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Showing metabocard for Osmium (HMDB0303937)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 05:48:33 UTC
Update Date2021-09-24 05:48:33 UTC
HMDB IDHMDB0303937
Secondary Accession NumbersNone
Metabolite Identification
Common NameOsmium
DescriptionOsmium, also known as 76os or osmio, is a member of the class of compounds known as homogeneous transition metal compounds. Homogeneous transition metal compounds are inorganic compounds containing only metal atoms,with the largest atom being a transition metal atom. Osmium can be found in a number of food items such as garlic, dill, sunburst squash (pattypan squash), and green zucchini, which makes osmium a potential biomarker for the consumption of these food products. Osmium (from Greek ὀσμή osme, "smell") is a chemical element with symbol Os and atomic number 76. It is a hard, brittle, bluish-white transition metal in the platinum group that is found as a trace element in alloys, mostly in platinum ores. Osmium is the densest naturally occurring element, with a density of 22.59 g/cm3. Its alloys with platinum, iridium, and other platinum-group metals are employed in fountain pen nib tipping, electrical contacts, and other applications where extreme durability and hardness are needed .
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303937 (Osmium)


  Mrv0541 03031519452D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Os  0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for HMDB0303937 (Osmium)

HMDB0303937
     RDKit          3D
Osmium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Os  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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3D SDF for HMDB0303937 (Osmium)


  Mrv0541 03031519452D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Os  0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0303937

> <DATABASE_NAME>
hmdb

> <SMILES>
[Os]

> <INCHI_IDENTIFIER>
InChI=1S/Os

> <INCHI_KEY>
SYQBFIAQOQZEGI-UHFFFAOYSA-N

> <FORMULA>
Os

> <MOLECULAR_WEIGHT>
190.23

> <EXACT_MASS>
191.96148

> <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>
osmium

> <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>
osmium

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0303937 (Osmium)

HMDB0303937
     RDKit          3D
Osmium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Os  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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PDB for HMDB0303937 (Osmium)

HEADER    PROTEIN                                 03-MAR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAR-15         0                                  
HETATM    1 Os   UNK     0       0.000   0.000   0.000  0.00  0.00          Os+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0303937 (Osmium)

COMPND    HMDB0303937
HETATM    1 OS1  UNL     1       0.000   0.000   0.000  1.00  0.00          OS  
END
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SMILES for HMDB0303937 (Osmium)

[Os]
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INCHI for HMDB0303937 (Osmium)

InChI=1S/Os
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View in JSmolView Stereo Labels
Synonyms
ValueSource
76OsChEBI
OsChEBI
OsmioChEBI
OsmiumChEBI
Chemical FormulaOs
Average Molecular Weight190.23
Monoisotopic Molecular Weight191.96148
IUPAC Nameosmium
Traditional Nameosmium
CAS Registry NumberNot Available
SMILES
[Os]
InChI Identifier
InChI=1S/Os
InChI KeySYQBFIAQOQZEGI-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
Source
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
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]+158.24932859911
AllCCS[M+H-H2O]+154.96532859911
AllCCS[M+Na]+162.1932859911
AllCCS[M+NH4]+161.30832859911
AllCCS[M-H]-242.97332859911
AllCCS[M+Na-2H]-254.71332859911
AllCCS[M+HCOO]-267.47832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1015.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid469.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid211.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid387.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid245.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid356.7 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 Acid461.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)704.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid725.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid223.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid815.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid321.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid412.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate740.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA414.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water325.7 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030066
KNApSAcK IDNot Available
Chemspider ID22379
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound23937
PDB IDNot Available
ChEBI ID30687
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