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Record Information
StatusExpected but not Quantified
Creation Date2006-05-22 15:12:47 UTC
Update Date2020-02-26 21:24:29 UTC
Secondary Accession Numbers
  • HMDB03288
Metabolite Identification
Common NameSelenocysteine
DescriptionSelenocysteine, also known as 3-seleno-alanine, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. Selenocysteine is a drug. Selenocysteine is a very strong basic compound (based on its pKa). Selenocysteine exists in all living species, ranging from bacteria to humans. Within humans, selenocysteine participates in a number of enzymatic reactions. In particular, selenocysteine can be converted into L-alanine and hydrogen selenide; which is catalyzed by the enzyme selenocysteine lyase. In addition, selenocysteine and 2-ketobutyric acid can be biosynthesized from selenocystathionine through the action of the enzyme cystathionine gamma-lyase. In humans, selenocysteine is involved in selenoamino acid metabolism. Selenocysteine (symbol Sec or U, in older publications also as Se-Cys) is the 21st proteinogenic amino acid. Outside of the human body, selenocysteine has been detected, but not quantified in, several different foods, such as redcurrants, catjang pea, chickpea, european cranberries, and celery stalks. This could make selenocysteine a potential biomarker for the consumption of these foods. The selenocysteine tRNAs are initially charged with serine by seryl-tRNA ligase, but the resulting Ser-tRNASec is not used for translation because it is not recognised by the normal translation elongation factor (EF-Tu in bacteria, eEF1A in eukaryotes). The UGA codon is made to encode selenocysteine by the presence of a selenocysteine insertion sequence (SECIS) in the mRNA. Most selenoproteins contain a single selenocysteine residue.
(2R)-2-Amino-3-selanylpropanoic acidHMDB
Chemical FormulaC3H7NO2Se
Average Molecular Weight168.05
Monoisotopic Molecular Weight168.964200301
IUPAC Name(2R)-2-amino-3-selanylpropanoic acid
Traditional NameL-selenocysteine
CAS Registry Number3614-08-2
InChI Identifier
Chemical Taxonomy
Description belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
  • L-alpha-amino acid
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Organic oxide
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Selenol
  • Primary amine
  • Organoselenium compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors

Route of exposure:


Biological location:


Naturally occurring process:


Industrial application:

Physical Properties
Experimental Properties
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
Water Solubility325 g/LALOGPS
pKa (Strongest Acidic)1.27ChemAxon
pKa (Strongest Basic)8.42ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity33.45 m³·mol⁻¹ChemAxon
Polarizability10.67 ųChemAxon
Number of Rings0ChemAxon
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, Positivesplash10-00di-5900000000-827b47dc191649f521acSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00di-5900000000-32e999fe6e3d67e322cbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01b9-0900000000-fadd5a69b2b225d034acSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01b9-0900000000-8fe6412cebc1ca99fe59Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00dl-5900000000-2408222e037ff9db752aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0900000000-91ba91d891f89ff1fc23Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00kk-6900000000-67c579b8ba30e155bcb3Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-9200000000-0b58b77f13cec3df121dSpectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Tissue Locations
  • Fibroblasts
  • Kidney
  • Testes
  • Thyroid Gland
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02345
Phenol Explorer Compound IDNot Available
FoodDB IDFDB002262
KNApSAcK IDC00034230
Chemspider ID23436
KEGG Compound IDC05688
BiGG ID46290
Wikipedia LinkSelenocysteine
PubChem Compound25076
PDB IDNot Available
ChEBI ID16633
Food Biomarker OntologyNot Available
VMH IDNot Available
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Mostert V, Wolff S, Dreher I, Kohrle J, Abel J: Identification of an element within the promoter of human selenoprotein P responsive to transforming growth factor-beta. Eur J Biochem. 2001 Dec;268(23):6176-81. [PubMed:11733012 ]
  2. Zimmermann MB, Kohrle J: The impact of iron and selenium deficiencies on iodine and thyroid metabolism: biochemistry and relevance to public health. Thyroid. 2002 Oct;12(10):867-78. [PubMed:12487769 ]
  3. Sun QA, Su D, Novoselov SV, Carlson BA, Hatfield DL, Gladyshev VN: Reaction mechanism and regulation of mammalian thioredoxin/glutathione reductase. Biochemistry. 2005 Nov 8;44(44):14528-37. [PubMed:16262253 ]
  4. Chu FF, Esworthy RS, Doroshow JH, Doan K, Liu XF: Expression of plasma glutathione peroxidase in human liver in addition to kidney, heart, lung, and breast in humans and rodents. Blood. 1992 Jun 15;79(12):3233-8. [PubMed:1339300 ]
  5. Blotcky AJ, Ebrahim A, Rack EP: Determination of selenium metabolites in biological fluids using instrumental and molecular neutron activation analysis. Anal Chem. 1988 Dec 15;60(24):2734-7. [PubMed:3245598 ]
  6. Utomo A, Jiang X, Furuta S, Yun J, Levin DS, Wang YC, Desai KV, Green JE, Chen PL, Lee WH: Identification of a novel putative non-selenocysteine containing phospholipid hydroperoxide glutathione peroxidase (NPGPx) essential for alleviating oxidative stress generated from polyunsaturated fatty acids in breast cancer cells. J Biol Chem. 2004 Oct 15;279(42):43522-9. Epub 2004 Aug 4. [PubMed:15294905 ]
  7. Rooseboom M, Vermeulen NP, Andreadou I, Commandeur JN: Evaluation of the kinetics of beta-elimination reactions of selenocysteine Se-conjugates in human renal cytosol: possible implications for the use as kidney selective prodrugs. J Pharmacol Exp Ther. 2000 Aug;294(2):762-9. [PubMed:10900258 ]
  8. Zinoni F, Birkmann A, Stadtman TC, Bock A: Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli. Proc Natl Acad Sci U S A. 1986 Jul;83(13):4650-4. [PubMed:2941757 ]

