2'-Deoxycytidine
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Identification
- Generic Name
- 2'-Deoxycytidine
- DrugBank Accession Number
- DB02594
- Background
Not Available
- Type
- Small Molecule
- Groups
- Experimental, Investigational
- Structure
- Weight
- Average: 227.2172
Monoisotopic: 227.090605919 - Chemical Formula
- C9H13N3O4
- Synonyms
- 1-(2-deoxy-.beta.-d-ribofuranosyl)cytosine
- 4-amino-1-(2-deoxy-.beta.-d-erythro-pentofuranosyl)-2(1h)-pyrimidinone
- dC
- dCYD
- Deoxyribose cytidine
Pharmacology
- Indication
Not Available
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- Pharmacodynamics
Not Available
- Mechanism of action
Target Actions Organism UThymidine kinase 2, mitochondrial Not Available Humans UClass B acid phosphatase Not Available Escherichia coli (strain K12) UDeoxycytidine kinase Not Available Humans - 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 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
- Kingdom
- Organic compounds
- Super Class
- Nucleosides, nucleotides, and analogues
- Class
- Pyrimidine nucleosides
- Sub Class
- Pyrimidine 2'-deoxyribonucleosides
- Direct Parent
- Pyrimidine 2'-deoxyribonucleosides
- Alternative Parents
- Pyrimidones / Aminopyrimidines and derivatives / Imidolactams / Hydropyrimidines / Tetrahydrofurans / Heteroaromatic compounds / Secondary alcohols / Oxacyclic compounds / Azacyclic compounds / Primary amines show 4 more
- Substituents
- Alcohol / Amine / Aminopyrimidine / Aromatic heteromonocyclic compound / Azacycle / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Imidolactam / Organic nitrogen compound show 14 more
- Molecular Framework
- Aromatic heteromonocyclic compounds
- External Descriptors
- pyrimidine 2'-deoxyribonucleoside (CHEBI:15698) / Deoxyribonucleosides (C00881)
- Affected organisms
- Not Available
Chemical Identifiers
- UNII
- 0W860991D6
- CAS number
- 951-77-9
- InChI Key
- CKTSBUTUHBMZGZ-SHYZEUOFSA-N
- InChI
- InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1
- IUPAC Name
- 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
- SMILES
- NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1
References
- Synthesis Reference
Graham A. Mock, Douglas H. Lovern, "N.sup.4 -substituted 2'-deoxycytidine compounds, oligonucleotides including N.sup.4 -labeled 2'-deoxycytidines, and a process for making oligonucleotides with N-modified 2'-deoxycytidines." U.S. Patent US5633364, issued April, 1995.
US5633364- General References
- Not Available
- External Links
- Human Metabolome Database
- HMDB0000014
- KEGG Compound
- C00881
- PubChem Compound
- 13711
- PubChem Substance
- 46508326
- ChemSpider
- 13117
- BindingDB
- 50367094
- ChEBI
- 15698
- ChEMBL
- CHEMBL66115
- ZINC
- ZINC000018286013
- PDBe Ligand
- DCZ
- Wikipedia
- Deoxycytidine
- PDB Entries
- 1j90 / 1p60 / 1p61 / 1rmy / 1vq5 / 1vqp / 2a2z / 2a30 / 2no1 / 2vp5 … show 18 more
Clinical Trials
- Clinical Trials
Pharmacoeconomics
- Manufacturers
- Not Available
- Packagers
- Not Available
- Dosage Forms
- Not Available
- Prices
- Not Available
- Patents
- Not Available
Properties
- State
- Solid
- Experimental Properties
Property Value Source logP -1.77 HANSCH,C ET AL. (1995) - Predicted Properties
Property Value Source Water Solubility 15.9 mg/mL ALOGPS logP -1.9 ALOGPS logP -1.9 Chemaxon logS -1.2 ALOGPS pKa (Strongest Acidic) 13.89 Chemaxon pKa (Strongest Basic) 4.34 Chemaxon Physiological Charge 0 Chemaxon Hydrogen Acceptor Count 6 Chemaxon Hydrogen Donor Count 3 Chemaxon Polar Surface Area 108.38 Å2 Chemaxon Rotatable Bond Count 2 Chemaxon Refractivity 53.03 m3·mol-1 Chemaxon Polarizability 21.65 Å3 Chemaxon Number of Rings 2 Chemaxon Bioavailability 1 Chemaxon Rule of Five Yes Chemaxon Ghose Filter No Chemaxon Veber's Rule No Chemaxon MDDR-like Rule No Chemaxon - Predicted ADMET Features
