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Showing metabocard for Selenocysteine (HMDB0003288)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-05-22 15:12:47 UTC
Update Date2023-02-21 17:16:35 UTC
HMDB IDHMDB0003288
Secondary Accession Numbers
  • HMDB03288
Metabolite Identification
Common NameSelenocysteine
DescriptionSelenocysteine is an amino acid that is present in several enzymes (for example glutathione peroxidases, tetraiodothyronine 5' deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases and some hydrogenases). Selenocysteine has a structure similar to cysteine, but with an atom of selenium taking the place of the usual sulfur. Proteins that include a selenocysteine residue are called selenoproteins (Wikipedia ). Selenocysteine is a naturally occurring amino acid in both eukaryotic and prokaryotic organisms. It is found in tRNAs and in the catalytic site of some enzymes. The genes for glutathione peroxidase and formate dehydrogenase contain the TGA codon, which codes for this amino acid (Pubchem).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003288 (Selenocysteine)

  Mrv1652309042000282D          

  7  6  0  0  1  0            999 V2000
    1.0312   -0.3167    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0312    0.5082    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7456    0.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4602    0.5082    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
    0.3167    0.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3977    0.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3167    1.7457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
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3D MOL for HMDB0003288 (Selenocysteine)

HMDB0003288
     RDKit          3D
Selenocysteine
 14 13  0  0  0  0  0  0  0  0999 V2000
   -0.7287   -1.2138    1.2619 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2380   -0.1081    0.5002 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1159   -0.4035   -0.1013 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7087    1.1220   -1.1065 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -1.1635    0.2065   -0.5905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2049   -0.4685   -0.7340 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9273    1.2508   -1.4965 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1272   -1.4943    2.0498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7168   -1.0479    1.5219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0932    0.7443    1.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8096   -0.7220    0.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0495   -1.2726   -0.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2005    1.4597   -0.8309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6844    1.9476   -1.5495 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  1
  3 11  1  0
  3 12  1  0
  4 13  1  0
  7 14  1  0
M  END
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3D SDF for HMDB0003288 (Selenocysteine)

  Mrv1652309042000282D          

  7  6  0  0  1  0            999 V2000
    1.0312   -0.3167    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0312    0.5082    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7456    0.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4602    0.5082    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
    0.3167    0.9207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3977    0.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3167    1.7457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003288

> <DATABASE_NAME>
hmdb

> <SMILES>
N[C@@H](C[SeH])C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H7NO2Se/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1

> <INCHI_KEY>
ZKZBPNGNEQAJSX-REOHCLBHSA-N

> <FORMULA>
C3H7NO2Se

> <MOLECULAR_WEIGHT>
168.05

> <EXACT_MASS>
168.964200301

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.672622939777279

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-selanylpropanoic acid

> <ALOGPS_LOGP>
-3.20

> <JCHEM_LOGP>
-4.06647676757644

> <ALOGPS_LOGS>
0.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.079176189051655

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2678685745362661

> <JCHEM_PKA_STRONGEST_BASIC>
8.395568600611247

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
33.44690000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.25e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-selenocysteine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0003288 (Selenocysteine)

HMDB0003288
     RDKit          3D
Selenocysteine
 14 13  0  0  0  0  0  0  0  0999 V2000
   -0.7287   -1.2138    1.2619 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2380   -0.1081    0.5002 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1159   -0.4035   -0.1013 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7087    1.1220   -1.1065 Se  0  0  0  0  0  2  0  0  0  0  0  0
   -1.1635    0.2065   -0.5905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2049   -0.4685   -0.7340 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9273    1.2508   -1.4965 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1272   -1.4943    2.0498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7168   -1.0479    1.5219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0932    0.7443    1.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8096   -0.7220    0.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0495   -1.2726   -0.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2005    1.4597   -0.8309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6844    1.9476   -1.5495 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  1
  3 11  1  0
  3 12  1  0
  4 13  1  0
  7 14  1  0
M  END
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PDB for HMDB0003288 (Selenocysteine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       1.925  -0.591   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.925   0.949   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.258   1.719   0.000  0.00  0.00           C+0
HETATM    4 Se   UNK     0       4.592   0.949   0.000  0.00  0.00          Se+0
HETATM    5  C   UNK     0       0.591   1.719   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.742   0.949   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.591   3.259   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0003288 (Selenocysteine)

