NAV

Cytidine 5'-diphosphoglycerol

Identification

Generic Name
Cytidine 5'-diphosphoglycerol
DrugBank Accession Number
DB02484
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 477.255
Monoisotopic: 477.054960797
Chemical Formula
C12H21N3O13P2
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
UGlycerol-3-phosphate cytidylyltransferaseNot AvailableBacillus subtilis (strain 168)
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 cdp-glycerols. These are glycerolipids with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part. As is the case with diacylglycerols, phosphatidylserines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 atoms.
Kingdom
Organic compounds
Super Class
Lipids and lipid-like molecules
Class
Glycerophospholipids
Sub Class
CDP-glycerols
Direct Parent
CDP-glycerols
Alternative Parents
Pyrimidine ribonucleoside diphosphates / Pentose phosphates / Glycosylamines / Monosaccharide phosphates / Organic pyrophosphates / Aminopyrimidines and derivatives / Pyrimidones / Monoalkyl phosphates / Hydropyrimidines / Imidolactams
show 10 more
Substituents
Alcohol / Alkyl phosphate / Amine / Aminopyrimidine / Aromatic heteromonocyclic compound / Azacycle / Cdp-glycerol / Glycosyl compound / Heteroaromatic compound / Hydrocarbon derivative
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
HHPOUCCVONEPRK-CNYIRLTGSA-N
InChI
InChI=1S/C12H21N3O13P2/c13-8-1-2-15(12(20)14-8)11-10(19)9(18)7(27-11)5-26-30(23,24)28-29(21,22)25-4-6(17)3-16/h1-2,6-7,9-11,16-19H,3-5H2,(H,21,22)(H,23,24)(H2,13,14,20)/t6-,7+,9+,10+,11+/m0/s1
IUPAC Name
{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2S)-2,3-dihydroxypropoxy](hydroxy)phosphoryl}oxy)phosphinic acid
SMILES
[H]N([H])C1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OC[C@@H](O)CO)[C@@H](O)[C@H]1O

References

General References
Not Available
PubChem Compound
447253
PubChem Substance
46505163
ChemSpider
394400
ZINC
ZINC000008551188
PDBe Ligand
C2G
PDB Entries
1n1d / 4q7c

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 Solubility12.2 mg/mLALOGPS
logP-1.6ALOGPS
logP-4.5Chemaxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.82Chemaxon
pKa (Strongest Basic)4.34Chemaxon
Physiological Charge-2Chemaxon
Hydrogen Acceptor Count12Chemaxon
Hydrogen Donor Count7Chemaxon
Polar Surface Area251.13 Å2Chemaxon
Rotatable Bond Count10Chemaxon
Refractivity93.03 m3·mol-1Chemaxon
Polarizability39.59 Å3Chemaxon
Number of Rings2Chemaxon
Bioavailability0Chemaxon
Rule of FiveNoChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.7848
Blood Brain Barrier+0.8575
Caco-2 permeable-0.7668
P-glycoprotein substrateNon-substrate0.7245
P-glycoprotein inhibitor INon-inhibitor0.9178
P-glycoprotein inhibitor IINon-inhibitor0.9771
Renal organic cation transporterNon-inhibitor0.9686
CYP450 2C9 substrateNon-substrate0.7849
CYP450 2D6 substrateNon-substrate0.8404
CYP450 3A4 substrateNon-substrate0.5998
CYP450 1A2 substrateNon-inhibitor0.9147
CYP450 2C9 inhibitorNon-inhibitor0.9098
CYP450 2D6 inhibitorNon-inhibitor0.8966
CYP450 2C19 inhibitorNon-inhibitor0.8935
CYP450 3A4 inhibitorNon-inhibitor0.8738
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9673
Ames testNon AMES toxic0.8177
CarcinogenicityNon-carcinogens0.8635
BiodegradationNot ready biodegradable0.7747
Rat acute toxicity2.2403 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9697
hERG inhibition (predictor II)Non-inhibitor0.7535
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/MSsplash10-0w4l-0000900000-ccb81e01e16f55930576
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-0000900000-b85c1ccda5e153558d50
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-003r-6203900000-103170a3187aeefe01bb
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-03fu-0593100000-c0ca95545b8ca3316c04
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-0006-0931100000-d9f6507fb2f78d4c0512
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-056r-9405200000-7109629dc5ade0f8e301
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]-164.70198
predicted
DeepCCS 1.0 (2019)
[M+H]+166.52644
predicted
DeepCCS 1.0 (2019)
[M+Na]+172.2365
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. Glycerol-3-phosphate cytidylyltransferase
Kind
Protein
Organism
Bacillus subtilis (strain 168)
Pharmacological action
Unknown
General Function
Metal ion binding
Specific Function
Provides activated glycerol phosphate for teichoic acid synthesis, via incorporation into both the linkage unit and the teichoic acid polymer by TagB and TagF.
Gene Name
tagD
Uniprot ID
P27623
Uniprot Name
Glycerol-3-phosphate cytidylyltransferase
Molecular Weight
15271.45 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 July 02, 2020 13:17