0 (2019)
[M+H]+186.13814
predicted
DeepCCS 1.0 (2019)
[M+Na]+191.9933
predicted
DeepCCS 1.0 (2019)

Targets

Build, predict & validate machine-learning models
Use our structured and evidence-based datasets to unlock new
insights and accelerate drug research.
Learn more
Use our structured and evidence-based datasets to unlock new insights and accelerate drug research.
Learn more
Details1. CDP-glucose 4,6-dehydratase
Kind
Protein
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Pharmacological action
Unknown
General Function
Cdp-glucose 4,6-dehydratase activity
Specific Function
Not Available
Gene Name
rfbG
Uniprot ID
P26397
Uniprot Name
CDP-glucose 4,6-dehydratase
Molecular Weight
41021.34 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]

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