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Showing metabocard for Yttrium (HMDB0013667)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-01-26 16:10:12 UTC
Update Date2020-02-26 21:39:01 UTC
HMDB IDHMDB0013667
Secondary Accession Numbers
  • HMDB13667
Metabolite Identification
Common NameYttrium
DescriptionYttrium, also known as 39Y or ytrio, 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. Yttrium is possibly neutral. In conjunction with other rare earths, yttrium is used as a phosphor in television receivers and is a component of the yttrium-aluminum garnet (YAG) lasers. Outside of the human body, Yttrium is found, on average, in the highest concentration within a few different foods, such as milk (cow), spinachs, and red beetroots and in a lower concentration in yellow zucchinis, japanese pumpkins, and carrots. Yttrium has also been detected, but not quantified in, cucumbers. This could make yttrium a potential biomarker for the consumption of these foods. An element of the rare earth family of metals. It has the atomic symbol Y, atomic number 39, and atomic weight 88.91.
Structure
Data?1582753141
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013667 (Yttrium)


  Mrv0541 02271201192D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Y   0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for HMDB0013667 (Yttrium)

HMDB0013667
     RDKit          3D
Yttrium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Y   0  0  0  0  0 15  0  0  0  0  0  0
M  END
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3D SDF for HMDB0013667 (Yttrium)


  Mrv0541 02271201192D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Y   0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013667

> <DATABASE_NAME>
hmdb

> <SMILES>
[Y]

> <INCHI_IDENTIFIER>
InChI=1S/Y

> <INCHI_KEY>
VWQVUPCCIRVNHF-UHFFFAOYSA-N

> <FORMULA>
Y

> <MOLECULAR_WEIGHT>
88.9059

> <EXACT_MASS>
88.905847902

> <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>
yttrium

> <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>
yttrium

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0013667 (Yttrium)

HMDB0013667
     RDKit          3D
Yttrium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Y   0  0  0  0  0 15  0  0  0  0  0  0
M  END
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PDB for HMDB0013667 (Yttrium)

HEADER    PROTEIN                                 27-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-FEB-12         0                                  
HETATM    1  Y   UNK     0       0.000   0.000   0.000  0.00  0.00           Y+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0013667 (Yttrium)

COMPND    HMDB0013667
HETATM    1  Y1  UNL     1       0.000   0.000   0.000  1.00  0.00           Y  
END
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SMILES for HMDB0013667 (Yttrium)

[Y]
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INCHI for HMDB0013667 (Yttrium)

InChI=1S/Y
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View in JSmolView Stereo Labels
Synonyms
ValueSource
39YChEBI
YChEBI
YtrioChEBI
Yttrium y 90 epratuzumabHMDB
YttriumChEBI
Chemical FormulaY
Average Molecular Weight88.9059
Monoisotopic Molecular Weight88.905847902
IUPAC Nameyttrium
Traditional Nameyttrium
CAS Registry Number7440-65-5
SMILES
[Y]
InChI Identifier
InChI=1S/Y
InChI KeyVWQVUPCCIRVNHF-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 Point1526 °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]+123.432859911
AllCCS[M+H-H2O]+119.732859911
AllCCS[M+NH4]+126.832859911
AllCCS[M+Na]+127.832859911
AllCCS[M-H]-139.732859911
AllCCS[M+Na-2H]-151.332859911
AllCCS[M+HCOO]-164.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Yttrium[Y]695.2Standard polar33892256
Yttrium[Y]237.8Standard non polar33892256
Yttrium[Y]72.1Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yttrium 10V, Positive-QTOFsplash10-000i-9000000000-597609eca3b881292a212016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yttrium 20V, Positive-QTOFsplash10-000i-9000000000-597609eca3b881292a212016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yttrium 40V, Positive-QTOFsplash10-000i-9000000000-597609eca3b881292a212016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yttrium 10V, Negative-QTOFsplash10-000i-9000000000-288c3d6979fa1d89b6c32016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yttrium 20V, Negative-QTOFsplash10-000i-9000000000-288c3d6979fa1d89b6c32016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Yttrium 40V, Negative-QTOFsplash10-000i-9000000000-288c3d6979fa1d89b6c32016-08-04Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Cerebrospinal Fluid (CSF)
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Cerebrospinal Fluid (CSF)Detected and Quantified0.004 +/- 0.001 uMAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected and Quantified0.005 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030035
KNApSAcK IDNot Available
Chemspider ID22429
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkYttrium
METLIN IDNot Available
PubChem Compound23993
PDB IDNot Available
ChEBI ID33331
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