Showing metabocard for Phosphoroselenoic acid (MMDBc0029732)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2021-11-17 23:39:24 UTC
Update Date2024-04-30 19:41:34 UTC
Metabolite IDMMDBc0029732
Metabolite Identification
Common NamePhosphoroselenoic acid
DescriptionPhosphoroselenoic acid, H3SePO3, is the activated selenium donor compound required for the biosynthesis of selenocysteyl-tRNA, the precursor of specific selenocysteine residues in bacterial and mammalian selenoproteins. Selenocysteine is often called the 21st amino acid, because Sec has a specific tRNA and codon UGA, and shares a major stop codon UGA. A number of enzymes have selenocysteine, residues and in some cases at their active sites. Proteins containing the 21st amino acid, selenocysteine (Sec), have been described in all three domains of life. (PMID: 18156471 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9ab958a8f8>


  Mrv1652305171817442D          

  5  4  0  0  0  0            999 V2000
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.0000    0.0000 Se  0  0  0  0  0  2  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  2  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9ab958a8f8>

HMDB0003840
     RDKit          3D
Phosphoroselenoic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
    1.5287   -0.1969   -0.4970 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1310    0.4962    0.1461 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.1163    0.5743   -1.0050 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4781   -0.4127    1.4459 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6041    2.2822    0.7327 Se  0  0  0  0  0  2  0  0  0  0  0  0
    1.4593   -1.1773   -0.5335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2682   -0.3339   -1.3406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8605   -1.2320    1.0516 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  2  0
  1  6  1  0
  3  7  1  0
  4  8  1  0
M  END
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3D SDF for #<Metabolite:0x00007f9ab958a8f8>


  Mrv1652305171817442D          

  5  4  0  0  0  0            999 V2000
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.0000    0.0000 Se  0  0  0  0  0  2  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  2  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029732

> <DATABASE_NAME>
MIME

> <SMILES>
OP(O)(O)=[Se]

> <INCHI_IDENTIFIER>
InChI=1S/H3O3PSe/c1-4(2,3)5/h(H3,1,2,3,5)

> <INCHI_KEY>
JRPHGDYSKGJTKZ-UHFFFAOYSA-N

> <FORMULA>
H3O3PSe

> <MOLECULAR_WEIGHT>
160.96

> <EXACT_MASS>
161.898502302

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
7.233680377305243

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
hydroxy(selanylidene)phosphonous acid

> <JCHEM_LOGP>
-1.1304999999999996

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
-3.1645280069565223

> <JCHEM_PKA_STRONGEST_ACIDIC>
-6.266789329064495

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
26.323899999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
selenophosphoric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9ab958a8f8>

HMDB0003840
     RDKit          3D
Phosphoroselenoic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
    1.5287   -0.1969   -0.4970 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1310    0.4962    0.1461 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.1163    0.5743   -1.0050 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4781   -0.4127    1.4459 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6041    2.2822    0.7327 Se  0  0  0  0  0  2  0  0  0  0  0  0
    1.4593   -1.1773   -0.5335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2682   -0.3339   -1.3406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8605   -1.2320    1.0516 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  2  0
  1  6  1  0
  3  7  1  0
  4  8  1  0
M  END
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PDB for #<Metabolite:0x00007f9ab958a8f8>

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM    2  P   UNK     0       1.540   0.000   0.000  0.00  0.00           P+0
HETATM    3  O   UNK     0       1.540   1.540   0.000  0.00  0.00           O+0
HETATM    4 Se   UNK     0       3.080  -0.000   0.000  0.00  0.00          Se+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for #<Metabolite:0x00007f9ab958a8f8>

COMPND    HMDB0003840
HETATM    1  O1  UNL     1       1.529  -0.197  -0.497  1.00  0.00           O  
HETATM    2  P1  UNL     1       0.131   0.496   0.146  1.00  0.00           P  
HETATM    3  O2  UNL     1      -1.116   0.574  -1.005  1.00  0.00           O  
HETATM    4  O3  UNL     1      -0.478  -0.413   1.446  1.00  0.00           O  
HETATM    5 SE1  UNL     1       0.604   2.282   0.733  1.00  0.00          SE  
HETATM    6  H1  UNL     1       1.459  -1.177  -0.534  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.268  -0.334  -1.341  1.00  0.00           H  
HETATM    8  H3  UNL     1      -0.860  -1.232   1.052  1.00  0.00           H  
CONECT    1    2    6
CONECT    2    3    4    5    5
CONECT    3    7
CONECT    4    8
END
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SMILES for #<Metabolite:0x00007f9ab958a8f8>

OP(O)(O)=[Se]
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INCHI for #<Metabolite:0x00007f9ab958a8f8>

InChI=1S/H3O3PSe/c1-4(2,3)5/h(H3,1,2,3,5)
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Synonyms
ValueSource
[p(OH)3Se]ChEBI
SelenophosphateChEBI
Selenophosphoric acidGenerator
PhosphoroselenoateGenerator
Monoselenophosphoric acidHMDB
SePO3HMDB
TrihydroxidoselenidophosphorusHMDB
Molecular FormulaH3O3PSe
Average Mass160.96
Monoisotopic Mass161.898502302
IUPAC Namehydroxy(selanylidene)phosphonous acid
Traditional Nameselenophosphoric acid
CAS Registry Number25758-66-1
SMILES
OP(O)(O)=[Se]
InChI Identifier
InChI=1S/H3O3PSe/c1-4(2,3)5/h(H3,1,2,3,5)
InChI KeyJRPHGDYSKGJTKZ-UHFFFAOYSA-N