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Showing metabocard for Ruthenium (HMDB0013668)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-01-26 17:21:25 UTC
Update Date2020-02-26 21:39:01 UTC
HMDB IDHMDB0013668
Secondary Accession Numbers
  • HMDB13668
Metabolite Identification
Common NameRuthenium
DescriptionRuthenium, also known as 44RU or rutenio, 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. Ruthenium is found, on average, in the highest concentration within a few different foods, such as yellow zucchinis (Cucurbita pepo var. cylindrica), dills (Anethum graveolens), and spinaches (Spinacia oleracea) and in a lower concentration in garden tomatoes (Solanum lycopersicum), red beetroots (Beta vulgaris var. rubra), and carrots (Daucus carota ssp. sativus). Ruthenium has also been detected, but not quantified in, cucumbers (Cucumis sativus) and romaine lettuces (Lactuca sativa L. var. longifolia). This could make ruthenium a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Ruthenium.
Structure
Data?1582753141
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013668 (Ruthenium)

23950
  Mrv0541 02271202152D          

  1  0  0  0  0  0            999 V2000
    2.0000    0.0000    0.0000 Ru  0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for HMDB0013668 (Ruthenium)

HMDB0013668
     RDKit          3D
Ruthenium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Ru  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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3D SDF for HMDB0013668 (Ruthenium)

23950
  Mrv0541 02271202152D          

  1  0  0  0  0  0            999 V2000
    2.0000    0.0000    0.0000 Ru  0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013668

> <DATABASE_NAME>
hmdb

> <SMILES>
[Ru]

> <INCHI_IDENTIFIER>
InChI=1S/Ru

> <INCHI_KEY>
KJTLSVCANCCWHF-UHFFFAOYSA-N

> <FORMULA>
Ru

> <MOLECULAR_WEIGHT>
101.07

> <EXACT_MASS>
101.904349503

> <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>
ruthenium

> <JCHEM_LOGP>
0

> <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>
ruthenium

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0013668 (Ruthenium)

HMDB0013668
     RDKit          3D
Ruthenium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Ru  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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PDB for HMDB0013668 (Ruthenium)

HEADER    PROTEIN                                 27-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 23950                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-FEB-12         0                                  
HETATM    1 Ru   UNK     0       3.733   0.000   0.000  0.00  0.00          Ru+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0013668 (Ruthenium)

COMPND    HMDB0013668
HETATM    1 RU1  UNL     1       0.000   0.000   0.000  1.00  0.00          RU  
END
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SMILES for HMDB0013668 (Ruthenium)

[Ru]
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INCHI for HMDB0013668 (Ruthenium)

InChI=1S/Ru
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View in JSmolView Stereo Labels
Synonyms
ValueSource
44RUChEBI
RuChEBI
RutenioChEBI
RutheniumChEBI
Chemical FormulaRu
Average Molecular Weight101.07
Monoisotopic Molecular Weight101.904349503
IUPAC Nameruthenium
Traditional Nameruthenium
CAS Registry Number7440-18-8
SMILES
[Ru]
InChI Identifier
InChI=1S/Ru
InChI KeyKJTLSVCANCCWHF-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
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point2334 °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]+146.832859911
AllCCS[M+H-H2O]+142.632859911
AllCCS[M+NH4]+150.832859911
AllCCS[M+Na]+151.932859911
AllCCS[M-H]-353.932859911
AllCCS[M+Na-2H]-366.032859911
AllCCS[M+HCOO]-379.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Ruthenium[Ru]704.9Standard polar33892256
Ruthenium[Ru]239.1Standard non polar33892256
Ruthenium[Ru]69.8Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ruthenium 10V, Positive-QTOFsplash10-0udi-0900000000-f8430a41a6e0f81da7782016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ruthenium 20V, Positive-QTOFsplash10-0udi-0900000000-f8430a41a6e0f81da7782016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ruthenium 40V, Positive-QTOFsplash10-0udi-0900000000-f8430a41a6e0f81da7782016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ruthenium 10V, Negative-QTOFsplash10-0udi-0900000000-a1a5c18d1fdb0876b9aa2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ruthenium 20V, Negative-QTOFsplash10-0udi-0900000000-a1a5c18d1fdb0876b9aa2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ruthenium 40V, Negative-QTOFsplash10-0udi-0900000000-a1a5c18d1fdb0876b9aa2016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
Cerebrospinal Fluid (CSF)Detected and Quantified0.005 +/- 0.002 uMAdult (>18 years old)Not SpecifiedNormal details
UrineDetected and Quantified0.0002 (0.0001-0.0009) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030039
KNApSAcK IDNot Available
Chemspider ID22390
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkRuthenium
METLIN IDNot Available
PubChem Compound23950
PDB IDNot Available
ChEBI ID30682
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 ReferencesNot Available