Only showing the first 10 proteins. There are 25 proteins in total.


General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination.
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Molecular weight:
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  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. [PubMed:17016423 ]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]
General function:
Involved in oxidoreductase activity
Specific function:
Isoform 1 may possess glutaredoxin activity as well as thioredoxin reductase activity and induces actin and tubulin polymerization, leading to formation of cell membrane protrusions. Isoform 4 enhances the transcriptional activity of estrogen receptors alpha and beta while isoform 5 enhances the transcriptional activity of the beta receptor only. Isoform 5 also mediates cell death induced by a combination of interferon-beta and retinoic acid.
Gene Name:
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General function:
Involved in oxidoreductase activity
Specific function:
Maintains thioredoxin in a reduced state. Implicated in the defenses against oxidative stress. May play a role in redox-regulated cell signaling.
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General function:
Involved in pyridoxal phosphate binding
Specific function:
Catalyzes the last step in the trans-sulfuration pathway from methionine to cysteine. Has broad substrate specificity. Converts cystathionine to cysteine, ammonia and 2-oxobutanoate. Converts two cysteine molecules to lanthionine and hydrogen sulfide. Can also accept homocysteine as substrate. Specificity depends on the levels of the endogenous substrates. Generates the endogenous signaling molecule hydrogen sulfide (H2S), and so contributes to the regulation of blood pressure. Acts as a cysteine-protein sulfhydrase by mediating sulfhydration of target proteins: sulfhydration consists of converting -SH groups into -SSH on specific cysteine residues of target proteins such as GAPDH, PTPN1 and NF-kappa-B subunit RELA, thereby regulating their function.
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Molecular weight:
Selenocystathionine + Water → Selenocysteine + Ammonia + 2-Ketobutyric aciddetails
General function:
Involved in catalytic activity
Specific function:
Synthesizes selenophosphate from selenide and ATP.
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General function:
Involved in glutathione peroxidase activity
Specific function:
Protects the hemoglobin in erythrocytes from oxidative breakdown.
Gene Name:
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General function:
Involved in glutathione peroxidase activity
Specific function:
Protects cells against membrane lipid peroxidation and cell death. Required for normal sperm development and male fertility. Could play a major role in protecting mammals from the toxicity of ingested lipid hydroperoxides. Essential for embryonic development. Protects from radiation and oxidative damage (By similarity).
Gene Name:
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General function:
Involved in glutathione peroxidase activity
Specific function:
Protects cells and enzymes from oxidative damage, by catalyzing the reduction of hydrogen peroxide, lipid peroxides and organic hydroperoxide, by glutathione.
Gene Name:
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Molecular weight:
General function:
Involved in glutathione peroxidase activity
Specific function:
Could play a major role in protecting mammals from the toxicity of ingested organic hydroperoxides. Tert-butyl hydroperoxide, cumene hydroperoxide and linoleic acid hydroperoxide but not phosphatidycholine hydroperoxide, can act as acceptors.
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General function:
Involved in thyroxine 5'-deiodinase activity
Specific function:
Responsible for the deiodination of T4 (3,5,3',5'-tetraiodothyronine) into T3 (3,5,3'-triiodothyronine) and of T3 into T2 (3,3'-diiodothyronine). Plays a role in providing a source of plasma T3 by deiodination of T4 in peripheral tissues such as liver and kidney.
Gene Name:
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Molecular weight:

Only showing the first 10 proteins. There are 25 proteins in total.