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Showing metabocard for Palladium (HMDB0013670)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-01-27 11:43:36 UTC
Update Date2020-02-26 21:39:01 UTC
HMDB IDHMDB0013670
Secondary Accession Numbers
  • HMDB13670
Metabolite Identification
Common NamePalladium
DescriptionPalladium, also known as 46PD or paladio, 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. Palladium is found, on average, in the highest concentration within a few different foods, such as milk (cow), garlics (Allium sativum), and broccolis (Brassica oleracea var. italica) and in a lower concentration in romaine lettuces (Lactuca sativa L. var. longifolia), spinaches (Spinacia oleracea), and orange bell peppers (Capsicum annuum). This could make palladium a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Palladium.
Structure
Data?1582753141
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013670 (Palladium)


  Mrv0541 09051414492D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Pd  0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for HMDB0013670 (Palladium)

HMDB0013670
     RDKit          3D
Palladium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Pd  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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3D SDF for HMDB0013670 (Palladium)


  Mrv0541 09051414492D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Pd  0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013670

> <DATABASE_NAME>
hmdb

> <SMILES>
[Pd]

> <INCHI_IDENTIFIER>
InChI=1S/Pd

> <INCHI_KEY>
KDLHZDBZIXYQEI-UHFFFAOYSA-N

> <FORMULA>
Pd

> <MOLECULAR_WEIGHT>
106.42

> <EXACT_MASS>
105.903483087

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
palladium

> <JCHEM_LOGP>
0.0

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
0.0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
palladium

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0013670 (Palladium)

HMDB0013670
     RDKit          3D
Palladium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Pd  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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PDB for HMDB0013670 (Palladium)

HEADER    PROTEIN                                 05-SEP-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-14         0                                  
HETATM    1 Pd   UNK     0       0.000   0.000   0.000  0.00  0.00          Pd+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0013670 (Palladium)

COMPND    HMDB0013670
HETATM    1 PD1  UNL     1       0.000   0.000   0.000  1.00  0.00          PD  
END
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SMILES for HMDB0013670 (Palladium)

[Pd]
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INCHI for HMDB0013670 (Palladium)

InChI=1S/Pd
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View in JSmolView Stereo Labels
Synonyms
ValueSource
46pdChEBI
PaladioChEBI
PdChEBI
Chemical FormulaPd
Average Molecular Weight106.42
Monoisotopic Molecular Weight105.903483087
IUPAC Namepalladium
Traditional Namepalladium
CAS Registry Number7440-05-3
SMILES
[Pd]
InChI Identifier
InChI=1S/Pd
InChI KeyKDLHZDBZIXYQEI-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
Disposition

Biological location

Source

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point1554.9 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP0Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0ChemAxon
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]+126.832859911
AllCCS[M+H-H2O]+123.232859911
AllCCS[M+NH4]+130.132859911
AllCCS[M+Na]+131.132859911
AllCCS[M-H]-148.732859911
AllCCS[M+Na-2H]-160.332859911
AllCCS[M+HCOO]-173.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Palladium[Pd]698.6Standard polar33892256
Palladium[Pd]236.6Standard non polar33892256
Palladium[Pd]72.3Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Palladium 10V, Positive-QTOFsplash10-0a4i-0900000000-cfbea5880bde44122df52016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Palladium 20V, Positive-QTOFsplash10-0a4i-0900000000-cfbea5880bde44122df52016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Palladium 40V, Positive-QTOFsplash10-0a4i-0900000000-cfbea5880bde44122df52016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Palladium 10V, Negative-QTOFsplash10-0udi-0900000000-e5a383c648e39dd19c112016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Palladium 20V, Negative-QTOFsplash10-0udi-0900000000-e5a383c648e39dd19c112016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Palladium 40V, Negative-QTOFsplash10-0udi-0900000000-e5a383c648e39dd19c112016-08-03Wishart 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
Cerebrospinal Fluid (CSF)Detected and Quantified0.036 +/- 0.018 uMAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected and Quantified0.947 +/- 0.86 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
UrineDetected and Quantified0.0110 (0.0011-0.1410) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified< 0.00001 - 0.2538 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030040
KNApSAcK IDNot Available
Chemspider ID22380
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPalladium
METLIN IDNot Available
PubChem Compound23938
PDB IDNot Available
ChEBI ID33363
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General ReferencesNot Available