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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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22546835)
  • Saliva (HMDB: HMDB0013667)
  • Cerebrospinal fluid (HMDB: HMDB0013667)
    • Source
    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 Retention Times

    Underivatized

    Chromatographic MethodRetention TimeReference
    AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid272.5 seconds40023050
    Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid862.1 seconds40023050
    Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid410.3 seconds40023050
    Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid187.3 seconds40023050
    Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid340.6 seconds40023050
    RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid202.8 seconds40023050
    Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid300.3 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 Acid387.8 seconds40023050
    HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)567.0 seconds40023050
    UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid634.8 seconds40023050
    BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid162.7 seconds40023050
    UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid708.1 seconds40023050
    SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid276.7 seconds40023050
    RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid361.4 seconds40023050
    MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate644.2 seconds40023050
    KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA350.2 seconds40023050
    Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water282.0 seconds40023050

    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