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Showing metabocard for Zirconium (HMDB0001475)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-02-26 21:23:24 UTC
HMDB IDHMDB0001475
Secondary Accession Numbers
  • HMDB01475
Metabolite Identification
Common NameZirconium
DescriptionThe action of Zirconium (Zr) on biological systems presents an enigma. It is ubiquitous, being present in nature in amounts higher than most trace elements. It is taken up by plants from soil and water and accumulated in certain tissues. The entry into animal systems in vivo is related to the mode of exposure and the concentration in the surrounding environment. Retention is initially in soft tissues and then slowly in the bone. The metal is able to cross the blood brain-barrier and is deposited in the brain and the placental barrier to enter milk. Physiologically, it exists as an ion in the body. The daily human uptake has been known to be as high as 125 mg. The level of toxicity has been found to be moderately low, both in histological and cytological studies. The toxic effects induced by very high concentrations are nonspecific in nature. Despite the presence and retention in relatively high quantities in biological systems, Zr has not yet been associated with any specific metabolic function. Very little information is available about its interaction with the compounds of the genetical systems, such as nucleic acids. Apparently, the metal is neither an essential nor toxic element in the conventional sense. However, the increasing exposure to this element through its increasing use in new materials and following radioactive fallout, has increased the importance of the study of its effects on living organisms. The tetravalent nature of the ionic state and the high stability of the compounds formed are important factors that need to be considered, as also the accumulation of this element in the brain, reminiscent of the relationship between Aluminum and Alzheimer's disease. Zirconium is a metallic element with the atomic number 40 and mol wt 91.99, and belongs to the group IVB and second transition series of the fifth period of Mendeleyev's periodic table. It was named from Arabic zargun, meaning gold color. Discovered in the semiprecious gem zircon, as orthosilicate, by Klaproth in 1789, Zr was isolated as an element by Berzelius in 1824. In its metal form, Zr is hard and resistant to corrosion, heat, and acid. Zirconium behaves like an essential trace metal in the biosphere, although the possibility that it is a natural contaminant with no considerable physiological effects must be considered (PMID: 1283692 , Biol Trace Elem Res. 1992 Dec;35(3):247-71.).
Structure
Data?1582752204
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001475 (Zirconium)


  Mrv0541 02231219092D          

  1  0  0  0  0  0            999 V2000
   26.7353  -16.9068    0.0000 Zr  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 HMDB0001475 (Zirconium)

HMDB0001475
     RDKit          3D
Zirconium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Zr  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 HMDB0001475 (Zirconium)


  Mrv0541 02231219092D          

  1  0  0  0  0  0            999 V2000
   26.7353  -16.9068    0.0000 Zr  0  0  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   4
M  END
> <DATABASE_ID>
HMDB0001475

> <DATABASE_NAME>
hmdb

> <SMILES>
[Zr+4]

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

> <INCHI_KEY>
GBNDTYKAOXLLID-UHFFFAOYSA-N

> <FORMULA>
Zr

> <MOLECULAR_WEIGHT>
91.224

> <EXACT_MASS>
89.904703679

> <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>
zirconium(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>
zirconium(4+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0001475 (Zirconium)

HMDB0001475
     RDKit          3D
Zirconium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Zr  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 HMDB0001475 (Zirconium)

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 Zr   UNK     0      49.906 -31.559   0.000  0.00  0.00          Zr+4
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0001475 (Zirconium)

COMPND    HMDB0001475
HETATM    1 ZR1  UNL     1       0.000   0.000   0.000  1.00  0.00          ZR4+
END
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SMILES for HMDB0001475 (Zirconium)

[Zr+4]
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INCHI for HMDB0001475 (Zirconium)

InChI=1S/Zr/q+4
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View in JSmolView Stereo Labels
Synonyms
ValueSource
CirconioHMDB
ZircatHMDB
ZirconioHMDB
ZirkoniumHMDB
ZrHMDB
Chemical FormulaZr
Average Molecular Weight91.224
Monoisotopic Molecular Weight89.904703679
IUPAC Namezirconium(4+) ion
Traditional Namezirconium(4+) ion
CAS Registry Number7440-67-7
SMILES
[Zr+4]
InChI Identifier
InChI=1S/Zr/q+4
InChI KeyGBNDTYKAOXLLID-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 DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point1857 °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]+123.5632859911
AllCCS[M-H]-140.19132859911
AllCCS[M+H]+123.632859911
AllCCS[M+H-H2O]+119.932859911
AllCCS[M+NH4]+127.032859911
AllCCS[M+Na]+128.032859911
AllCCS[M-H]-140.232859911
AllCCS[M+Na-2H]-151.932859911
AllCCS[M+HCOO]-164.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Zirconium[Zr+4]697.3Standard polar33892256
Zirconium[Zr+4]230.0Standard non polar33892256
Zirconium[Zr+4]44.2Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zirconium 10V, Positive-QTOFsplash10-0006-9000000000-eeb5929a6e02556f62fb2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zirconium 20V, Positive-QTOFsplash10-0006-9000000000-eeb5929a6e02556f62fb2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zirconium 40V, Positive-QTOFsplash10-0006-9000000000-eeb5929a6e02556f62fb2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zirconium 10V, Negative-QTOFsplash10-000i-9000000000-40db25c0ee17df55c09e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zirconium 20V, Negative-QTOFsplash10-000i-9000000000-40db25c0ee17df55c09e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zirconium 40V, Negative-QTOFsplash10-000i-9000000000-40db25c0ee17df55c09e2016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.00077-0.0050 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.00132 +/- 0.00055 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.00526 +/- 0.00274 uMAdult (>18 years old)Both
Normal		 details
Cerebrospinal Fluid (CSF)Detected and Quantified0.277 +/- 0.086 uMAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected and Quantified0.237 +/- 0.10 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
UrineDetected and Quantified0.021 (0.004-0.083) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.0012-0.0074 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.00099 +/- 0.00077 uMElderly (>65 years old)Both
Parkinson's disease		 details
BloodDetected and Quantified0.00417 +/- 0.00186 uMElderly (>65 years old)Both
Parkinson's disease		 details
Associated Disorders and Diseases
Disease References
Parkinson's disease
  1. Forte G, Alimonti A, Pino A, Stanzione P, Brescianini S, Brusa L, Sancesario G, Violante N, Bocca B: Metals and oxidative stress in patients with Parkinson's disease. Ann Ist Super Sanita. 2005;41(2):189-95. [PubMed:16244392 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB004189
KNApSAcK IDNot Available
Chemspider ID103026
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkZirconium
METLIN IDNot Available
PubChem Compound115139
PDB IDNot Available
ChEBI ID33342
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Ghosh S, Sharma A, Talukder G: Zirconium. An abnormal trace element in biology. Biol Trace Elem Res. 1992 Dec;35(3):247-71. [PubMed:1283692 ]