ContaminantDB: Emtricitabine

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-05-22 04:26:05 UTC

Update Date

2016-11-09 01:15:36 UTC

Accession Number

CHEM017526

Identification

Common Name

Emtricitabine

Class

Small Molecule

Description

An organofluorine compound that is 5-fluorocytosine substituted at the 1 position by a 2-(hydroxymethyl)-1,3-oxathiolan-5-yl group (2R,5S configuration). It is used in combination therapy for the treatment of HIV-1 infection.

Contaminant Sources

HMDB Contaminants - Urine
STOFF IDENT Compounds
ToxCast & Tox21 Chemicals

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(-)-(2R,5S)-5-Fluoro-1-[2-(hydroxymethyl)-1,3-oxathiolan-5-yl]cytosine	ChEBI
(-)-2'-Deoxy-5-fluoro-3'-thiacytidine	ChEBI
(-)-beta-2',3'-Dideoxy-5-fluoro-3'-thiacytidine	ChEBI
(-)-cis-4-Amino-5-fluoro-1-(2-hydroxymethyl-1,3-oxathiolan-5-yl)-(1H)-pyrimidin-2-one	ChEBI
(-)-FTC	ChEBI
(2R-cis)-4-Amino-5-fluoro-1-(2-(hydroxymethyl)-1,3-oxathiolan-5-yl)-2(1H)-pyrimidinone	ChEBI
4-Amino-5-fluoro-1-((2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl)pyrimidin-2(1H)-one	ChEBI
4-Amino-5-fluoro-1-((2R,5S)-2-hydroxymethyl-[1,3]oxathiolan-5-yl)-1H-pyrimidin-2-one	ChEBI
5-Fluoro-1-((2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl)cytosine	ChEBI
Emtriva	Kegg
ABBR FTC	Kegg
(-)-b-2',3'-Dideoxy-5-fluoro-3'-thiacytidine	Generator
(-)-Β-2',3'-dideoxy-5-fluoro-3'-thiacytidine	Generator
(-)-2',3'-Dideoxy-5-fluoro-3'-thiacytidine	HMDB
(-)-Emtricitabine	HMDB
Coviracil	HMDB
Emtricitabine	HMDB
Beta L 2',3' Dideoxy 5 fluoro 3' thiacytidine	MeSH
beta-L-2',3'-Dideoxy-5-fluoro-3'-thiacytidine	MeSH

Chemical Formula

C₈H₁₀FN₃O₃S

Average Molecular Mass

247.247 g/mol

Monoisotopic Mass

247.043 g/mol

CAS Registry Number

143491-57-0

IUPAC Name

4-amino-5-fluoro-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

emtricitabine

SMILES

NC1=NC(=O)N(C=C1F)[C@@H]1CS[C@H](CO)O1

InChI Identifier

InChI=1S/C8H10FN3O3S/c9-4-1-12(8(14)11-7(4)10)5-3-16-6(2-13)15-5/h1,5-6,13H,2-3H2,(H2,10,11,14)/t5-,6+/m0/s1

InChI Key

XQSPYNMVSIKCOC-NTSWFWBYSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as 3'-thia pyrimidine nucleosides. These are nucleoside analogues with a structure that consists of a pyrimidine base, which is N-substituted at the 1-position with a 3'-thia derivative (1,3-oxazolidine) of the ribose moiety that is characteristic of nucleosides.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Nucleoside and nucleotide analogues

Sub Class

3'-thia pyrimidine nucleosides

Direct Parent

3'-thia pyrimidine nucleosides

Alternative Parents

Substituents

3'-thia pyrimidine nucleoside
Aminopyrimidine
Halopyrimidine
Pyrimidone
Aryl fluoride
Aryl halide
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Monothioacetal
Oxathiolane
Oxacycle
Azacycle
Organoheterocyclic compound
Amine
Organooxygen compound
Organonitrogen compound
Organofluoride
Organohalogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Primary alcohol
Primary amine
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organofluorine compound (CHEBI:31536 )
pyrimidone (CHEBI:31536 )
nucleoside analogue (CHEBI:31536 )
monothioacetal (CHEBI:31536 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	2 g/L	ALOGPS
logP	-0.8	ALOGPS
logP	-0.9	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	14.29	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	88.15 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.37 m³·mol⁻¹	ChemAxon
Polarizability	21.79 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

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-005c-9840000000-916eed674e8dde443d6e	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0fep-8292000000-b2dcf9a13b9a869927cc	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-0udi-0900000000-70cf3fd58a0517da4a55	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-0udi-0900000000-94b3e0720e27e6745a1f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-0udi-0900000000-8dbfc14b46cc1f58e910	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-0udi-0900000000-2dad282fe8707980881d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-0udi-1900000000-efef9ecafd739446f7ae	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-0udi-2900000000-349c2005cbcd9008b160	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-001i-0900000000-6dae6d5531a8a2f408cd	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-001i-0900000000-b8b0b2a41b04924a3ae6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-001i-0900000000-b0b20b1959137a52d9c7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-001i-0900000000-bd2c9f863694963a9078	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-001i-1900000000-9903921aee7742b373e7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-001i-1900000000-8857a02a53df79efbd5c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-001i-0900000000-961f6f9132af62bc5e1e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 15V, Positive	splash10-001i-0900000000-09ba1f683ca6a306fa48	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 45V, Positive	splash10-001i-0900000000-85e4574e24a912428e0d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 75V, Negative	splash10-0udi-1900000000-98f516d8a1dfac9bd187	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 90V, Negative	splash10-0udi-2900000000-d38aba7b54ffd5599634	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 60V, Positive	splash10-001i-0900000000-77bf43e48b391e0cc9e6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-0udi-0900000000-f3f824943162b24c1e4f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-0920000000-810d7a7def89643865a6	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-1900000000-009baab415006b7bc307	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-6900000000-4ee98d10e3447b6c66ac	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002b-2390000000-77ee7291923983e61f8b	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ukl-1910000000-fa4bf50b1d66f4072746	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9100000000-634ee8be27db1e259199	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum