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Showing metabocard for Tetraphosphorus (HMDB0258930)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:46:19 UTC
Update Date2022-11-23 22:29:20 UTC
HMDB IDHMDB0258930
Secondary Accession NumbersNone
Metabolite Identification
Common NameTetraphosphorus
DescriptionWhite Phosphorus, also known as phosphorus or P4, belongs to the class of inorganic compounds known as homogeneous other non-metal compounds. These are inorganic non-metallic compounds in which the largest atom belongs to the class of 'other non-metals'. Based on a literature review very few articles have been published on White Phosphorus. This compound has been identified in human blood as reported by (PMID: 31557052 ). Tetraphosphorus is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Tetraphosphorus 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0258930 (Tetraphosphorus)


  Mrv0541 10041417142D          

  4  6  0  0  0  0            999 V2000
    0.0000    0.4530    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230   -0.4530    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -0.4530    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.1510    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  3  4  1  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  1  1  0  0  0  0
  1  4  1  0  0  0  0
  4  2  1  0  0  0  0
M  END
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3D MOL for HMDB0258930 (Tetraphosphorus)

HMDB0258930
     RDKit          3D
tetraphosphorus
  4  6  0  0  0  0  0  0  0  0999 V2000
    0.2773    0.7978   -0.7146 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9503   -0.7206   -0.4356 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6302    0.4170    0.8864 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.3032   -0.4941    0.2638 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  1  1  0
  4  1  1  0
  4  2  1  0
M  END
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3D SDF for HMDB0258930 (Tetraphosphorus)


  Mrv0541 10041417142D          

  4  6  0  0  0  0            999 V2000
    0.0000    0.4530    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230   -0.4530    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -0.4530    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.1510    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  3  4  1  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  1  1  0  0  0  0
  1  4  1  0  0  0  0
  4  2  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258930

> <DATABASE_NAME>
hmdb

> <SMILES>
P12P3P1P23

> <INCHI_IDENTIFIER>
InChI=1S/P4/c1-2-3(1)4(1)2

> <INCHI_KEY>
OBSZRRSYVTXPNB-UHFFFAOYSA-N

> <FORMULA>
P4

> <MOLECULAR_WEIGHT>
123.895

> <EXACT_MASS>
123.895046048

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
5.766265667337508

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
tricyclo[1.1.0.0²,⁴]tetraphosphane

> <JCHEM_LOGP>
1.3232

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
7.1840599913279615

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
27.344

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
phosphorus

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0258930 (Tetraphosphorus)

HMDB0258930
     RDKit          3D
tetraphosphorus
  4  6  0  0  0  0  0  0  0  0999 V2000
    0.2773    0.7978   -0.7146 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9503   -0.7206   -0.4356 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6302    0.4170    0.8864 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.3032   -0.4941    0.2638 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  1  1  0
  4  1  1  0
  4  2  1  0
M  END
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PDB for HMDB0258930 (Tetraphosphorus)

HEADER    PROTEIN                                 04-OCT-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-OCT-14         0                                  
HETATM    1  P   UNK     0       0.000   0.846   0.000  0.00  0.00           P+0
HETATM    2  P   UNK     0      -0.976  -0.846   0.000  0.00  0.00           P+0
HETATM    3  P   UNK     0       0.976  -0.846   0.000  0.00  0.00           P+0
HETATM    4  P   UNK     0       0.000  -0.282   0.000  0.00  0.00           P+0
CONECT    1    2    3    4                                                  
CONECT    2    1    3    4                                                  
CONECT    3    4    2    1                                                  
CONECT    4    3    1    2                                                  
MASTER        0    0    0    0    0    0    0    0    4    0   12    0
END
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3D PDB for HMDB0258930 (Tetraphosphorus)

COMPND    HMDB0258930
HETATM    1  P1  UNL     1       0.277   0.798  -0.715  1.00  0.00           P  
HETATM    2  P2  UNL     1      -0.950  -0.721  -0.436  1.00  0.00           P  
HETATM    3  P3  UNL     1      -0.630   0.417   0.886  1.00  0.00           P  
HETATM    4  P4  UNL     1       1.303  -0.494   0.264  1.00  0.00           P  
CONECT    1    2    3    4
CONECT    2    3    4
CONECT    3    4
END
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SMILES for HMDB0258930 (Tetraphosphorus)

P12P3P1P23
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INCHI for HMDB0258930 (Tetraphosphorus)

InChI=1S/P4/c1-2-3(1)4(1)2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Molecular phosphorusChEBI
P4ChEBI
PhosphorusChEBI
Phosphorus tetraatomic moleculeChEBI
Phosphorus tetramerChEBI
Tetraatomic phosphorusChEBI
Tetrameric phosphorusChEBI
Phosphorus, blackMeSH
Phosphorus, redMeSH
Phosphorus, whiteMeSH
Black phosphorusMeSH
Phosphorus 31MeSH
Phosphorus, yellowMeSH
Red phosphorusMeSH
Phosphorus-31MeSH
Yellow phosphorusMeSH
Chemical FormulaP4
Average Molecular Weight123.895
Monoisotopic Molecular Weight123.895046048
IUPAC Nametricyclo[1.1.0.0²,⁴]tetraphosphane
Traditional Namephosphorus
CAS Registry NumberNot Available
SMILES
P12P3P1P23
InChI Identifier
InChI=1S/P4/c1-2-3(1)4(1)2
InChI KeyOBSZRRSYVTXPNB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous other non-metal compounds. These are inorganic non-metallic compounds in which the largest atom belongs to the class of 'other non-metals'.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassHomogeneous other non-metal compounds
Sub ClassNot Available
Direct ParentHomogeneous other non-metal compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous other non metal
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP1.32ChemAxon
pKa (Strongest Basic)7.18ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity27.34 m³·mol⁻¹ChemAxon
Polarizability5.77 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-150.76430932474
DeepCCS[M+Na]+124.5930932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
tetraphosphorusP12P3P1P23691.7Standard polar33892256
tetraphosphorusP12P3P1P23705.7Standard non polar33892256
tetraphosphorusP12P3P1P23808.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Tetraphosphorus GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-0900000000-28572b58b528d5280e992021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Tetraphosphorus GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetraphosphorus 10V, Positive-QTOFsplash10-00di-0900000000-554ba802daa412f7566b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetraphosphorus 20V, Positive-QTOFsplash10-00di-0900000000-554ba802daa412f7566b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetraphosphorus 40V, Positive-QTOFsplash10-00di-0900000000-554ba802daa412f7566b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetraphosphorus 10V, Negative-QTOFsplash10-00di-0900000000-ed7439d5980f85d06aba2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetraphosphorus 20V, Negative-QTOFsplash10-00di-0900000000-ed7439d5980f85d06aba2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetraphosphorus 40V, Negative-QTOFsplash10-00di-0900000000-ed7439d5980f85d06aba2016-08-03Wishart 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 ID109894
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAllotropes of phosphorus
METLIN IDNot Available
PubChem Compound123286
PDB IDNot Available
ChEBI ID35895
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 ]