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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:51 UTC
Update Date2021-09-14 14:57:36 UTC
HMDB IDHMDB0015017
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.
Structure
Data?1582753248
Synonyms
ValueSource
(-)-(2R,5S)-5-Fluoro-1-[2-(hydroxymethyl)-1,3-oxathiolan-5-yl]cytosineChEBI
(-)-2'-Deoxy-5-fluoro-3'-thiacytidineChEBI
(-)-beta-2',3'-Dideoxy-5-fluoro-3'-thiacytidineChEBI
(-)-cis-4-Amino-5-fluoro-1-(2-hydroxymethyl-1,3-oxathiolan-5-yl)-(1H)-pyrimidin-2-oneChEBI
(-)-FTCChEBI
(2R-cis)-4-Amino-5-fluoro-1-(2-(hydroxymethyl)-1,3-oxathiolan-5-yl)-2(1H)-pyrimidinoneChEBI
4-Amino-5-fluoro-1-((2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl)pyrimidin-2(1H)-oneChEBI
4-Amino-5-fluoro-1-((2R,5S)-2-hydroxymethyl-[1,3]oxathiolan-5-yl)-1H-pyrimidin-2-oneChEBI
5-Fluoro-1-((2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl)cytosineChEBI
EmtrivaKegg
ABBR FTCKegg
(-)-b-2',3'-Dideoxy-5-fluoro-3'-thiacytidineGenerator
(-)-Β-2',3'-dideoxy-5-fluoro-3'-thiacytidineGenerator
(-)-2',3'-Dideoxy-5-fluoro-3'-thiacytidineHMDB
(-)-EmtricitabineHMDB
CoviracilHMDB
EmtricitabineHMDB
Beta L 2',3' Dideoxy 5 fluoro 3' thiacytidineMeSH
beta-L-2',3'-Dideoxy-5-fluoro-3'-thiacytidineMeSH
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
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 KeyXQSPYNMVSIKCOC-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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassNucleoside and nucleotide analogues
Sub Class3'-thia pyrimidine nucleosides
Direct Parent3'-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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point136 - 140 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility2 g/LNot Available
LogP-1.4Not Available
Experimental Spectral PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility2 g/LALOGPS
logP10(-0.8) g/LALOGPS
logP10(-0.9) g/LChemAxon
logS10(-2.1) 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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Emtricitabine,1TMS,#1C[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N)=NC2=O)CS12286.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Emtricitabine,1TMS,#2C[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F2310.0Semi standard non polarhttps://arxiv.org/abs/1905.12712
Emtricitabine,1TBDMS,#1CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N)=NC2=O)CS12536.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Emtricitabine,1TBDMS,#2CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F2553.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Emtricitabine GC-MS (Non-derivatized) - 70eV, Positivesplash10-005c-9840000000-916eed674e8dde443d6e2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Emtricitabine GC-MS (1 TMS) - 70eV, Positivesplash10-0fep-8292000000-b2dcf9a13b9a869927cc2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Emtricitabine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Emtricitabine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOFsplash10-0udi-0900000000-70cf3fd58a0517da4a552017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOFsplash10-0udi-0900000000-94b3e0720e27e6745a1f2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOFsplash10-0udi-0900000000-8dbfc14b46cc1f58e9102017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOFsplash10-0udi-0900000000-2dad282fe8707980881d2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOFsplash10-0udi-1900000000-efef9ecafd739446f7ae2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOFsplash10-0udi-2900000000-349c2005cbcd9008b1602017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOFsplash10-001i-0900000000-6dae6d5531a8a2f408cd2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOFsplash10-001i-0900000000-b8b0b2a41b04924a3ae62017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOFsplash10-001i-0900000000-b0b20b1959137a52d9c72017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOFsplash10-001i-0900000000-bd2c9f863694963a90782017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOFsplash10-001i-1900000000-9903921aee7742b373e72017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOFsplash10-001i-1900000000-8857a02a53df79efbd5c2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine 30V, Positive-QTOFsplash10-001i-0900000000-961f6f9132af62bc5e1e2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine 15V, Positive-QTOFsplash10-001i-0900000000-09ba1f683ca6a306fa482021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine 45V, Positive-QTOFsplash10-001i-0900000000-85e4574e24a912428e0d2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine 75V, Negative-QTOFsplash10-0udi-1900000000-98f516d8a1dfac9bd1872021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine 90V, Negative-QTOFsplash10-0udi-2900000000-d38aba7b54ffd55996342021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine 60V, Positive-QTOFsplash10-001i-0900000000-77bf43e48b391e0cc9e62021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Emtricitabine 30V, Negative-QTOFsplash10-0udi-0900000000-f3f824943162b24c1e4f2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Emtricitabine 10V, Positive-QTOFsplash10-001i-0920000000-810d7a7def89643865a62016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Emtricitabine 20V, Positive-QTOFsplash10-001i-1900000000-009baab415006b7bc3072016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Emtricitabine 40V, Positive-QTOFsplash10-001i-6900000000-4ee98d10e3447b6c66ac2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Emtricitabine 10V, Negative-QTOFsplash10-002b-2390000000-77ee7291923983e61f8b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Emtricitabine 20V, Negative-QTOFsplash10-0ukl-1910000000-fa4bf50b1d66f40727462016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Emtricitabine 40V, Negative-QTOFsplash10-00di-9100000000-634ee8be27db1e2591992016-08-03Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00879 details
UrineExpected but not QuantifiedNot QuantifiedNot 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
MarkerDB IDNot Available
Good Scents IDNot Available
References
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 ]

Enzymes

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:
DCK
Uniprot ID:
P27707
Molecular weight:
30518.315
References
  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 ]