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Showing metabocard for Gadolinium (HMDB0041899)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-13 11:46:51 UTC
Update Date2022-03-07 02:57:13 UTC
HMDB IDHMDB0041899
Secondary Accession Numbers
  • HMDB41899
Metabolite Identification
Common NameGadolinium
DescriptionAlthough gadolinium agents have proved useful for patients with renal impairment, in patients with severe renal failure requiring dialysis, there is a risk of a rare but serious illnesses, called nephrogenic systemic fibrosis (NSF) or nephrogenic fibrosing dermopathy, that has been linked to the use of four gadolinium-containing MRI contrast agents. The disease resembles scleromyxedema and to some extent scleroderma. It may occur months after contrast has been injected. Its association with gadolinium and not the carrier molecule is confirmed by its occurrence in from contrast materials in which gadolinium is carried by very different carrier molecules. Gadolinium is a chemical element with symbol Gd and atomic number 64. It is a silvery-white, malleable and ductile rare-earth metal. It is found in nature only in combined (salt) form. Gadolinium was first detected spectroscopically in 1880 by de Marignac who separated its oxide and is credited with its discovery. It is named for gadolinite, one of the minerals in which it was found, in turn named for chemist Johan Gadolin. The metal was isolated by Lecoq de Boisbaudran in 1886. Gadolinium as a phosphor is also used in other imaging. In X-ray systems, gadolinium is contained in the phosphor layer, suspended in a polymer matrix at the detector. Terbium-doped gadolinium oxysulfide (Gd2O2S: Tb) at the phosphor layer converts the X-rays released from the source into light. This material emits green light at 540 nm due to the presence of Tb3+, which is very useful for enhancing the imaging quality. The energy conversion of Gd is up to 20%, which means that one-fifth of the X-rays striking the phosphor layer can be converted into light photons. Gadolinium oxyorthosilicate (Gd2SiO5, GSO; usually doped by 0.1-1% of Ce) is a single crystal that is used as a scintillator in medical imaging such as positron emission tomography or for detecting neutrons. Gadolinium is a constituent in many minerals such as monazite and bastnasite, which are oxides. The metal is too reactive to exist naturally. Ironically, as noted above, the mineral gadolinite actually contains only traces of Gd. The abundance in the earth crust is about 6.2 mg/kg. The main mining areas are China, USA, Brazil, Sri Lanka, India and Australia with reserves expected to exceed one million tonnes. World production of pure gadolinium is about 400 tonnes per year. Gadolinium is a silvery-white malleable and ductile rare-earth metal. It crystallizes in hexagonal, close-packed 1- form at room temperature, but, when heated to temperatures above 1235 °C, it transforms into its 2- form, which has a body-centered cubic structure. Gadolinium is a strong reducing agent, which reduces oxides of several metals into their elements. Gadolinium is quite electropositive and reacts slowly with cold water and quite quickly with hot water to form gadolinium hydroxide:
Structure
Data?1563863712
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0041899 (Gadolinium)


  Mrv0541 09131211462D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Gd  0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for HMDB0041899 (Gadolinium)

HMDB0041899
     RDKit          3D
Gadolinium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Gd  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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3D SDF for HMDB0041899 (Gadolinium)


  Mrv0541 09131211462D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Gd  0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0041899

> <DATABASE_NAME>
hmdb

> <SMILES>
[Gd]

> <INCHI_IDENTIFIER>
InChI=1S/Gd

> <INCHI_KEY>
UIWYJDYFSGRHKR-UHFFFAOYSA-N

> <FORMULA>
Gd

> <MOLECULAR_WEIGHT>
157.25

> <EXACT_MASS>
157.924100533

> <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>
gadolinium

> <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>
gadolinium

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0041899 (Gadolinium)

HMDB0041899
     RDKit          3D
Gadolinium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Gd  0  0  0  0  0 15  0  0  0  0  0  0
M  END
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PDB for HMDB0041899 (Gadolinium)

HEADER    PROTEIN                                 13-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-SEP-12         0                                  
HETATM    1 Gd   UNK     0       0.000   0.000   0.000  0.00  0.00          Gd+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0041899 (Gadolinium)

COMPND    HMDB0041899
HETATM    1 GD1  UNL     1       0.000   0.000   0.000  1.00  0.00          GD  
END
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SMILES for HMDB0041899 (Gadolinium)

[Gd]
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INCHI for HMDB0041899 (Gadolinium)

InChI=1S/Gd
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View in JSmolView Stereo Labels
Synonyms
ValueSource
64GDChEBI
GadolinioChEBI
GdChEBI
Motexafin gadoliniumHMDB
GadoliniumChEBI
Chemical FormulaGd
Average Molecular Weight157.25
Monoisotopic Molecular Weight157.924100533
IUPAC Namegadolinium
Traditional Namegadolinium
CAS Registry Number7440-54-2
SMILES
[Gd]
InChI Identifier
InChI=1S/Gd
InChI KeyUIWYJDYFSGRHKR-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
Role
Industrial applicationBiological role
Physical Properties
StateLiquid
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]+136.932859911
AllCCS[M+H-H2O]+133.532859911
AllCCS[M+NH4]+140.232859911
AllCCS[M+Na]+141.132859911
AllCCS[M-H]-176.232859911
AllCCS[M+Na-2H]-187.832859911
AllCCS[M+HCOO]-200.432859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid282.6 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid928.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid432.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid194.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid357.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid208.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid326.0 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 Acid418.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)605.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid662.2 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid182.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid762.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid292.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid387.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate698.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA368.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water308.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Gadolinium[Gd]697.9Standard polar33892256
Gadolinium[Gd]241.4Standard non polar33892256
Gadolinium[Gd]69.7Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gadolinium 10V, Positive-QTOFsplash10-0a4i-0900000000-572da205f8e2e1264df12017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gadolinium 20V, Positive-QTOFsplash10-0a4i-0900000000-572da205f8e2e1264df12017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gadolinium 40V, Positive-QTOFsplash10-0a4i-0900000000-572da205f8e2e1264df12017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gadolinium 10V, Negative-QTOFsplash10-0a4i-0900000000-d2f64f0c400dfa0135032017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gadolinium 20V, Negative-QTOFsplash10-0a4i-0900000000-d2f64f0c400dfa0135032017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gadolinium 40V, Negative-QTOFsplash10-0a4i-0900000000-d2f64f0c400dfa0135032017-07-26Wishart LabView Spectrum
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 IDDB12091
Phenol Explorer Compound IDNot Available
FooDB IDFDB030054
KNApSAcK IDNot Available
Chemspider ID22418
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGadolinium
METLIN IDNot Available
PubChem Compound23982
PDB IDNot Available
ChEBI ID33375
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