2'-Deoxycytidine

Identification

Name
2'-Deoxycytidine
Accession Number
DB02594  (EXPT01140)
Type
Small Molecule
Groups
Experimental, Investigational
Description
Not Available
Structure
Thumb
Synonyms
  • 1-(2-deoxy-.beta.-d-ribofuranosyl)cytosine
  • 4-amino-1-(2-deoxy-.beta.-d-erythro-pentofuranosyl)-2(1h)-pyrimidinone
  • dC
  • dCYD
  • Deoxyribose cytidine
Categories
Not Available
UNII
0W860991D6
CAS number
951-77-9
Weight
Average: 227.2172
Monoisotopic: 227.090605919
Chemical Formula
C9H13N3O4
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)[[email protected]]1C[[email protected]](O)[[email protected]@H](CO)O1

Pharmacology

Indication
Not Available
Structured Indications
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UThymidine kinase 2, mitochondrialNot AvailableHuman
UClass B acid phosphataseNot AvailableEscherichia coli (strain K12)
UDeoxycytidine kinaseNot AvailableHuman
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
Toxicity
Not Available
Affected organisms
Not Available
Pathways
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

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
HMDB00014
KEGG Compound
C00881
PubChem Compound
13711
PubChem Substance
46508326
ChemSpider
13117
BindingDB
50367094
ChEBI
15698
ChEMBL
CHEMBL66115
HET
DCZ
Wikipedia
Deoxycytidine
PDB Entries
1j90 / 1p60 / 1p61 / 1rmy / 1vq5 / 1vqp / 2a2z / 2a30 / 2no1 / 2vp5
show 12 more

Clinical Trials

Clinical Trials
PhaseStatusPurposeConditionsCount
1CompletedPreventionNeoplasms, Brain1
1CompletedTreatmentDrug/Agent Toxicity by Tissue/Organ / Leukemias / Malignant Lymphomas / Multiple Myeloma and Plasma Cell Neoplasm1
1CompletedTreatmentHealthy Volunteers1
2RecruitingTreatmentMalignant Neoplasm of Stomach1
Not AvailableCompletedTreatmentAbdominal Subcutaneous Fat1

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
PropertyValueSource
logP-1.77HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
Water Solubility15.9 mg/mLALOGPS
logP-1.9ALOGPS
logP-1.9ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)13.89ChemAxon
pKa (Strongest Basic)-0.0012ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area108.38 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity53.03 m3·mol-1ChemAxon
Polarizability21.65 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption+0.9895
Blood Brain Barrier+0.9493
Caco-2 permeable-0.8497
P-glycoprotein substrateNon-substrate0.7317
P-glycoprotein inhibitor INon-inhibitor0.9441
P-glycoprotein inhibitor IINon-inhibitor0.936
Renal organic cation transporterNon-inhibitor0.9081
CYP450 2C9 substrateNon-substrate0.8204
CYP450 2D6 substrateNon-substrate0.8544
CYP450 3A4 substrateNon-substrate0.549
CYP450 1A2 substrateNon-inhibitor0.9569
CYP450 2C9 inhibitorNon-inhibitor0.9449
CYP450 2D6 inhibitorNon-inhibitor0.9436
CYP450 2C19 inhibitorNon-inhibitor0.9492
CYP450 3A4 inhibitorNon-inhibitor0.9546
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9602
Ames testNon AMES toxic0.9039
CarcinogenicityNon-carcinogens0.8058
BiodegradationNot ready biodegradable0.8507
Rat acute toxicity1.8867 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9714
hERG inhibition (predictor II)Non-inhibitor0.9099
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 GC-MS Spectrum - GC-MSPredicted GC-MSNot Available
MS/MS Spectrum - Quattro_QQQ 10V, PositiveLC-MS/MSsplash10-03di-0900000000-27431bdd2327f6f2b886
MS/MS Spectrum - Quattro_QQQ 25V, PositiveLC-MS/MSsplash10-03di-1900000000-0ea85f3f3940843e385b
MS/MS Spectrum - Quattro_QQQ 40V, PositiveLC-MS/MSsplash10-03dl-9500000000-569e473eba0b700f5b6e
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, NegativeLC-MS/MSsplash10-004i-0090000000-5c8c0fde4f2163fbc335
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, NegativeLC-MS/MSsplash10-0006-9420000000-28279714b575d59761ce
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, NegativeLC-MS/MSsplash10-0006-9200000000-df7c76b755c9fac5267b
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, NegativeLC-MS/MSsplash10-0006-9100000000-acbd1d7557be6d716a19
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, NegativeLC-MS/MSsplash10-00kf-9100000000-056ef35d3aa743e0d5cf
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, PositiveLC-MS/MSsplash10-03di-0910000000-52e9d173bb94576f7d9e
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, PositiveLC-MS/MSsplash10-03di-0900000000-e06e5a9f19c4162aa24f
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, PositiveLC-MS/MSsplash10-03di-0900000000-551d8ee9679ef3fb65fa
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, PositiveLC-MS/MSsplash10-03di-3900000000-4c62633283ba566dbee0
LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , PositiveLC-MS/MSsplash10-03di-0900000000-bac3656523b118a2c1bc
LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , PositiveLC-MS/MSsplash10-03dj-6900000000-dfa8435d3dd8b8981621
LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , PositiveLC-MS/MSsplash10-01t9-0690000000-72302b09c51553dde169
LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, PositiveLC-MS/MSsplash10-03fr-0930000000-f5c80400a73719f6211f
LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , NegativeLC-MS/MSsplash10-0006-9130000000-c7f95a478d22e3cc83f4
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSNot Available
LC-MS/MS Spectrum - LC-ESI-QQ , negativeLC-MS/MSsplash10-004i-0090000000-af75883dba546c82e7bc
LC-MS/MS Spectrum - LC-ESI-QQ , negativeLC-MS/MSsplash10-0006-9420000000-562a675c6278a4ae2bc4
LC-MS/MS Spectrum - LC-ESI-QQ , negativeLC-MS/MSsplash10-0006-9200000000-297a4fef750eac4c8d96
LC-MS/MS Spectrum - LC-ESI-QQ , negativeLC-MS/MSsplash10-0006-9100000000-acbd1d7557be6d716a19
LC-MS/MS Spectrum - LC-ESI-QQ , negativeLC-MS/MSsplash10-00kf-9100000000-c8d290006792e43e5246
LC-MS/MS Spectrum - LC-ESI-QTOF , negativeLC-MS/MSsplash10-0006-9130000000-441cdea7b1e92a12d0f9
MS/MS Spectrum - , negativeLC-MS/MSsplash10-0006-9100000000-860c1c1204e23d4b2b74
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-03di-0910000000-52e9d173bb94576f7d9e
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-03di-0900000000-e06e5a9f19c4162aa24f
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-03di-0900000000-551d8ee9679ef3fb65fa
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-03di-3900000000-6d5290db43d9b03bdf61
LC-MS/MS Spectrum - LC-ESI-IT , positiveLC-MS/MSsplash10-03di-0900000000-05258818a022f0a66a09
LC-MS/MS Spectrum - LC-ESI-QTOF , positiveLC-MS/MSsplash10-01t9-0690000000-811636cc0d40f8dbc6f9
LC-MS/MS Spectrum - LC-ESI-QTOF , positiveLC-MS/MSsplash10-03fr-0930000000-f5c80400a73719f6211f
MS/MS Spectrum - , positiveLC-MS/MSsplash10-03di-0900000000-f0442ccd83b2ddf8260a
1H NMR Spectrum1D NMRNot Applicable
13C NMR Spectrum1D NMRNot Applicable
[1H,13C] 2D NMR Spectrum2D NMRNot Applicable

Taxonomy

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
Pyrimidine 2'-deoxyribonucleoside / Aminopyrimidine / Pyrimidone / Hydropyrimidine / Pyrimidine / Imidolactam / Heteroaromatic compound / Tetrahydrofuran / Secondary alcohol / Azacycle
show 14 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
pyrimidine 2'-deoxyribonucleoside (CHEBI:15698) / Deoxyribonucleosides (C00881)

Targets

Kind
Protein
Organism
Human
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
  1. 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]
  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. [PubMed:17016423]
  3. 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. [PubMed:10592235]
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
  1. 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]
  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. [PubMed:17016423]
Kind
Protein
Organism
Human
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

Kind
Protein
Organism
Human
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

Drug created on June 13, 2005 07:24 / Updated on November 09, 2017 03:16