Cytidine-5'-Diphosphate
Identification
- Name
- Cytidine-5'-Diphosphate
- Accession Number
- DB04555
- Description
Cytidine 5'-(trihydrogen diphosphate). A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. Synonyms: CRPP; cytidine pyrophosphate. [PubChem]
- Type
- Small Molecule
- Groups
- Experimental
- Structure
Structure for Cytidine-5'-Diphosphate (DB04555)
- Weight
- Average: 403.1764
Monoisotopic: 403.018181361 - Chemical Formula
- C9H15N3O11P2
- Synonyms
- Not Available
Pharmacology
Accelerate your drug discovery research with the industry’s only fully connected ADMET dataset, ideal for:Accelerate your drug discovery research with our fully connected ADMET dataset- Indication
- Not Available
- Contraindications & Blackbox Warnings
Contraindications & Blackbox WarningsWith our commercial data, access important information on dangerous risks, contraindications, and adverse effects.Our Blackbox Warnings cover Risks, Contraindications, and Adverse Effects- Pharmacodynamics
- Not Available
- Mechanism of action
Target Actions Organism U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Not Available Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) UN-acylneuraminate cytidylyltransferase Not Available Neisseria meningitidis UCytidylate kinase Not Available Escherichia coli (strain K12) UCDP-paratose 2-epimerase Not Available Salmonella typhi U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Not Available Shigella flexneri U3-deoxy-manno-octulosonate cytidylyltransferase Not Available Escherichia coli - 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
Reduce medical errorsand improve treatment outcomes with our comprehensive & structured data on drug adverse effects.Reduce medical errors & improve treatment outcomes with our adverse effects data- Toxicity
- Not Available
- Affected organisms
- 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 / Organic pyrophosphates / Monosaccharide phosphates / Aminopyrimidines and derivatives / Pyrimidones / Monoalkyl phosphates / Hydropyrimidines / Imidolactams / Tetrahydrofurans show 9 more
- Substituents
- 1,2-diol / Alcohol / Alkyl phosphate / Amine / Aminopyrimidine / Aromatic heteromonocyclic compound / Azacycle / Glycosyl compound / Heteroaromatic compound / Hydrocarbon derivative show 26 more
- Molecular Framework
- Aromatic heteromonocyclic compounds
- External Descriptors
- cytidine 5'-phosphate, pyrimidine ribonucleoside 5'-diphosphate (CHEBI:17239) / Ribonucleotides (C00112)
Chemical Identifiers
- UNII
- 1ZH821MXU5
- CAS number
- 63-38-7
- InChI Key
- ZWIADYZPOWUWEW-XVFCMESISA-N
- InChI
- InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/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)phosphoryl)oxy]phosphonic acid
- SMILES
- NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O
References
- General References
- Not Available
- External Links
- Human Metabolome Database
- HMDB0001546
- KEGG Compound
- C00112
- PubChem Compound
- 6132
- PubChem Substance
- 46508856
- ChemSpider
- 5902
- BindingDB
- 50194153
- ChEBI
- 17239
- ChEMBL
- CHEMBL425252
- ZINC
- ZINC000008215624
- PDBe Ligand
- CDP
- PDB Entries
- 1eyr / 1ffu / 1gx1 / 1h7h / 1iv2 / 1orr / 1u3l / 1xjn / 1yqn / 2az3 … show 48 more
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 Water Solubility 10.1 mg/mL ALOGPS logP -1.4 ALOGPS logP -3.6 ChemAxon logS -1.6 ALOGPS pKa (Strongest Acidic) 1.77 ChemAxon pKa (Strongest Basic) -0.52 ChemAxon Physiological Charge -2 ChemAxon Hydrogen Acceptor Count 11 ChemAxon Hydrogen Donor Count 6 ChemAxon Polar Surface Area 221.67 Å2 ChemAxon Rotatable Bond Count 6 ChemAxon Refractivity 76.29 m3·mol-1 ChemAxon Polarizability 31.39 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 - 0.8988 Blood Brain Barrier + 0.9126 Caco-2 permeable - 0.7763 P-glycoprotein substrate Non-substrate 0.7622 P-glycoprotein inhibitor I Non-inhibitor 0.9175 P-glycoprotein inhibitor II Non-inhibitor 0.9806 Renal organic cation transporter Non-inhibitor 0.96 CYP450 2C9 substrate Non-substrate 0.7402 CYP450 2D6 substrate Non-substrate 0.8462 CYP450 3A4 substrate Non-substrate 0.596 CYP450 1A2 substrate Non-inhibitor 0.9167 CYP450 2C9 inhibitor Non-inhibitor 0.9233 CYP450 2D6 inhibitor Non-inhibitor 0.9134 CYP450 2C19 inhibitor Non-inhibitor 0.9043 CYP450 3A4 inhibitor Non-inhibitor 0.9438 CYP450 inhibitory promiscuity Low CYP Inhibitory Promiscuity 0.974 Ames test Non AMES toxic 0.9125 Carcinogenicity Non-carcinogens 0.9062 Biodegradation Not ready biodegradable 0.7826 Rat acute toxicity 2.2404 LD50, mol/kg Not applicable hERG inhibition (predictor I) Weak inhibitor 0.9834 hERG inhibition (predictor II) Non-inhibitor 0.8137
Spectra
- Mass Spec (NIST)
- Not Available
- Spectra
Targets
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- Kind
- Protein
- Organism
- Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
- 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
- Q8RQP5
- Uniprot Name
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- Molecular Weight
- 16519.835 Da
References
- Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
- 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. [PubMed:17016423]
- Kind
- Protein
- Organism
- Neisseria meningitidis
- Pharmacological action
- Unknown
- General Function
- N-acylneuraminate cytidylyltransferase activity
- Specific Function
- Not Available
- Gene Name
- neuA
- Uniprot ID
- P0A0Z8
- Uniprot Name
- N-acylneuraminate cytidylyltransferase
- Molecular Weight
- 24892.155 Da
References
- Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
- 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. [PubMed:17016423]
- Kind
- Protein
- Organism
- Escherichia coli (strain K12)
- Pharmacological action
- Unknown
- General Function
- Cytidylate kinase activity
- Specific Function
- ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors.
- Gene Name
- cmk
- Uniprot ID
- P0A6I0
- Uniprot Name
- Cytidylate kinase
- Molecular Weight
- 24746.03 Da
References
- Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
- 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. [PubMed:17016423]
- Kind
- Protein
- Organism
- Salmonella typhi
- Pharmacological action
- Unknown
- General Function
- Cdp-abequose epimerase activity
- Specific Function
- Catalyzes the isomeration of CDP-paratose to CDP-tyvelose.
- Gene Name
- rfbE
- Uniprot ID
- P14169
- Uniprot Name
- CDP-paratose 2-epimerase
- Molecular Weight
- 37957.675 Da
References
- Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
- 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. [PubMed:17016423]
- 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
- Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
- 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. [PubMed:17016423]
- Kind
- Protein
- Organism
- Escherichia coli
- Pharmacological action
- Unknown
- General Function
- 3-deoxy-manno-octulosonate cytidylyltransferase activity
- Specific Function
- Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria.
- Gene Name
- kpsU
- Uniprot ID
- P42216
- Uniprot Name
- 3-deoxy-manno-octulosonate cytidylyltransferase
- Molecular Weight
- 27158.885 Da
References
- Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
- 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. [PubMed:17016423]
Drug created on June 13, 2005 13:24 / Updated on June 12, 2020 16:52