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Showing metabocard for Nickel (HMDB0002457)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
enzymes (3) Show 3 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:53 UTC
Update Date2020-10-09 21:10:37 UTC
HMDB IDHMDB0002457
Secondary Accession Numbers
  • HMDB02457
Metabolite Identification
Common NameNickel
DescriptionNickel is a solid, silver-white, hard, malleable transition metal with an atomic number of 28. It resists corrosion even at high temperatures. It is present in many alloys in widespread use, including stainless steels. It may also be present as an impurity in any alloy. Nickel is used in the production of coins, jewellery, and nickel-cadmium batteries, and as a catalyst for the hydrogenation of liquid oils to solid fats such as oleomargarine and vegetable shortening. Nickel-containing dental alloys continue to be used successfully in the provision of various forms of dental care. Many of these alloys have applications in the construction of restorations designed to remain in clinical service for many years, including crowns, fixed bridgework, and removable partial dentures. Furthermore, nickel containing alloys find extensive application in orthodontics, including metallic brackets, arch wires, bands, springs and ligature wires. Many instruments and devises, for example, endodontic instruments also contain nickel. Allergic responses are mediated through the immune system. In a sensitized individual, allergic responses can be initiated by relatively small amounts of the allergen; for example, if nickel ions are released from a nickel plated material following direct and prolonged contact with the skin. Individuals are first sensitized to the allergen. Subsequent exposures, if sufficiently high, may then result in an allergic reaction. A number of allergens are used in the clinical practice of dentistry, notably eugenol, mercury, nickel, chromium, cobalt, components of resin-based materials and a host of other chemical agents. The majority of dental allergies, including allergic responses to nickel-containing dental alloys, comprise Type IV hypersensitivity reactions, cell-mediated by T-lymphocytes. Physiologically, it exists as an ion in the body.(PMID: 17243350 , 16405986 ).
Structure
Data?1582752250
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002457 (Nickel)


  Mrv0541 02231219322D          

  1  0  0  0  0  0            999 V2000
   15.9758  -17.6858    0.0000 Ni  0  2  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   2
M  END
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3D MOL for HMDB0002457 (Nickel)

HMDB0002457
     RDKit          3D
Nickel
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Ni  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   2
M  END
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3D SDF for HMDB0002457 (Nickel)


  Mrv0541 02231219322D          

  1  0  0  0  0  0            999 V2000
   15.9758  -17.6858    0.0000 Ni  0  2  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   2
M  END
> <DATABASE_ID>
HMDB0002457

> <DATABASE_NAME>
hmdb

> <SMILES>
[Ni++]

> <INCHI_IDENTIFIER>
InChI=1S/Ni/q+2

> <INCHI_KEY>
VEQPNABPJHWNSG-UHFFFAOYSA-N

> <FORMULA>
Ni

> <MOLECULAR_WEIGHT>
58.6934

> <EXACT_MASS>
57.935347922

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
nickel(2+) ion

> <JCHEM_LOGP>
0.156

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
nickel(2+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0002457 (Nickel)

HMDB0002457
     RDKit          3D
Nickel
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Ni  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   2
M  END
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PDB for HMDB0002457 (Nickel)

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 Ni   UNK     0      29.821 -33.013   0.000  0.00  0.00          Ni+2
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0002457 (Nickel)

COMPND    HMDB0002457
HETATM    1 NI1  UNL     1       0.000   0.000   0.000  1.00  0.00          NI2+
END
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SMILES for HMDB0002457 (Nickel)

[Ni++]
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INCHI for HMDB0002457 (Nickel)