COMPND    HMDB0003288
HETATM    1  N1  UNL     1      -0.729  -1.214   1.262  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.238  -0.108   0.500  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.116  -0.404  -0.101  1.00  0.00           C  
HETATM    4 SE1  UNL     1       1.709   1.122  -1.106  1.00  0.00          SE  
HETATM    5  C3  UNL     1      -1.164   0.207  -0.591  1.00  0.00           C  
HETATM    6  O1  UNL     1      -2.205  -0.469  -0.734  1.00  0.00           O  
HETATM    7  O2  UNL     1      -0.927   1.251  -1.497  1.00  0.00           O  
HETATM    8  H1  UNL     1      -0.127  -1.494   2.050  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.717  -1.048   1.522  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.093   0.744   1.200  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.810  -0.722   0.691  1.00  0.00           H  
HETATM   12  H5  UNL     1       1.049  -1.273  -0.817  1.00  0.00           H  
HETATM   13  H6  UNL     1       3.200   1.460  -0.831  1.00  0.00           H  
HETATM   14  H7  UNL     1      -1.684   1.948  -1.550  1.00  0.00           H  
CONECT    1    2    8    9
CONECT    2    3    5   10
CONECT    3    4   11   12
CONECT    4   13
CONECT    5    6    6    7
CONECT    7   14
END
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SMILES for HMDB0003288 (Selenocysteine)

N[C@@H](C[SeH])C(O)=O
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INCHI for HMDB0003288 (Selenocysteine)

InChI=1S/C3H7NO2Se/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-Selenyl-L-alanineChEBI
L-SelenocysteinChEBI
L-SelenozysteinChEBI
(2R)-2-Amino-3-selanylpropanoateHMDB
(2R)-2-Amino-3-selanylpropanoic acidHMDB
3-Seleno-alanineHMDB
3-SelenoalanineHMDB
L-SelenocysteineHMDB
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
SMILES
N[C@@H](C[SeH])C(O)=O
InChI Identifier
InChI=1S/C3H7NO2Se/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
InChI KeyZKZBPNGNEQAJSX-REOHCLBHSA-N
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
Substituents
  • 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
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Tissue Locations
  • Fibroblasts
  • Kidney
  • Testis
  • Thyroid Gland
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02345
Phenol Explorer Compound IDNot Available
FooDB IDFDB002262
KNApSAcK IDC00034230
Chemspider ID23436
KEGG Compound IDC05688
BioCyc IDL-SELENOCYSTEINE
BiGG ID46290
Wikipedia LinkSelenocysteine
METLIN ID3292
PubChem Compound25076
PDB IDNot Available
ChEBI ID16633
Food Biomarker OntologyNot Available
VMH IDSELCYS
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References

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

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Nucleoside diphosphate kinase A
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.
Gene Name:
NME1
Uniprot ID:
P15531
Molecular weight:
17148.635
References
  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 ]
Enzyme Details
2. Thioredoxin reductase 1, cytoplasmic
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:
TXNRD1
Uniprot ID:
Q16881
Molecular weight:
70905.58
Enzyme Details
3. Thioredoxin reductase 2, mitochondrial
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.
Gene Name:
TXNRD2
Uniprot ID:
Q9NNW7
Molecular weight:
56506.275
Enzyme Details
4. Cystathionine gamma-lyase
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.
Gene Name:
CTH
Uniprot ID:
P32929
Molecular weight:
41259.91
Reactions
Selenocystathionine + Water → Selenocysteine + Ammonia + 2-Ketobutyric aciddetails
Enzyme Details
5. Selenide, water dikinase 2
General function:
Involved in catalytic activity
Specific function:
Synthesizes selenophosphate from selenide and ATP.
Gene Name:
SEPHS2
Uniprot ID:
Q99611
Molecular weight:
47304.695
Enzyme Details
6. Glutathione peroxidase 1
General function:
Involved in glutathione peroxidase activity
Specific function:
Protects the hemoglobin in erythrocytes from oxidative breakdown.
Gene Name:
GPX1
Uniprot ID:
P07203
Molecular weight:
22087.94
Enzyme Details
7. Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
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:
GPX4
Uniprot ID:
P36969
Molecular weight:
25046.57
Enzyme Details
8. Glutathione peroxidase 3
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:
GPX3
Uniprot ID:
P22352
Molecular weight:
25552.185
Enzyme Details
9. Glutathione peroxidase 2
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.
Gene Name:
GPX2
Uniprot ID:
P18283
Molecular weight:
21953.835
Enzyme Details
10. Type I iodothyronine deiodinase
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:
DIO1
Uniprot ID:
P49895
Molecular weight:
28924.21

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

Show all enzymes and transporters