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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:51 UTC

Update Date

2022-03-07 02:51:49 UTC

HMDB ID

HMDB0015017

Secondary Accession Numbers

HMDB15017

Metabolite Identification

Common Name

Emtricitabine

Description

Emtricitabine 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

879
  Mrv0541 02231215042D          

 16 17  0  0  1  0            999 V2000
    2.6665   -1.4952    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    2.2494    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.7465   -0.7106    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6409   -2.9164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.5994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.5994    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    1.8369    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    3.0744    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.2256    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4115   -0.7106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4916   -1.4952    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9764   -2.1627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    1.0119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    1.0119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    1.8369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    2.2494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  1 11  1  0  0  0  0
  2 15  1  0  0  0  0
  3  9  1  0  0  0  0
  3 11  1  0  0  0  0
  4 12  1  0  0  0  0
  5 14  2  0  0  0  0
  9  6  1  1  0  0  0
  6 13  1  0  0  0  0
  6 14  1  0  0  0  0
  7 14  1  0  0  0  0
  7 16  2  0  0  0  0
  8 16  1  0  0  0  0
  9 10  1  0  0  0  0
 11 12  1  1  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0015017

> <DATABASE_NAME>
hmdb

> <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

> <FORMULA>
C8H10FN3O3S

> <MOLECULAR_WEIGHT>
247.247

> <EXACT_MASS>
247.042690096

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
21.791009606969588

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.80

> <JCHEM_LOGP>
-0.8956646779999999

> <ALOGPS_LOGS>
-2.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.294605874877231

> <JCHEM_PKA_STRONGEST_BASIC>
-3.107339390328698

> <JCHEM_POLAR_SURFACE_AREA>
88.15

> <JCHEM_REFRACTIVITY>
55.367399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
emtricitabine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 879                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  S   UNK     0       4.977  -2.791   0.000  0.00  0.00           S+0
HETATM    2  F   UNK     0       8.415   4.199   0.000  0.00  0.00           F+0
HETATM    3  O   UNK     0       6.993  -1.326   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       6.796  -5.444   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       3.080   1.119   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       5.748   1.119   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       4.414   3.429   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       5.748   5.739   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       5.748  -0.421   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.501  -1.326   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.518  -2.791   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.423  -4.037   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.081   1.889   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.414   1.889   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.081   3.429   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.748   4.199   0.000  0.00  0.00           C+0
CONECT    1   10   11                                                       
CONECT    2   15                                                            
CONECT    3    9   11                                                       
CONECT    4   12                                                            
CONECT    5   14                                                            
CONECT    6    9   13   14                                                  
CONECT    7   14   16                                                       
CONECT    8   16                                                            
CONECT    9    3    6   10                                                  
CONECT   10    1    9                                                       
CONECT   11    1    3   12                                                  
CONECT   12    4   11                                                       
CONECT   13    6   15                                                       
CONECT   14    5    6    7                                                  
CONECT   15    2   13   16                                                  
CONECT   16    7    8   15                                                  
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol View NMR Assignments View Stereo Labels

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 Weight

247.247

Monoisotopic Molecular Weight

247.042690096

IUPAC Name

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

Traditional Name

emtricitabine

CAS Registry Number

143491-57-0

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 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 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Cytoplasm (HMDB: HMDB0015017)

Source

Exogenous

Exogenous (HMDB: HMDB0015017)

Process

Naturally occurring process

Biological process

Biochemical pathway

Drug action pathway

Emtricitabine Action Pathway (PathBank: SMP0000741)

