Showing metabocard for Se-Methylselenocysteine (MMDBc0030225)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:59:05 UTC
Update Date2024-04-30 19:44:55 UTC
Metabolite IDMMDBc0030225
Metabolite Identification
Common NameSe-Methylselenocysteine
DescriptionSe-Methylselenocysteine (SeMSC) is a naturally occurring seleno-amino acid that is synthesized by plants such as garlic, astragalus, onions and broccoli. SeMSC is an intermediate in selenoamino acid metabolism. Unlike selenomethionine, which is incorporated into proteins in place of methionine, SeMSC is not incorporated into any proteins, thereby being fully available for the synthesis of selenium-containing enzymes such as glutathione peroxidase.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005634c27f65c8>


  Mrv1652304202019322D          

  8  7  0  0  0  0            999 V2000
   -1.7632    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4776   -0.1339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7632    1.1035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0487   -0.1339    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0487   -0.9589    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3342    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3802   -0.1339    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
    1.0946    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  4  5  1  6  0  0  0
M  END
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3D MOL for #<Metabolite:0x00005634c27f65c8>

HMDB0004113
     RDKit          3D
Se-Methylselenocysteine
 17 16  0  0  0  0  0  0  0  0999 V2000
    3.2973   -0.4439    0.1272 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4809   -1.1621    0.1515 Se  0  0  0  0  0  2  0  0  0  0  0  0
    0.2478    0.2395    0.6873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9481    0.2768   -0.2471 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8610    1.3227    0.1583 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6877   -1.0103   -0.1896 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1290   -2.0991   -0.4949 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0233   -1.0905    0.1993 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2792    0.4828   -0.4731 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9639   -1.1700   -0.3648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6120   -0.2770    1.1826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1409    0.0363    1.7135 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7517    1.2254    0.7210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6002    0.4120   -1.3014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3850    2.0938    0.6751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4422    1.6543   -0.6283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4153   -0.4908    0.9049 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
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  6
  5 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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3D SDF for #<Metabolite:0x00005634c27f65c8>


  Mrv1652304202019322D          

  8  7  0  0  0  0            999 V2000
   -1.7632    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4776   -0.1339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7632    1.1035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0487   -0.1339    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0487   -0.9589    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3342    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3802   -0.1339    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
    1.0946    0.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  4  5  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030225

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO2Se/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m0/s1

> <INCHI_KEY>
XDSSPSLGNGIIHP-VKHMYHEASA-N

> <FORMULA>
C4H9NO2Se

> <MOLECULAR_WEIGHT>
182.08

> <EXACT_MASS>
182.979850365

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.89093551048972

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-(methylselanyl)propanoic acid

> <ALOGPS_LOGP>
-2.83

> <JCHEM_LOGP>
-3.4965590832336657

> <ALOGPS_LOGS>
-0.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.455656581832642

> <JCHEM_PKA_STRONGEST_BASIC>
8.399279194736632

> <JCHEM_POLAR_SURFACE_AREA>
63.31999999999999

> <JCHEM_REFRACTIVITY>
38.19600000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.56e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylselenocysteine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00005634c27f65c8>

HMDB0004113
     RDKit          3D
Se-Methylselenocysteine
 17 16  0  0  0  0  0  0  0  0999 V2000
    3.2973   -0.4439    0.1272 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4809   -1.1621    0.1515 Se  0  0  0  0  0  2  0  0  0  0  0  0
    0.2478    0.2395    0.6873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9481    0.2768   -0.2471 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8610    1.3227    0.1583 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6877   -1.0103   -0.1896 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1290   -2.0991   -0.4949 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0233   -1.0905    0.1993 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2792    0.4828   -0.4731 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9639   -1.1700   -0.3648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6120   -0.2770    1.1826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1409    0.0363    1.7135 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7517    1.2254    0.7210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6002    0.4120   -1.3014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3850    2.0938    0.6751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4422    1.6543   -0.6283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4153   -0.4908    0.9049 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
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  6
  5 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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PDB for #<Metabolite:0x00005634c27f65c8>

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0      -3.291   0.520   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -4.625  -0.250   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -3.291   2.060   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.958  -0.250   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -1.958  -1.790   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -0.624   0.520   0.000  0.00  0.00           C+0
HETATM    7 Se   UNK     0       0.710  -0.250   0.000  0.00  0.00          Se+0
HETATM    8  C   UNK     0       2.043   0.520   0.000  0.00  0.00           C+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    6    5                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00005634c27f65c8>

COMPND    HMDB0004113
HETATM    1  C1  UNL     1       3.297  -0.444   0.127  1.00  0.00           C  
HETATM    2 SE1  UNL     1       1.481  -1.162   0.152  1.00  0.00          SE  
HETATM    3  C2  UNL     1       0.248   0.239   0.687  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.948   0.277  -0.247  1.00  0.00           C  
HETATM    5  N1  UNL     1      -1.861   1.323   0.158  1.00  0.00           N  
HETATM    6  C4  UNL     1      -1.688  -1.010  -0.190  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.129  -2.099  -0.495  1.00  0.00           O  
HETATM    8  O2  UNL     1      -3.023  -1.090   0.199  1.00  0.00           O  
HETATM    9  H1  UNL     1       3.279   0.483  -0.473  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.964  -1.170  -0.365  1.00  0.00           H  
HETATM   11  H3  UNL     1       3.612  -0.277   1.183  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.141   0.036   1.714  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.752   1.225   0.721  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.600   0.412  -1.301  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.385   2.094   0.675  1.00  0.00           H  
HETATM   16  H8  UNL     1      -2.442   1.654  -0.628  1.00  0.00           H  
HETATM   17  H9  UNL     1      -3.415  -0.491   0.905  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3
CONECT    3    4   12   13
CONECT    4    5    6   14
CONECT    5   15   16
CONECT    6    7    7    8
CONECT    8   17
END
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SMILES for #<Metabolite:0x00005634c27f65c8>

C[Se]C[C@H](N)C(O)=O
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INCHI for #<Metabolite:0x00005634c27f65c8>

InChI=1S/C4H9NO2Se/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m0/s1
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Synonyms
ValueSource
L-MethylselenocysteineChEBI
Methyl-L-selenocysteineChEBI
MethylselenocysteineChEBI
Se-methyl-seleno-L-cysteineChEBI
Se-methyl-selenocysteineChEBI
Selenium methyl cysteineChEBI
Selenium-methylselenocystineChEBI
SelenohomocysteineChEBI
SelenomethylselenocysteineChEBI
3-(Methylseleno)-L-alanineHMDB
Se-methyl-L-selenocysteineHMDB
L-Methyl-selenocysteineHMDB
Methyl selenocysteineHMDB
Selenomethylselenocysteine, (D,L)-isomerHMDB
Selenomethylselenocysteine, (L)-isomer, 75Se-labeledHMDB
SeMCysHMDB
Selenomethylselenocysteine, (L)-isomerHMDB
Methylseleno-L-cysteineHMDB
Selenomethyl selenocysteineHMDB
Se-MethylselenocysteineHMDB
Molecular FormulaC4H9NO2Se
Average Mass182.08
Monoisotopic Mass182.979850365
IUPAC Name(2R)-2-amino-3-(methylselanyl)propanoic acid
Traditional Namemethylselenocysteine
CAS Registry Number26046-90-2
SMILES
C[Se]C[C@H](N)C(O)=O
InChI Identifier
InChI=1S/C4H9NO2Se/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m0/s1
InChI KeyXDSSPSLGNGIIHP-VKHMYHEASA-N