InChI=1S/Ni/q+2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Ni2+ChEBI
Ni(2+)ChEBI
NICKEL (II) ionChEBI
Nickel, ion (ni2+)ChEBI
Nickelous ionChEBI
Ni(II)Kegg
Carbonyl nickel powderHMDB
Malleable nickelHMDB
NIHMDB
NichelHMDB
Nickel 200HMDB
Nickel 201HMDB
Nickel 204HMDB
Nickel 205HMDB
Nickel 211HMDB
Nickel 212HMDB
Nickel 213HMDB
Nickel 222HMDB
Nickel 223HMDB
Nickel 229HMDB
Nickel 270HMDB
Nickel particlesHMDB
Nickel spongeHMDB
Raney alloyHMDB
Raney nickelHMDB
Chemical FormulaNi
Average Molecular Weight58.6934
Monoisotopic Molecular Weight57.935347922
IUPAC Namenickel(2+) ion
Traditional Namenickel(2+) ion
CAS Registry Number7440-02-0
SMILES
[Ni++]
InChI Identifier
InChI=1S/Ni/q+2
InChI KeyVEQPNABPJHWNSG-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 Parents
Substituents
  • Homogeneous transition metal
  • Inorganic nickel compound
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point1455 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.16ChemAxon
Physiological Charge2ChemAxon
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 Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Nickel[Ni++]696.1Standard polar33892256
Nickel[Ni++]328.8Standard non polar33892256
Nickel[Ni++]46.1Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nickel 10V, Positive-QTOFsplash10-0a4i-9000000000-08256b3c9e2cc1750f602015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nickel 20V, Positive-QTOFsplash10-0a4i-9000000000-08256b3c9e2cc1750f602015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nickel 40V, Positive-QTOFsplash10-0a4i-9000000000-08256b3c9e2cc1750f602015-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nickel 10V, Negative-QTOFsplash10-0a4i-9000000000-4648ffc6f53552c415032015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nickel 20V, Negative-QTOFsplash10-0a4i-9000000000-4648ffc6f53552c415032015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nickel 40V, Negative-QTOFsplash10-0a4i-9000000000-4648ffc6f53552c415032015-09-15Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.64 +/- 0.72 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.01415(0.01122-0.01743) uMNot AvailableBothNormal
    • Report on Human B...
 details
BloodDetected and Quantified0.01277(0.01053-0.01536) uMAdult (>18 years old)BothNormal
    • Report on Human B...
 details
BloodDetected and Quantified0.026-0.066 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
BloodDetected and Quantified0.053 +/- 0.017 uMAdult (>18 years old)MaleNormal
    • Geigy Scientific ...
 details
BloodDetected and Quantified0.046 +/- 0.02 uMAdult (>18 years old)FemaleNormal
    • Geigy Scientific ...
 details
Cerebrospinal Fluid (CSF)Detected and Quantified0.097 +/- 0.109 uMAdult (>18 years old)Not SpecifiedNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified<0.004 uMAdult (>18 years old)BothNormal details
SalivaDetected and Quantified0.108 +/- 0.035 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
SalivaDetected and Quantified0.341 +/- 0.170 uMAdult (>18 years old)Not SpecifiedNormal
    • Natheer H. Al-Raw...
 details
UrineDetected and Quantified0.00420 (0.00302-0.00572) umol/mmol creatinineNot AvailableBothNormal
    • Report on Human B...
 details
UrineDetected and Quantified0.00345(0.00254-0.00447) umol/mmol creatinineAdult (>18 years old)BothNormal
    • Report on Human B...
 details
UrineDetected and Quantified0.0080 (0.0015-0.0450) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.0028 +/- 0.0015 umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
    • West Cadwell, N.J...
    • Basel, Switzerlan...
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.022 +/- 0.011 uMAdult (>18 years old)BothMultiple sclerosis details
BloodDetected and Quantified0.011 +/- 0.0057 uMAdult (>18 years old)BothParkinson's disease details
BloodDetected and Quantified0.01 +/- 0.0062 uMAdult (>18 years old)BothAlzheimer's disease details