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	136 - 140 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	2 g/L	Not Available
LogP	-1.4	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular 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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	150.376	30932474
DeepCCS	[M-H]-	147.981	30932474
DeepCCS	[M-2H]-	181.044	30932474
DeepCCS	[M+Na]+	156.395	30932474
AllCCS	[M+H]+	152.3	32859911
AllCCS	[M+H-H2O]+	148.6	32859911
AllCCS	[M+NH4]+	155.7	32859911
AllCCS	[M+Na]+	156.7	32859911
AllCCS	[M-H]-	150.0	32859911
AllCCS	[M+Na-2H]-	150.2	32859911
AllCCS	[M+HCOO]-	150.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	2.26 minutes	32390414
Predicted by Siyang on May 30, 2022	9.9118 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.37 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	29.9 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	877.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	275.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	95.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	170.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	70.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	302.3 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	326.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	115.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	729.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	275.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	807.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	228.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	203.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	380.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	251.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	114.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Emtricitabine	NC1=NC(=O)N(C=C1F)[C@@H]1CS[C@H](CO)O1	3529.9	Standard polar	33892256
Emtricitabine	NC1=NC(=O)N(C=C1F)[C@@H]1CS[C@H](CO)O1	2246.4	Standard non polar	33892256
Emtricitabine	NC1=NC(=O)N(C=C1F)[C@@H]1CS[C@H](CO)O1	2481.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Emtricitabine,1TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N)=NC2=O)CS1	2286.5	Semi standard non polar	33892256
Emtricitabine,1TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F	2310.0	Semi standard non polar	33892256
Emtricitabine,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO[Si](C)(C)C)O2)C=C1F	2378.8	Semi standard non polar	33892256
Emtricitabine,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO[Si](C)(C)C)O2)C=C1F	2048.1	Standard non polar	33892256
Emtricitabine,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO[Si](C)(C)C)O2)C=C1F	3158.8	Standard polar	33892256
Emtricitabine,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F)[Si](C)(C)C	2336.6	Semi standard non polar	33892256
Emtricitabine,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F)[Si](C)(C)C	2239.2	Standard non polar	33892256
Emtricitabine,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F)[Si](C)(C)C	3225.2	Standard polar	33892256
Emtricitabine,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CS1	2382.5	Semi standard non polar	33892256
Emtricitabine,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CS1	2318.6	Standard non polar	33892256
Emtricitabine,3TMS,isomer #1	C[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CS1	2803.2	Standard polar	33892256
Emtricitabine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N)=NC2=O)CS1	2536.5	Semi standard non polar	33892256
Emtricitabine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F	2553.1	Semi standard non polar	33892256
Emtricitabine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1F	2816.7	Semi standard non polar	33892256
Emtricitabine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1F	2428.4	Standard non polar	33892256
Emtricitabine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2CS[C@H](CO[Si](C)(C)C(C)(C)C)O2)C=C1F	3218.1	Standard polar	33892256
Emtricitabine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F)[Si](C)(C)C(C)(C)C	2765.6	Semi standard non polar	33892256
Emtricitabine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F)[Si](C)(C)C(C)(C)C	2755.4	Standard non polar	33892256
Emtricitabine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@@H]2CS[C@H](CO)O2)C=C1F)[Si](C)(C)C(C)(C)C	3195.9	Standard polar	33892256
Emtricitabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CS1	3003.8	Semi standard non polar	33892256
Emtricitabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CS1	3009.9	Standard non polar	33892256
Emtricitabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@@H]1O[C@H](N2C=C(F)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CS1	3023.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Emtricitabine GC-MS (Non-derivatized) - 70eV, Positive	splash10-005c-9840000000-916eed674e8dde443d6e	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Emtricitabine GC-MS (1 TMS) - 70eV, Positive	splash10-0fep-8292000000-b2dcf9a13b9a869927cc	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Emtricitabine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Emtricitabine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOF	splash10-0udi-0900000000-70cf3fd58a0517da4a55	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOF	splash10-0udi-0900000000-94b3e0720e27e6745a1f	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOF	splash10-0udi-0900000000-8dbfc14b46cc1f58e910	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOF	splash10-0udi-0900000000-2dad282fe8707980881d	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOF	splash10-0udi-1900000000-efef9ecafd739446f7ae	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , negative-QTOF	splash10-0udi-2900000000-349c2005cbcd9008b160	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOF	splash10-001i-0900000000-6dae6d5531a8a2f408cd	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOF	splash10-001i-0900000000-b8b0b2a41b04924a3ae6	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOF	splash10-001i-0900000000-b0b20b1959137a52d9c7	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOF	splash10-001i-0900000000-bd2c9f863694963a9078	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOF	splash10-001i-1900000000-9903921aee7742b373e7	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine LC-ESI-QFT , positive-QTOF	splash10-001i-1900000000-8857a02a53df79efbd5c	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine 30V, Positive-QTOF	splash10-001i-0900000000-961f6f9132af62bc5e1e	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine 15V, Positive-QTOF	splash10-001i-0900000000-09ba1f683ca6a306fa48	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine 45V, Positive-QTOF	splash10-001i-0900000000-85e4574e24a912428e0d	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine 75V, Negative-QTOF	splash10-0udi-1900000000-98f516d8a1dfac9bd187	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine 90V, Negative-QTOF	splash10-0udi-2900000000-d38aba7b54ffd5599634	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine 60V, Positive-QTOF	splash10-001i-0900000000-77bf43e48b391e0cc9e6	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Emtricitabine 30V, Negative-QTOF	splash10-0udi-0900000000-f3f824943162b24c1e4f	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Emtricitabine 10V, Positive-QTOF	splash10-001i-0920000000-810d7a7def89643865a6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Emtricitabine 20V, Positive-QTOF	splash10-001i-1900000000-009baab415006b7bc307	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Emtricitabine 40V, Positive-QTOF	splash10-001i-6900000000-4ee98d10e3447b6c66ac	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Emtricitabine 10V, Negative-QTOF	splash10-002b-2390000000-77ee7291923983e61f8b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Emtricitabine 20V, Negative-QTOF	splash10-0ukl-1910000000-fa4bf50b1d66f4072746	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Emtricitabine 40V, Negative-QTOF	splash10-00di-9100000000-634ee8be27db1e259199	2016-08-03	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Emtricitabine Action Pathway		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00879	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00879	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00879

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

54859

KEGG Compound ID

C12599

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Emtricitabine

METLIN ID

Not Available

PubChem Compound

60877

PDB ID

Not Available

ChEBI ID

31536

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Authors unspecified: Emtricitabine/tenofovir disoproxil fumarate. Drugs R D. 2004;5(3):160-1. [PubMed:15139777 ]
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 ]
Masho SW, Wang CL, Nixon DE: Review of tenofovir-emtricitabine. Ther Clin Risk Manag. 2007 Dec;3(6):1097-104. [PubMed:18516268 ]
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

Enzyme Details

1. Deoxycytidine kinase

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

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 ]

Showing metabocard for Emtricitabine (HMDB0015017)

MOL for HMDB0015017 (Emtricitabine)

3D MOL for HMDB0015017 (Emtricitabine)

3D SDF for HMDB0015017 (Emtricitabine)

3D-SDF for HMDB0015017 (Emtricitabine)

PDB for HMDB0015017 (Emtricitabine)

3D PDB for HMDB0015017 (Emtricitabine)

SMILES for HMDB0015017 (Emtricitabine)

INCHI for HMDB0015017 (Emtricitabine)

Structure for HMDB0015017 (Emtricitabine)

3D Structure for HMDB0015017 (Emtricitabine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

References