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Showing metabocard for Phosphoroselenoic acid (HMDB0003840)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-08-13 05:42:32 UTC
Update Date2023-02-21 17:16:49 UTC
HMDB IDHMDB0003840
Secondary Accession Numbers
  • HMDB0006407
  • HMDB03840
  • HMDB06407
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. Phosphoroselenoic acid is also the selenium donor used to synthesize selenocysteine (Sec), the 21st amino acid, which is co-translationally incorporated into selenoproteins at in-frame UGA codons. A number of enzymes have selenocysteine residues and, in some cases, the residues are located at their active sites. Proteins containing selenocysteine have been described in all three domains of life (PMID: 18156471 ). Selenophosphate synthetase (EC 2.7.9.3, human SPS1, the product of the selD gene) produces monoselenophosphate from selenide and ATP. The SPS1-encoded enzyme depends on a selenium salvage system that recycles L-selenocysteine. Selenophosphate synthetase genes play a role in a cancer cell's response to ionizing radiation and its reaction product, selenophosphate, might be involved in cancer prevention in a p53-dependent manner and could be applied to the development of a novel cancer therapy (PMID: 8986768 , 10609888 , 16786570 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003840 (Phosphoroselenoic acid)

  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 HMDB0003840 (Phosphoroselenoic acid)

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 HMDB0003840 (Phosphoroselenoic acid)

  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>
HMDB0003840

> <DATABASE_NAME>
hmdb

> <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 HMDB0003840 (Phosphoroselenoic acid)

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 HMDB0003840 (Phosphoroselenoic acid)

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 HMDB0003840 (Phosphoroselenoic acid)

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 HMDB0003840 (Phosphoroselenoic acid)

OP(O)(O)=[Se]
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INCHI for HMDB0003840 (Phosphoroselenoic acid)

InChI=1S/H3O3PSe/c1-4(2,3)5/h(H3,1,2,3,5)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[p(OH)3Se]ChEBI
SelenophosphateChEBI
Selenophosphoric acidGenerator
PhosphoroselenoateGenerator
Monoselenophosphoric acidHMDB
SePO3HMDB
TrihydroxidoselenidophosphorusHMDB
Chemical FormulaH3O3PSe
Average Molecular Weight160.96
Monoisotopic Molecular Weight161.898502302
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
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as non-metal selenophosphates. These are inorganic compounds in which the largest oxoanion is selenophosphate, and in which the heaviest atom not in an oxoanion is a non-metal element.
KingdomInorganic compounds
Super ClassMixed metal/non-metal compounds
ClassOther mixed metal/non-metal oxoanionic compounds
Sub ClassNon-metal selenophosphates
Direct ParentNon-metal selenophosphates
Alternative ParentsNot Available
Substituents
  • Non-metal selenophosphate
Molecular FrameworkNot Available
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
PropertyValueSource
logP-1.1ChemAxon
pKa (Strongest Acidic)-6.3ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area60.69 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.32 m³·mol⁻¹ChemAxon
Polarizability7.23 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023234
KNApSAcK IDNot Available
Chemspider ID1061
KEGG Compound IDC05172
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1092
PDB IDNot Available
ChEBI ID29269
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceEphraim, F.; Majler, E. Selenophosphates. Berichte der Deutschen Chemischen Gesellschaft (1910), 43 277-85.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Guimaraes MJ, Peterson D, Vicari A, Cocks BG, Copeland NG, Gilbert DJ, Jenkins NA, Ferrick DA, Kastelein RA, Bazan JF, Zlotnik A: Identification of a novel selD homolog from eukaryotes, bacteria, and archaea: is there an autoregulatory mechanism in selenocysteine metabolism? Proc Natl Acad Sci U S A. 1996 Dec 24;93(26):15086-91. [PubMed:8986768 ]
  2. Lacourciere GM: Biosynthesis of selenophosphate. Biofactors. 1999;10(2-3):237-44. [PubMed:10609888 ]
  3. Chung HJ, Yoon SI, Shin SH, Koh YA, Lee SJ, Lee YS, Bae S: p53-Mediated enhancement of radiosensitivity by selenophosphate synthetase 1 overexpression. J Cell Physiol. 2006 Oct;209(1):131-41. [PubMed:16786570 ]
  4. Lobanov AV, Hatfield DL, Gladyshev VN: Selenoproteinless animals: selenophosphate synthetase SPS1 functions in a pathway unrelated to selenocysteine biosynthesis. Protein Sci. 2008 Jan;17(1):176-82. [PubMed:18156471 ]

Enzymes

Enzyme Details
1. Selenide, water dikinase 1
General function:
Involved in catalytic activity
Specific function:
Synthesizes selenophosphate from selenide and ATP.
Gene Name:
SEPHS1
Uniprot ID:
P49903
Molecular weight:
42910.325
Reactions
Adenosine triphosphate + Hydrogen selenide + Water → Adenosine monophosphate + Phosphoroselenoic acid + Phosphatedetails
Enzyme Details
2. 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
Reactions
Adenosine triphosphate + Hydrogen selenide + Water → Adenosine monophosphate + Phosphoroselenoic acid + Phosphatedetails
Enzyme Details
3. O-phosphoseryl-tRNA(Sec) selenium transferase
General function:
Involved in catalytic activity
Specific function:
Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis.
Gene Name:
SEPSECS
Uniprot ID:
Q9HD40
Molecular weight:
55725.69
Reactions
O-phospho-L-seryl-tRNA(Sec) + Phosphoroselenoic acid → L-selenocysteinyl-tRNA(Sec) + Phosphatedetails
O-Phosphoseryl-tRNA(Sec) + Phosphoroselenoic acid + Water → L-Selenocysteinyl-tRNA(Sec) + Phosphatedetails