Property Value Probability Human Intestinal Absorption + 0.9895 Blood Brain Barrier + 0.9493 Caco-2 permeable - 0.8497 P-glycoprotein substrate Non-substrate 0.7317 P-glycoprotein inhibitor I Non-inhibitor 0.9441 P-glycoprotein inhibitor II Non-inhibitor 0.936 Renal organic cation transporter Non-inhibitor 0.9081 CYP450 2C9 substrate Non-substrate 0.8204 CYP450 2D6 substrate Non-substrate 0.8544 CYP450 3A4 substrate Non-substrate 0.549 CYP450 1A2 substrate Non-inhibitor 0.9569 CYP450 2C9 inhibitor Non-inhibitor 0.9449 CYP450 2D6 inhibitor Non-inhibitor 0.9436 CYP450 2C19 inhibitor Non-inhibitor 0.9492 CYP450 3A4 inhibitor Non-inhibitor 0.9546 CYP450 inhibitory promiscuity Low CYP Inhibitory Promiscuity 0.9602 Ames test Non AMES toxic 0.9039 Carcinogenicity Non-carcinogens 0.8058 Biodegradation Not ready biodegradable 0.8507 Rat acute toxicity 1.8867 LD50, mol/kg Not applicable hERG inhibition (predictor I) Weak inhibitor 0.9714 hERG inhibition (predictor II) Non-inhibitor 0.9099
Spectra
- Mass Spec (NIST)
- Not Available
- Spectra
- Chromatographic Properties
Collision Cross Sections (CCS)
Adduct CCS Value (Å2) Source type Source [M-H]- 159.3121992 predictedDarkChem Lite v0.1.0 [M-H]- 159.4940992 predictedDarkChem Lite v0.1.0 [M-H]- 158.9509992 predictedDarkChem Lite v0.1.0 [M-H]- 150.08359 predictedDeepCCS 1.0 (2019) [M+H]+ 159.8305992 predictedDarkChem Lite v0.1.0 [M+H]+ 159.7274992 predictedDarkChem Lite v0.1.0 [M+H]+ 159.8479992 predictedDarkChem Lite v0.1.0 [M+H]+ 152.47914 predictedDeepCCS 1.0 (2019) [M+Na]+ 159.0596992 predictedDarkChem Lite v0.1.0 [M+Na]+ 159.7014992 predictedDarkChem Lite v0.1.0 [M+Na]+ 159.6809992 predictedDarkChem Lite v0.1.0 [M+Na]+ 158.77092 predictedDeepCCS 1.0 (2019)
Targets
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1. DetailsThymidine kinase 2, mitochondrial
- Kind
- Protein
- Organism
- Humans
- Pharmacological action
- Unknown
- General Function
- Thymidine kinase activity
- Specific Function
- Deoxyribonucleoside kinase that phosphorylates thymidine, deoxycytidine, and deoxyuridine. Also phosphorylates anti-viral and anti-cancer nucleoside analogs.
- Gene Name
- TK2
- Uniprot ID
- O00142
- Uniprot Name
- Thymidine kinase 2, mitochondrial
- Molecular Weight
- 31004.53 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. [Article]
- 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]
- Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [Article]
2. DetailsClass B acid phosphatase
- Kind
- Protein
- Organism
- Escherichia coli (strain K12)
- Pharmacological action
- Unknown
- General Function
- Phosphoserine phosphatase activity
- Specific Function
- Dephosphorylates several organic phosphate monoesters including 3'- and 5'-nucleotides, 2'-deoxy-5'-nucleotides, pNPP, phenyl phosphate, glycerol 2-phosphate, ribose 5-phosphate, O-phospho-L-amino ...
- Gene Name
- aphA
- Uniprot ID
- P0AE22
- Uniprot Name
- Class B acid phosphatase
- Molecular Weight
- 26103.29 Da
References
3. DetailsDeoxycytidine kinase
- Kind
- Protein
- Organism
- Humans
- Pharmacological action
- Unknown
- General Function
- Protein homodimerization activity
- Specific Function
- Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based...
- Gene Name
- DCK
- Uniprot ID
- P27707
- Uniprot Name
- Deoxycytidine kinase
- Molecular Weight
- 30518.315 Da
Enzymes
1. DetailsDeoxycytidine kinase
- Kind
- Protein
- Organism
- Humans
- Pharmacological action
- Unknown
- Actions
- Substrate
- General Function
- Protein homodimerization activity
- Specific Function
- Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based...
- Gene Name
- DCK
- Uniprot ID
- P27707
- Uniprot Name
- Deoxycytidine kinase
- Molecular Weight
- 30518.315 Da
References
- Shewach DS, Reynolds KK, Hertel L: Nucleotide specificity of human deoxycytidine kinase. Mol Pharmacol. 1992 Sep;42(3):518-24. [Article]
- Weber G, Singhal RL, Abonyi M, Prajda N, Hata Y, Szekeres T, Yeh A, Look KY: Regulation of deoxycytidine kinase activity and inhibition by DFDC. Adv Enzyme Regul. 1993;33:39-59. [Article]
Drug created at June 13, 2005 13:24 / Updated at January 14, 2023 19:02