Showing metabocard for Selenocysteine (MMDBc0000232)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:40:41 UTC
Update Date2024-10-06 22:41:37 UTC
Metabolite IDMMDBc0000232
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f920322a758>


  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 #<Metabolite:0x00007f920322a758>

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 #<Metabolite:0x00007f920322a758>


  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>
MMDBc0000232

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f920322a758>

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 #<Metabolite:0x00007f920322a758>

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 #<Metabolite:0x00007f920322a758>

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 #<Metabolite:0x00007f920322a758>

N[C@@H](C[SeH])C(O)=O
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INCHI for #<Metabolite:0x00007f920322a758>

InChI=1S/C3H7NO2Se/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
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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
Molecular FormulaC3H7NO2Se
Average Mass168.05
Monoisotopic Mass168.964200301
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