Hmdb loader

Showing metabocard for Phosphorothioic acid (HMDB0256494)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:59:16 UTC
Update Date2021-09-26 23:12:10 UTC
HMDB IDHMDB0256494
Secondary Accession NumbersNone
Metabolite Identification
Common NamePhosphorothioic acid
Descriptionphosphorothioic O,O,O-acid, also known as p(S)(OH)3 or thiophosphoric O,O,O-acid, belongs to the class of inorganic compounds known as non-metal thiophosphates. These are inorganic compounds in which the largest oxoanion is thiophosphate, and in which the heaviest atom not in an oxoanion is a non-metal element. Based on a literature review very few articles have been published on phosphorothioic O,O,O-acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Phosphorothioic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Phosphorothioic acid is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256494 (Phosphorothioic acid)


  Mrv0541 05041412172D          

  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    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.0000    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
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  2  0  0  0  0
M  END
Download

3D MOL for HMDB0256494 (Phosphorothioic acid)

HMDB0256494
     RDKit          3D
Phosphorothioic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
   -0.4632    1.3921    0.4569 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0773   -0.1837    0.2183 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.0914   -1.1282   -0.5931 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4751   -0.2548   -0.7169 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2989   -0.8984    1.7763 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.7973   -0.4084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9403   -0.6444   -0.5112 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2985   -0.0799   -0.2221 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
Download

3D SDF for HMDB0256494 (Phosphorothioic acid)


  Mrv0541 05041412172D          

  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    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.0000    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
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256494

> <DATABASE_NAME>
hmdb

> <SMILES>
OP(O)(O)=S

> <INCHI_IDENTIFIER>
InChI=1S/H3O3PS/c1-4(2,3)5/h(H3,1,2,3,5)

> <INCHI_KEY>
RYYWUUFWQRZTIU-UHFFFAOYSA-N

> <FORMULA>
H3O3PS

> <MOLECULAR_WEIGHT>
114.061

> <EXACT_MASS>
113.954051164

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
7.95633562265159

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
phosphorothioic acid

> <JCHEM_LOGP>
-0.13023423833333322

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.1473461176440045

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.418571919592014

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
22.6428

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
phosphorothioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0256494 (Phosphorothioic acid)

HMDB0256494
     RDKit          3D
Phosphorothioic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
   -0.4632    1.3921    0.4569 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0773   -0.1837    0.2183 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.0914   -1.1282   -0.5931 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4751   -0.2548   -0.7169 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2989   -0.8984    1.7763 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.7973   -0.4084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9403   -0.6444   -0.5112 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2985   -0.0799   -0.2221 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
Download

PDB for HMDB0256494 (Phosphorothioic acid)

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    4  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM    5  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
CONECT    1    4                                                            
CONECT    2    4                                                            
CONECT    3    4                                                            
CONECT    4    1    2    3    5                                             
CONECT    5    4                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
Download

3D PDB for HMDB0256494 (Phosphorothioic acid)

COMPND    HMDB0256494
HETATM    1  O1  UNL     1      -0.463   1.392   0.457  1.00  0.00           O  
HETATM    2  P1  UNL     1       0.077  -0.184   0.218  1.00  0.00           P  
HETATM    3  O2  UNL     1      -1.091  -1.128  -0.593  1.00  0.00           O  
HETATM    4  O3  UNL     1       1.475  -0.255  -0.717  1.00  0.00           O  
HETATM    5  S1  UNL     1       0.299  -0.898   1.776  1.00  0.00           S  
HETATM    6  H1  UNL     1      -0.655   1.797  -0.408  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.940  -0.644  -0.511  1.00  0.00           H  
HETATM    8  H3  UNL     1       2.298  -0.080  -0.222  1.00  0.00           H  
CONECT    1    2    6
CONECT    2    3    4    5    5
CONECT    3    7
CONECT    4    8
END
Download

SMILES for HMDB0256494 (Phosphorothioic acid)

OP(O)(O)=S
Download

INCHI for HMDB0256494 (Phosphorothioic acid)

