4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
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Identification
- Generic Name
- 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
- DrugBank Accession Number
- DB03687
- Background
Not Available
- Type
- Small Molecule
- Groups
- Experimental
- Structure
- Weight
- Average: 521.3075
Monoisotopic: 521.081175547 - Chemical Formula
- C14H25N3O14P2
- Synonyms
- 4-CDP-2-C-methyl-D-erythritol
- 4-Diphosphocytidyl-2-C-methyl-D-erythritol
Pharmacology
- Indication
Not Available
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- Pharmacodynamics
Not Available
- Mechanism of action
Target Actions Organism U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Not Available Shigella flexneri U4-diphosphocytidyl-2-C-methyl-D-erythritol kinase Not Available Shigella flexneri U2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase Not Available Escherichia coli (strain K12) - 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 outcomesWith structured adverse effects data, including: blackbox warnings, adverse reactions, warning & precautions, & incidence rates. View sample adverse effects data in our new Data Library!Improve decision support & research outcomes with our structured adverse effects data.
- 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 / Monoalkyl phosphates / Pyrimidones / Hydropyrimidines / Imidolactams / Tetrahydrofurans show 11 more
- Substituents
- Alcohol / Alkyl phosphate / Amine / Aminopyrimidine / Aromatic heteromonocyclic compound / Azacycle / Glycosyl compound / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine show 28 more
- Molecular Framework
- Aromatic heteromonocyclic compounds
- External Descriptors
- alditol 4-phosphate, tetritol phosphate, nucleotide-alditol (CHEBI:16578)
- Affected organisms
- Not Available
Chemical Identifiers
- UNII
- FB44VKC5JD
- CAS number
- 263016-94-0
- InChI Key
- YFAUKWZNPVBCFF-XHIBXCGHSA-N
- InChI
- InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1
- IUPAC Name
- {[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphoryl}oxy)phosphinic acid
- SMILES
- C[C@](O)(CO)[C@H](O)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O
References
- General References
- Not Available
- External Links
- KEGG Compound
- C11435
- PubChem Compound
- 443199
- PubChem Substance
- 46508868
- ChemSpider
- 391471
- ChEBI
- 16578
- ChEMBL
- CHEMBL1231708
- ZINC
- ZINC000008419042
- PDBe Ligand
- CDM
- PDB Entries
- 1ini / 1oj4 / 1u40 / 2v2z / 3pye / 3q80
Clinical Trials
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
Property Value Source logP -3.9 Chemaxon pKa (Strongest Acidic) 1.84 Chemaxon pKa (Strongest Basic) 3.56 Chemaxon Physiological Charge -2 Chemaxon Hydrogen Acceptor Count 14 Chemaxon Hydrogen Donor Count 9 Chemaxon Polar Surface Area 272.35 Å2 Chemaxon Rotatable Bond Count 11 Chemaxon Refractivity 115.04 m3·mol-1 Chemaxon Polarizability 44.23 Å3 Chemaxon Number of Rings 2 Chemaxon Bioavailability 0 Chemaxon Rule of Five No Chemaxon Ghose Filter No Chemaxon Veber's Rule No Chemaxon MDDR-like Rule No Chemaxon - Predicted ADMET Features
Property Value Probability Human Intestinal Absorption + 0.6071 Blood Brain Barrier + 0.7006 Caco-2 permeable - 0.7175 P-glycoprotein substrate Substrate 0.5456 P-glycoprotein inhibitor I Non-inhibitor 0.8692 P-glycoprotein inhibitor II Non-inhibitor 0.9936 Renal organic cation transporter Non-inhibitor 0.9762 CYP450 2C9 substrate Non-substrate 0.7196 CYP450 2D6 substrate Non-substrate 0.8283 CYP450 3A4 substrate Non-substrate 0.554 CYP450 1A2 substrate Non-inhibitor 0.8618 CYP450 2C9 inhibitor Non-inhibitor 0.8617 CYP450 2D6 inhibitor Non-inhibitor 0.866 CYP450 2C19 inhibitor Non-inhibitor 0.8366 CYP450 3A4 inhibitor Non-inhibitor 0.9137 CYP450 inhibitory promiscuity Low CYP Inhibitory Promiscuity 0.9658 Ames test Non AMES toxic 0.7107 Carcinogenicity Non-carcinogens 0.8258 Biodegradation Not ready biodegradable 0.9652 Rat acute toxicity 2.3188 LD50, mol/kg Not applicable hERG inhibition (predictor I) Weak inhibitor 0.9623 hERG inhibition (predictor II) Non-inhibitor 0.7904
Spectra
- Mass Spec (NIST)
- Not Available
- Spectra
- Chromatographic Properties
Collision Cross Sections (CCS)
Adduct CCS Value (Å2) Source type Source [M-H]- 214.6289813 predictedDarkChem Lite v0.1.0 [M-H]- 188.76128 predictedDeepCCS 1.0 (2019) [M+H]+ 214.8925813 predictedDarkChem Lite v0.1.0 [M+H]+ 190.70747 predictedDeepCCS 1.0 (2019) [M+Na]+ 213.9020813 predictedDarkChem Lite v0.1.0 [M+Na]+ 196.62047 predictedDeepCCS 1.0 (2019)
Targets
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- Kind
- Protein
- Organism
- Shigella flexneri
- Pharmacological action
- Unknown
- General Function
- Metal ion binding
- Specific Function
- Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidy...
- Gene Name
- ispF
- Uniprot ID
- P62619
- Uniprot Name
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- Molecular Weight
- 16897.37 Da
References
- Kind
- Protein
- Organism
- Shigella flexneri
- Pharmacological action
- Unknown
- General Function
- Atp binding
- Specific Function
- Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol.
- Gene Name
- ispE
- Uniprot ID
- Q83LD8
- Uniprot Name
- 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
- Molecular Weight
- 30953.11 Da
References
- Kind
- Protein
- Organism
- Escherichia coli (strain K12)
- Pharmacological action
- Unknown
- General Function
- Magnesium ion binding
- Specific Function
- Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP).
- Gene Name
- ispD
- Uniprot ID
- Q46893
- Uniprot Name
- 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
- Molecular Weight
- 25736.995 Da
References
Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52