SalivaDetected and Quantified2.896 +/- 1.533 uMAdult (>18 years old)Not SpecifiedOral squamous cell carcinoma
    • Natheer H. Al-Raw...
 details
SalivaDetected and Quantified3.237 +/- 1.704 uMAdult (>18 years old)Not Specified
Oral squamous cell carcinoma
    • Natheer H. Al-Raw...
 details
SalivaDetected and Quantified2.215 +/- 0.682 uMAdult (>18 years old)Not Specified
Oral squamous cell carcinoma
    • Natheer H. Al-Raw...
 details
Associated Disorders and Diseases
Disease References
Alzheimer's disease
  1. Bocca B, Forte G, Petrucci F, Pino A, Marchione F, Bomboi G, Senofonte O, Giubilei F, Alimonti A: Monitoring of chemical elements and oxidative damage in patients affected by Alzheimer's disease. Ann Ist Super Sanita. 2005;41(2):197-203. [PubMed:16244393 ]
Multiple sclerosis
  1. Forte G, Visconti A, Santucci S, Ghazaryan A, Figa-Talamanca L, Cannoni S, Bocca B, Pino A, Violante N, Alimonti A, Salvetti M, Ristori G: Quantification of chemical elements in blood of patients affected by multiple sclerosis. Ann Ist Super Sanita. 2005;41(2):213-6. [PubMed:16244395 ]
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 IDFDB013444
KNApSAcK IDNot Available
Chemspider ID909
KEGG Compound IDC19609
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNickel
METLIN IDNot Available
PubChem Compound934
PDB IDNot Available
ChEBI ID49786
Food Biomarker OntologyNot Available
VMH IDNI2
MarkerDB IDMDB00030002
Good Scents IDNot Available
References
Synthesis ReferenceLightner, David A.; Crist, B. Vincent; Kalyanam, Nagabushanam; May, Leslie M.; Jackman, Dennis E. The octant rule. 15. Antioctant effects: synthesis and circular dichroism of 2-exo- and 2-endo-alkylbicyclo[2.2.1]heptan-7-ones and bicyclo[3.2.1]octan-8-one. J. Org. Chem. 1985,50, 3867-3878. DOI: 10.1021/jo00220a037
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. Uthus EO, Seaborn CD: Deliberations and evaluations of the approaches, endpoints and paradigms for dietary recommendations of the other trace elements. J Nutr. 1996 Sep;126(9 Suppl):2452S-2459S. [PubMed:8811811 ]
  3. Biego GH, Joyeux M, Hartemann P, Debry G: Daily intake of essential minerals and metallic micropollutants from foods in France. Sci Total Environ. 1998 Jun 30;217(1-2):27-36. [PubMed:9695171 ]
  4. Hostynek JJ: Sensitization to nickel: etiology, epidemiology, immune reactions, prevention, and therapy. Rev Environ Health. 2006 Oct-Dec;21(4):253-80. [PubMed:17243350 ]
  5. Setcos JC, Babaei-Mahani A, Silvio LD, Mjor IA, Wilson NH: The safety of nickel containing dental alloys. Dent Mater. 2006 Dec;22(12):1163-8. Epub 2006 Jan 6. [PubMed:16405986 ]
  6. Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Drager A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO: Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. [PubMed:29457794 ]

Enzymes

Enzyme Details
1. Bis(5'-adenosyl)-triphosphatase
General function:
Involved in catalytic activity
Specific function:
Cleaves A-5'-PPP-5'A to yield AMP and ADP. Possible tumor suppressor for specific tissues.
Gene Name:
FHIT
Uniprot ID:
P49789
Molecular weight:
16858.11
Enzyme Details
2. Alpha-fetoprotein
General function:
Involved in transport
Specific function:
Binds copper, nickel, and fatty acids as well as, and bilirubin less well than, serum albumin. Only a small percentage (less than 2%) of the human AFP shows estrogen-binding properties
Gene Name:
AFP
Uniprot ID:
P02771
Molecular weight:
68676.9
Enzyme Details
3. 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
General function:
Involved in metal ion binding
Specific function:
Catalyzes the formation of formate and 2-keto-4-methylthiobutyrate (KMTB) from 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene). Also down-regulates cell migration mediated by MMP14. Necessary for hepatitis C virus replication in an otherwise non-permissive cell line.
Gene Name:
ADI1
Uniprot ID:
Q9BV57
Molecular weight:
21498.23