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Showing metabocard for Platinum (HMDB0013671)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-01-27 12:16:39 UTC
Update Date2020-02-26 21:39:01 UTC
HMDB IDHMDB0013671
Secondary Accession Numbers
  • HMDB13671
Metabolite Identification
Common NamePlatinum
DescriptionPlatinum, also known as 78PT, belongs to the class of inorganic compounds known as homogeneous transition metal compounds. These are inorganic compounds containing only metal atoms,with the largest atom being a transition metal atom. Platinum is found, on average, in the highest concentration within a few different foods, such as broccolis (Brassica oleracea var. italica), garlics (Allium sativum), and spinaches (Spinacia oleracea) and in a lower concentration in yellow bell peppers (Capsicum annuum), italian sweet red peppers (Capsicum annuum), and garden tomatoes (Solanum lycopersicum). This could make platinum a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Platinum.
Structure
Data?1582753141
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013671 (Platinum)

23939
  Mrv0541 02271202152D          

  1  0  0  0  0  0            999 V2000
    2.0000    0.0000    0.0000 Pt  0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for HMDB0013671 (Platinum)

HMDB0013671
     RDKit          3D
Platinum
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Pt  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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3D SDF for HMDB0013671 (Platinum)

23939
  Mrv0541 02271202152D          

  1  0  0  0  0  0            999 V2000
    2.0000    0.0000    0.0000 Pt  0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013671

> <DATABASE_NAME>
hmdb

> <SMILES>
[Pt]

> <INCHI_IDENTIFIER>
InChI=1S/Pt

> <INCHI_KEY>
BASFCYQUMIYNBI-UHFFFAOYSA-N

> <FORMULA>
Pt

> <MOLECULAR_WEIGHT>
195.084

> <EXACT_MASS>
194.964774449

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
platinum

> <JCHEM_LOGP>
0.029999999999999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
platinum

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0013671 (Platinum)

HMDB0013671
     RDKit          3D
Platinum
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Pt  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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PDB for HMDB0013671 (Platinum)

HEADER    PROTEIN                                 27-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 23939                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-FEB-12         0                                  
HETATM    1 Pt   UNK     0       3.733   0.000   0.000  0.00  0.00          Pt+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0013671 (Platinum)

COMPND    HMDB0013671
HETATM    1 PT1  UNL     1       0.000   0.000   0.000  1.00  0.00          PT  
END
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SMILES for HMDB0013671 (Platinum)

[Pt]
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INCHI for HMDB0013671 (Platinum)

InChI=1S/Pt
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View in JSmolView Stereo Labels
Synonyms
ValueSource
78PTChEBI
PtChEBI
Chemical FormulaPt
Average Molecular Weight195.084
Monoisotopic Molecular Weight194.964774449
IUPAC Nameplatinum
Traditional Nameplatinum
CAS Registry Number7440-06-4
SMILES
[Pt]
InChI Identifier
InChI=1S/Pt
InChI KeyBASFCYQUMIYNBI-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous transition metal compounds. These are inorganic compounds containing only metal atoms,with the largest atom being a transition metal atom.
KingdomInorganic compounds
Super ClassHomogeneous metal compounds
ClassHomogeneous transition metal compounds
Sub ClassNot Available
Direct ParentHomogeneous transition metal compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous transition metal
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point1768.3 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP0.03Extrapolated
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.03ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity0 m³·mol⁻¹ChemAxon
Polarizability1.78 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+143.932859911
AllCCS[M+H-H2O]+140.632859911
AllCCS[M+NH4]+147.132859911
AllCCS[M+Na]+148.032859911
AllCCS[M-H]-195.732859911
AllCCS[M+Na-2H]-207.232859911
AllCCS[M+HCOO]-219.732859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid315.2 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1066.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid498.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid222.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid411.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid268.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid378.6 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 Acid491.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)706.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid775.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid257.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid863.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid345.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid430.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate752.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA402.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water329.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Platinum[Pt]700.7Standard polar33892256
Platinum[Pt]242.7Standard non polar33892256
Platinum[Pt]77.4Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Platinum 10V, Positive-QTOFsplash10-0002-0900000000-2c75785e555aaa3eac6b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Platinum 20V, Positive-QTOFsplash10-0002-0900000000-2c75785e555aaa3eac6b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Platinum 40V, Positive-QTOFsplash10-0002-0900000000-2c75785e555aaa3eac6b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Platinum 10V, Negative-QTOFsplash10-0006-0900000000-1cf99af463a2b764673a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Platinum 20V, Negative-QTOFsplash10-0006-0900000000-1cf99af463a2b764673a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Platinum 40V, Negative-QTOFsplash10-0006-0900000000-1cf99af463a2b764673a2016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
BloodDetected and Quantified0.0000087-0.0020000 uMAdult (>18 years old)Both
Normal		 details
Cerebrospinal Fluid (CSF)Detected and Quantified0.041 +/- 0.012 uMAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected and Quantified0.004 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
UrineDetected and Quantified0.000155 (0.000031- 0.000560) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.0000656 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB12257
Phenol Explorer Compound IDNot Available
FooDB IDFDB030068
KNApSAcK IDNot Available
Chemspider ID22381
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPlatinum
METLIN IDNot Available
PubChem Compound23939
PDB IDNot Available
ChEBI ID33364
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1722211
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available