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Showing metabocard for Erbium (HMDB0303935)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 05:47:34 UTC
Update Date2021-09-24 05:47:34 UTC
HMDB IDHMDB0303935
Secondary Accession NumbersNone
Metabolite Identification
Common NameErbium
DescriptionErbium, also known as 68er or erbio, is a member of the class of compounds known as homogeneous lanthanide compounds. Homogeneous lanthanide compounds are inorganic compounds containing only metal atoms, with the largest atom being a lanthanide atom. Erbium can be found in red beetroot and spinach, which makes erbium a potential biomarker for the consumption of these food products. Erbium's principal uses involve its pink-colored Er3+ ions, which have optical fluorescent properties particularly useful in certain laser applications. Erbium-doped glasses or crystals can be used as optical amplification media, where Er3+ ions are optically pumped at around 980 or 1480 nm and then radiate light at 1530 nm in stimulated emission. This process results in an unusually mechanically simple laser optical amplifier for signals transmitted by fiber optics. The 1550 nm wavelength is especially important for optical communications because standard single mode optical fibers have minimal loss at this particular wavelength .
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303935 (Erbium)


  Mrv0541 03031519452D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Er  0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for HMDB0303935 (Erbium)

HMDB0303935
     RDKit          3D
Erbium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Er  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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3D SDF for HMDB0303935 (Erbium)


  Mrv0541 03031519452D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Er  0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0303935

> <DATABASE_NAME>
hmdb

> <SMILES>
[Er]

> <INCHI_IDENTIFIER>
InChI=1S/Er

> <INCHI_KEY>
UYAHIZSMUZPPFV-UHFFFAOYSA-N

> <FORMULA>
Er

> <MOLECULAR_WEIGHT>
167.259

> <EXACT_MASS>
165.9303

> <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>
erbium

> <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>
erbium

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0303935 (Erbium)

HMDB0303935
     RDKit          3D
Erbium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Er  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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PDB for HMDB0303935 (Erbium)

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 Er   UNK     0       0.000   0.000   0.000  0.00  0.00          Er+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0303935 (Erbium)

COMPND    HMDB0303935
HETATM    1 ER1  UNL     1       0.000   0.000   0.000  1.00  0.00          ER  
END
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SMILES for HMDB0303935 (Erbium)

[Er]
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INCHI for HMDB0303935 (Erbium)

InChI=1S/Er
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View in JSmolView Stereo Labels
Synonyms
ValueSource
68ErChEBI
ErChEBI
ErbioChEBI
Chemical FormulaEr
Average Molecular Weight167.259
Monoisotopic Molecular Weight165.9303
IUPAC Nameerbium
Traditional Nameerbium
CAS Registry NumberNot Available
SMILES
[Er]
InChI Identifier
InChI=1S/Er
InChI KeyUYAHIZSMUZPPFV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous lanthanide compounds. These are inorganic compounds containing only metal atoms, with the largest atom being a lanthanide atom.
KingdomInorganic compounds
Super ClassHomogeneous metal compounds
ClassHomogeneous lanthanide compounds
Sub ClassNot Available
Direct ParentHomogeneous lanthanide compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous lanthanide
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]+153.48732859911
AllCCS[M+H-H2O]+150.13332859911
AllCCS[M+Na]+157.51532859911
AllCCS[M+NH4]+156.61332859911
AllCCS[M-H]-229.00732859911
AllCCS[M+Na-2H]-240.80532859911
AllCCS[M+HCOO]-253.64332859911

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 IDFDB030058
KNApSAcK IDNot Available
Chemspider ID22416
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound23980
PDB IDNot Available
ChEBI ID33379
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