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Showing metabocard for Germanium (HMDB0002501)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:55 UTC
Update Date2022-03-07 02:49:16 UTC
HMDB IDHMDB0002501
Secondary Accession Numbers
  • HMDB02501
Metabolite Identification
Common NameGermanium
DescriptionGermanium is not an essential element. Physiologically, it exists as an ion in the body. Its acute toxicity is low. Germanium-containing dietary supplements became popular in the 1970s in Japan and later in other countries, as elixirs for certain diseases (e.g., cancer and AIDS). However, at least 31 reported human cases linked prolonged intake of germanium products with renal failure and even death.
Structure
Data?1582752251
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002501 (Germanium)


  Mrv0541 02231219332D          

  1  0  0  0  0  0            999 V2000
   15.7858  -14.5350    0.0000 Ge  0  0  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   4
M  END
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3D MOL for HMDB0002501 (Germanium)

HMDB0002501
     RDKit          3D
Germanium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Ge  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   4
M  END
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3D SDF for HMDB0002501 (Germanium)


  Mrv0541 02231219332D          

  1  0  0  0  0  0            999 V2000
   15.7858  -14.5350    0.0000 Ge  0  0  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   4
M  END
> <DATABASE_ID>
HMDB0002501

> <DATABASE_NAME>
hmdb

> <SMILES>
[Ge+4]

> <INCHI_IDENTIFIER>
InChI=1S/Ge/q+4

> <INCHI_KEY>
CULSIAXQVSZNSV-UHFFFAOYSA-N

> <FORMULA>
Ge

> <MOLECULAR_WEIGHT>
72.64

> <EXACT_MASS>
73.921178213

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
germanium(4+) ion

> <JCHEM_LOGP>
0

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
germanium(4+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0002501 (Germanium)

HMDB0002501
     RDKit          3D
Germanium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Ge  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   4
M  END
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PDB for HMDB0002501 (Germanium)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1 Ge   UNK     0      29.467 -27.132   0.000  0.00  0.00          Ge+4
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0002501 (Germanium)

COMPND    HMDB0002501
HETATM    1 GE1  UNL     1       0.000   0.000   0.000  1.00  0.00          GE4+
END
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SMILES for HMDB0002501 (Germanium)

[Ge+4]
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INCHI for HMDB0002501 (Germanium)

InChI=1S/Ge/q+4
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Ge(4+)ChEBI
GeHMDB
GermideHMDB
SerocionHMDB
Chemical FormulaGe
Average Molecular Weight72.64
Monoisotopic Molecular Weight73.921178213
IUPAC Namegermanium(4+) ion
Traditional Namegermanium(4+) ion
CAS Registry Number7440-56-4
SMILES
[Ge+4]
InChI Identifier
InChI=1S/Ge/q+4
InChI KeyCULSIAXQVSZNSV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous metalloid compounds. These are inorganic compounds containing only metal atoms,with the largest atom being a metalloid atom.
KingdomInorganic compounds
Super ClassHomogeneous metal compounds
ClassHomogeneous metalloid compounds
Sub ClassNot Available
Direct ParentHomogeneous metalloid compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous metalloid
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point938.3 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0ChemAxon
Physiological Charge4ChemAxon
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]+120.732859911
AllCCS[M+H-H2O]+117.032859911
AllCCS[M+NH4]+124.232859911
AllCCS[M+Na]+125.232859911
AllCCS[M-H]-131.132859911
AllCCS[M+Na-2H]-142.832859911
AllCCS[M+HCOO]-155.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid282.4 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid785.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid395.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid179.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid327.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid184.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid285.3 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 Acid362.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)543.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid603.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid129.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid683.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid263.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid353.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate642.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA345.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water294.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Germanium[Ge+4]686.0Standard polar33892256
Germanium[Ge+4]249.1Standard non polar33892256
Germanium[Ge+4]127.0Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Germanium 10V, Positive-QTOFsplash10-001i-9000000000-d30e86fb68c056ba94fa2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Germanium 20V, Positive-QTOFsplash10-001i-9000000000-d30e86fb68c056ba94fa2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Germanium 40V, Positive-QTOFsplash10-001i-9000000000-d30e86fb68c056ba94fa2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Germanium 10V, Negative-QTOFsplash10-001i-9000000000-0aec2ac48ffee5c3828a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Germanium 20V, Negative-QTOFsplash10-001i-9000000000-0aec2ac48ffee5c3828a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Germanium 40V, Negative-QTOFsplash10-001i-9000000000-0aec2ac48ffee5c3828a2016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
SalivaDetected and Quantified0.006 +/- 0.003 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
UrineDetected and Quantified1.58 (0.49-2.6) umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB003630
KNApSAcK IDNot Available
Chemspider ID10605699
KEGG Compound IDC15472
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGermanium
METLIN IDNot Available
PubChem Compound73608878
PDB IDNot Available
ChEBI ID30550
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 References
  1. Nielsen FH: How should dietary guidance be given for mineral elements with beneficial actions or suspected of being essential? J Nutr. 1996 Sep;126(9 Suppl):2377S-2385S. [PubMed:8811801 ]
  2. Tao SH, Bolger PM: Hazard assessment of germanium supplements. Regul Toxicol Pharmacol. 1997 Jun;25(3):211-9. [PubMed:9237323 ]