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Record Information
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:51 UTC
Update Date2020-02-26 21:40:48 UTC
Secondary Accession Numbers
  • HMDB15017
Metabolite Identification
Common NameEmtricitabine
DescriptionEmtricitabine is only found in individuals that have used or taken this drug. It is a nucleoside reverse transcriptase inhibitor (NRTI) for the treatment of human immunodeficiency virus type 1 (HIV-1) infection in adults. Emtricitabine works by inhibiting reverse transcriptase (RT), an enzyme that allows the virus to multiply by copying HIV RNA into new viral DNA. The drug competes with the reverse transcriptase's natural substrate deoxycytidine 5'-triphosphate and also becomes incorporated into viral DNA. This is a result of emtricitabine being a synthetic nucleoside analogue of cytidine. It is phosphorylated by cellular enzymes to form emtricitabine 5'-triphosphate which competes with the natural substrate deoxycytidine 5'-triphosphate and becomes incorporated into nascent viral DNA, resulting in early chain termination. By inhibiting HIV-1 reverse transcriptase, emtricitabine can help to lower the amount of HIV (viral load) in a patient's body and can indirectly increase the number of immune system cells (T cells or CD4+ T-cells). Both of these changes are associated with healthier immune systems and a decreased likelihood of serious illness. Emtricitabine is always used in conjunction with other HIV medicine to treat people with HIV infection.
Chemical FormulaC8H10FN3O3S
Average Molecular Weight247.247
Monoisotopic Molecular Weight247.042690096
IUPAC Name4-amino-5-fluoro-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-1,2-dihydropyrimidin-2-one
Traditional Nameemtricitabine
CAS Registry Number143491-57-0
InChI Identifier
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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassNucleoside and nucleotide analogues
Sub Class3'-thia pyrimidine nucleosides
Direct Parent3'-thia pyrimidine nucleosides
Alternative Parents
  • 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 FrameworkAromatic heteromonocyclic compounds
External Descriptors

Biological location:


Naturally occurring process:


Industrial application:

Physical Properties
Experimental Properties
Melting Point136 - 140 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility2 g/LNot Available
LogP-1.4Not Available
Predicted Properties
Water Solubility2 g/LALOGPS
pKa (Strongest Acidic)14.29ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area88.15 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity55.37 m³·mol⁻¹ChemAxon
Polarizability21.79 ųChemAxon
Number of Rings2ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-005c-9840000000-916eed674e8dde443d6eSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0fep-8292000000-b2dcf9a13b9a869927ccSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , negativesplash10-0udi-0900000000-70cf3fd58a0517da4a55Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , negativesplash10-0udi-0900000000-94b3e0720e27e6745a1fSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , negativesplash10-0udi-0900000000-8dbfc14b46cc1f58e910Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , negativesplash10-0udi-0900000000-2dad282fe8707980881dSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , negativesplash10-0udi-1900000000-efef9ecafd739446f7aeSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , negativesplash10-0udi-2900000000-349c2005cbcd9008b160Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , positivesplash10-001i-0900000000-6dae6d5531a8a2f408cdSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , positivesplash10-001i-0900000000-b8b0b2a41b04924a3ae6Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , positivesplash10-001i-0900000000-b0b20b1959137a52d9c7Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , positivesplash10-001i-0900000000-bd2c9f863694963a9078Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , positivesplash10-001i-1900000000-9903921aee7742b373e7Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT , positivesplash10-001i-1900000000-8857a02a53df79efbd5cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0920000000-810d7a7def89643865a6Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-1900000000-009baab415006b7bc307Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-6900000000-4ee98d10e3447b6c66acSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002b-2390000000-77ee7291923983e61f8bSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ukl-1910000000-fa4bf50b1d66f4072746Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-9100000000-634ee8be27db1e259199Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Normal Concentrations
BloodExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB00879 details
UrineExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB00879 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00879
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID54859
KEGG Compound IDC12599
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkEmtricitabine
METLIN IDNot Available
PubChem Compound60877
PDB IDNot Available
ChEBI ID31536
Food Biomarker OntologyNot Available
VMH IDNot Available
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Authors unspecified: Emtricitabine/tenofovir disoproxil fumarate. Drugs R D. 2004;5(3):160-1. [PubMed:15139777 ]
  2. Goicoechea M, Best B: Efavirenz/emtricitabine/tenofovir disoproxil fumarate fixed-dose combination: first-line therapy for all? Expert Opin Pharmacother. 2007 Feb;8(3):371-82. [PubMed:17266471 ]
  3. Masho SW, Wang CL, Nixon DE: Review of tenofovir-emtricitabine. Ther Clin Risk Manag. 2007 Dec;3(6):1097-104. [PubMed:18516268 ]
  4. Long MC, King JR, Acosta EP: Pharmacologic aspects of new antiretroviral drugs. Curr HIV/AIDS Rep. 2009 Feb;6(1):43-50. [PubMed:19149996 ]


General function:
Involved in ATP binding
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 on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.
Gene Name:
Uniprot ID:
Molecular weight:
  1. Bethell R, De Muys J, Lippens J, Richard A, Hamelin B, Ren C, Collins P: In vitro interactions between apricitabine and other deoxycytidine analogues. Antimicrob Agents Chemother. 2007 Aug;51(8):2948-53. Epub 2007 May 21. [PubMed:17517847 ]