NAV

2'-Deoxycytidine-5'-Monophosphate

Identification

Generic Name
2'-Deoxycytidine-5'-Monophosphate
DrugBank Accession Number
DB03798
Background

Deoxycytidine (dihydrogen phosphate). A deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions. [PubChem]

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 307.1971
Monoisotopic: 307.056936329
Chemical Formula
C9H14N3O7P
Synonyms
Not Available
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Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UThymidylate synthaseNot AvailableLactobacillus casei
UDeoxycytidylate 5-hydroxymethyltransferaseNot AvailableEnterobacteria phage T4
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
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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'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Pyrimidine nucleotides
Sub Class
Pyrimidine deoxyribonucleotides
Direct Parent
Pyrimidine 2'-deoxyribonucleoside monophosphates
Alternative Parents
Pyrimidones / Monoalkyl phosphates / Aminopyrimidines and derivatives / Imidolactams / Hydropyrimidines / Tetrahydrofurans / Heteroaromatic compounds / Secondary alcohols / Oxacyclic compounds / Azacyclic compounds
show 4 more
Substituents
Alcohol / Alkyl phosphate / Amine / Aminopyrimidine / Aromatic heteromonocyclic compound / Azacycle / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Imidolactam
show 17 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
2'-deoxycytidine phosphate, pyrimidine 2'-deoxyribonucleoside 5'-monophosphate (CHEBI:15918) / Deoxyribonucleotides (C00239)
Affected organisms
Not Available

Chemical Identifiers

UNII
W7A9174XQL
CAS number
1032-65-1
InChI Key
NCMVOABPESMRCP-SHYZEUOFSA-N
InChI
InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
IUPAC Name
{[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid
SMILES
NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1

References

General References
Not Available
Human Metabolome Database
HMDB0001202
KEGG Compound
C00239
PubChem Compound
13945
PubChem Substance
46506941
ChemSpider
13343
ChEBI
15918
ChEMBL
CHEMBL374699
ZINC
ZINC000003861759
PDBe Ligand
DC
PDB Entries
1b5d / 1b5e / 1nja / 1njc / 1nje / 1p3x / 2jat / 2qrn / 3g2r / 4p9c …
show 14 more

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 Solubility10.9 mg/mLALOGPS
logP-2.1ALOGPS
logP-2Chemaxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1.15Chemaxon
pKa (Strongest Basic)4.31Chemaxon
Physiological Charge-2Chemaxon
Hydrogen Acceptor Count8Chemaxon
Hydrogen Donor Count4Chemaxon
Polar Surface Area154.91 Å2Chemaxon
Rotatable Bond Count4Chemaxon
Refractivity63.91 m3·mol-1Chemaxon
Polarizability26.2 Å3Chemaxon
Number of Rings2Chemaxon
Bioavailability1Chemaxon
Rule of FiveYesChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption+0.6265
Blood Brain Barrier+0.9534
Caco-2 permeable-0.7477
P-glycoprotein substrateNon-substrate0.73
P-glycoprotein inhibitor INon-inhibitor0.8898
P-glycoprotein inhibitor IINon-inhibitor0.9777
Renal organic cation transporterNon-inhibitor0.9289
CYP450 2C9 substrateNon-substrate0.8188
CYP450 2D6 substrateNon-substrate0.8405
CYP450 3A4 substrateNon-substrate0.545
CYP450 1A2 substrateNon-inhibitor0.902
CYP450 2C9 inhibitorNon-inhibitor0.8715
CYP450 2D6 inhibitorNon-inhibitor0.9106
CYP450 2C19 inhibitorNon-inhibitor0.8763
CYP450 3A4 inhibitorNon-inhibitor0.9123
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9587
Ames testNon AMES toxic0.6365
CarcinogenicityNon-carcinogens0.8089
BiodegradationNot ready biodegradable0.8825
Rat acute toxicity2.3403 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9691
hERG inhibition (predictor II)Non-inhibitor0.8709
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-MSsplash10-0002-9410000000-f31bf162f5f972b9cf42
MS/MS Spectrum - Quattro_QQQ 10V, PositiveLC-MS/MSsplash10-03di-0900000000-01bb64efeca205daaf6e
MS/MS Spectrum - Quattro_QQQ 25V, PositiveLC-MS/MSsplash10-03di-1900000000-13c56ec900e188e10ddb
MS/MS Spectrum - Quattro_QQQ 40V, PositiveLC-MS/MSsplash10-03di-5900000000-4e6dd8fdc8a4142269a2
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-03di-0903000000-a66e39f0cbf3a7744ca5
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0a6r-4009000000-0f6b6ff10fea826feb5e
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-03di-1900000000-ec0f85a0fe0859dc0353
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9010000000-c552cbf0244546b3c386
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-03di-2900000000-d401a52f8cc81e24d2bd
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9310000000-2450ffdaba84f2270a1e
1H NMR Spectrum1D NMRNot Applicable
Predicted 1H NMR Spectrum1D NMRNot Applicable
Predicted 13C NMR Spectrum1D NMRNot Applicable
[1H,13C] 2D NMR Spectrum2D NMRNot Applicable
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-180.9882042
predicted
DarkChem Lite v0.1.0
[M-H]-180.7472042
predicted
DarkChem Lite v0.1.0
[M-H]-156.99477
predicted
DeepCCS 1.0 (2019)
[M+H]+181.6033042
predicted
DarkChem Lite v0.1.0
[M+H]+181.1717042
predicted
DarkChem Lite v0.1.0
[M+H]+159.39034
predicted
DeepCCS 1.0 (2019)
[M+Na]+181.1947042
predicted
DarkChem Lite v0.1.0
[M+Na]+180.5265042
predicted
DarkChem Lite v0.1.0
[M+Na]+165.8434
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. Thymidylate synthase
Kind
Protein
Organism
Lactobacillus casei
Pharmacological action
Unknown
General Function
Thymidylate synthase activity
Specific Function
Provides the sole de novo source of dTMP for DNA biosynthesis.
Gene Name
thyA
Uniprot ID
P00469
Uniprot Name
Thymidylate synthase
Molecular Weight
36579.235 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]
Details2. Deoxycytidylate 5-hydroxymethyltransferase
Kind
Protein
Organism
Enterobacteria phage T4
Pharmacological action
Unknown
General Function
Thymidylate synthase activity
Specific Function
Not Available
Gene Name
42
Uniprot ID
P08773
Uniprot Name
Deoxycytidylate 5-hydroxymethyltransferase
Molecular Weight
28489.065 Da

Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52