InChI=1S/H3O3PS/c1-4(2,3)5/h(H3,1,2,3,5)
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
p(S)(OH)3ChEBI
Thiophosphoric O,O,O-acidChEBI
Chemical FormulaH3O3PS
Average Molecular Weight114.061
Monoisotopic Molecular Weight113.954051164
IUPAC Namephosphorothioic acid
Traditional Namephosphorothioic acid
CAS Registry NumberNot Available
SMILES
OP(O)(O)=S
InChI Identifier
InChI=1S/H3O3PS/c1-4(2,3)5/h(H3,1,2,3,5)
InChI KeyRYYWUUFWQRZTIU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as non-metal thiophosphates. These are inorganic compounds in which the largest oxoanion is thiophosphate, and in which the heaviest atom not in an oxoanion is a non-metal element.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassNon-metal oxoanionic compounds
Sub ClassNon-metal thiophosphates
Direct ParentNon-metal thiophosphates
Alternative ParentsNot Available
Substituents
  • Non-metal thiophosphate
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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-0.13ChemAxon
pKa (Strongest Acidic)2.42ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area60.69 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity22.64 m³·mol⁻¹ChemAxon
Polarizability7.96 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+115.2630932474
DeepCCS[M-H]-113.41130932474
DeepCCS[M-2H]-148.75230932474
DeepCCS[M+Na]+122.84530932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20227.8723 minutes33406817
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid460.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid343.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid92.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid265.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid153.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid242.5 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid242.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)786.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid529.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid46.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid544.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid212.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid334.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate698.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA447.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water353.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Phosphorothioic acidOP(O)(O)=S1913.7Standard polar33892256
Phosphorothioic acidOP(O)(O)=S935.5Standard non polar33892256
Phosphorothioic acidOP(O)(O)=S1156.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Phosphorothioic acid,1TMS,isomer #1C[Si](C)(C)OP(O)(O)=S1201.5Semi standard non polar33892256
Phosphorothioic acid,1TMS,isomer #1C[Si](C)(C)OP(O)(O)=S1132.6Standard non polar33892256
Phosphorothioic acid,1TMS,isomer #1C[Si](C)(C)OP(O)(O)=S1828.8Standard polar33892256
Phosphorothioic acid,2TMS,isomer #1C[Si](C)(C)OP(O)(=S)O[Si](C)(C)C1251.4Semi standard non polar33892256
Phosphorothioic acid,2TMS,isomer #1C[Si](C)(C)OP(O)(=S)O[Si](C)(C)C1244.6Standard non polar33892256
Phosphorothioic acid,2TMS,isomer #1C[Si](C)(C)OP(O)(=S)O[Si](C)(C)C1532.6Standard polar33892256
Phosphorothioic acid,3TMS,isomer #1C[Si](C)(C)OP(=S)(O[Si](C)(C)C)O[Si](C)(C)C1310.8Semi standard non polar33892256
Phosphorothioic acid,3TMS,isomer #1C[Si](C)(C)OP(=S)(O[Si](C)(C)C)O[Si](C)(C)C1352.6Standard non polar33892256
Phosphorothioic acid,3TMS,isomer #1C[Si](C)(C)OP(=S)(O[Si](C)(C)C)O[Si](C)(C)C1376.7Standard polar33892256
Phosphorothioic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(O)(O)=S1425.9Semi standard non polar33892256
Phosphorothioic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(O)(O)=S1388.3Standard non polar33892256
Phosphorothioic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(O)(O)=S1995.5Standard polar33892256
Phosphorothioic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(O)(=S)O[Si](C)(C)C(C)(C)C1707.2Semi standard non polar33892256
Phosphorothioic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(O)(=S)O[Si](C)(C)C(C)(C)C1724.8Standard non polar33892256
Phosphorothioic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(O)(=S)O[Si](C)(C)C(C)(C)C1819.6Standard polar33892256
Phosphorothioic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=S)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C1944.6Semi standard non polar33892256
Phosphorothioic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=S)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C1993.8Standard non polar33892256
Phosphorothioic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=S)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C1775.6Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Phosphorothioic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-3900000000-e7e6bf472c44dd5f86c02021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Phosphorothioic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID146330
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID46611
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]