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Showing metabocard for Cobalt (HMDB0000608)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (23)transporters (4) Show 27 proteinsXML
enzymes (23)transporters (4) Show 27 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-16 08:41:04 UTC
Update Date2022-03-07 02:49:04 UTC
HMDB IDHMDB0000608
Secondary Accession Numbers
  • HMDB00608
Metabolite Identification
Common NameCobalt
DescriptionCobalt has a molecular weight of 58.9 and an atomic number of 27. In the Periodic Table, close to other transition metals, it is situated in group 8, together with rhodium and iridium and it can occur in four oxidation states (0, +2, +3 and +4). The +2 and the ground state are the most common. Cobalt occurs in the minerals cobaltite (Co, Fe) AsS, smaltite (CoAs2), and erythrite Co3(AsO4)2.8H2O, and is often associated with nickel, silver, lead, copper, and iron ores, from which it is most frequently obtained as a by-product. Depending on the considered species, cobalt has multiple industrial applications including the production of alloys and hard metal, diamond polishing, drying agents, pigments and catalysts. Hard metal or cemented carbide is a powder metallurgical product consisting of hard, wear-resistant carbide particles bound together (cemented) with a ductile metal binder (i.e. metallic Co) by liquid phase sintering. Tungsten carbide (WC) is produced by mixing tungsten powder with pure carbon powder at high temperature; hereafter WC is mixed with Co powder to which paraffin is added as a binder. Depending on specific requirements related to their use, hard metals might additionally contain small quantities of chromium, niobium, molybdenum, titanium, tantalum or vanadium carbides. Inhalation and skin contact are the main occupational exposure routes. Occupational exposure to cobalt may result in adverse health effects in different organs or tissues, including the respiratory tract, the skin, the hemapoietic tissues, the myocardium or the thyroid gland. In addition, teratogenic and carcinogenic effects have been observed in experimental systems and/or in humans. For the general population, the diet constitutes the main route of exposure to cobalt, since it is an essential component of Vitamin B12 (hydroxycolalamin). Cobalt functions as a co-factor in enzyme catalysed reactions and is involved in the production of erythropoietin, a hormone that stimulates the formation of erythrocytes. This last property of cobalt was applied in the past as a therapy for anaemia. The carcinogenic potential of cobalt and its compounds was evaluated in 1991 by the International Agency for Research on Cancer (IARC), which concluded that there was inadequate evidence for carcinogenicity in humans (lung cancer) but sufficient evidence in experimental animal studies. In most experimental studies considered, the routes of exposure were, however, of questionable relevance for cancer risk assessment in humans for example, local sarcomas after intra-muscular injection. The general conclusion was that cobalt and its compounds are possibly carcinogenic to humans (group 2B). Since this evaluation, additional data have been accumulated which generally indicate that, depending on the considered cobalt species, different outcomes regarding toxicity, mutagenicity and carcinogenicity can be observed. Physiologically, it exists as an ion in the body. Co(II) ions are genotoxic in vitro and in vivo, and carcinogenic in rodents. Co metal is genotoxic in vitro. Hard metal dust, of which occupational exposure is linked to an increased lung cancer risk, is proven to be genotoxic in vitro and in vivo. Possibly, production of active oxygen species and/or DNA repair inhibition are mechanisms involved. Given the recently provided proof for in vitro and in vivo genotoxic potential of hard metal dust, the mechanistic evidence of elevated production of active oxygen species and the epidemiological data on increased cancer risk, it may be advisable to consider the possibility of a new evaluation by IARC.(PMID: 14643417 ).
Structure
Data?1582752143
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000608 (Cobalt)


  Mrv1652309042000042D          

  1  0  0  0  0  0            999 V2000
   21.9133   -7.1092    0.0000 Co  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 HMDB0000608 (Cobalt)

HMDB0000608
     RDKit          3D
Cobalt
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Co  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 HMDB0000608 (Cobalt)


  Mrv1652309042000042D          

  1  0  0  0  0  0            999 V2000
   21.9133   -7.1092    0.0000 Co  0  2  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   2
M  END
> <DATABASE_ID>
HMDB0000608

> <DATABASE_NAME>
hmdb

> <SMILES>
[Co++]

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

> <INCHI_KEY>
XLJKHNWPARRRJB-UHFFFAOYSA-N

> <FORMULA>
Co

> <MOLECULAR_WEIGHT>
58.9332

> <EXACT_MASS>
58.933200194

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
lambda2-cobalt(2+) ion

> <JCHEM_LOGP>
0.22999999999999998

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
3.55

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.09

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
0.0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
lambda2-cobalt(2+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0000608 (Cobalt)

HMDB0000608
     RDKit          3D
Cobalt
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Co  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   2
M  END
Download

PDB for HMDB0000608 (Cobalt)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1 Co   UNK     0      40.905 -13.271   0.000  0.00  0.00          Co+2
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
Download

3D PDB for HMDB0000608 (Cobalt)

COMPND    HMDB0000608
HETATM    1 CO1  UNL     1       0.000   0.000   0.000  1.00  0.00          CO2+
END
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SMILES for HMDB0000608 (Cobalt)

[Co++]
Download

INCHI for HMDB0000608 (Cobalt)

InChI=1S/Co/q+2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Co(II)ChEBI
CO2+ChEBI
Co(2+)ChEBI
COBALT (II) ionChEBI
Cobalt(2+) ionChEBI
Cobalt(II) cationChEBI
Cobaltous ionChEBI
Cobalt(2+)Kegg
AquacatHMDB
CoHMDB
Cobalt-59HMDB
Cobatope-57HMDB
KobaltHMDB
Super cobaltHMDB
Chemical FormulaCo
Average Molecular Weight58.9332
Monoisotopic Molecular Weight58.933200194
IUPAC Namelambda2-cobalt(2+) ion
Traditional Namelambda2-cobalt(2+) ion
CAS Registry Number7440-48-4
SMILES
[Co++]
InChI Identifier
InChI=1S/Co/q+2
InChI KeyXLJKHNWPARRRJB-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 Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point1495 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.23ChemAxon
pKa (Strongest Acidic)3.09ChemAxon
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
Cobalt[Co++]701.5Standard polar33892256
Cobalt[Co++]276.2Standard non polar33892256
Cobalt[Co++]59.2Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cobalt 10V, Positive-QTOFsplash10-0a4i-9000000000-5ec55e9e276ff34b918f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cobalt 20V, Positive-QTOFsplash10-0a4i-9000000000-5ec55e9e276ff34b918f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cobalt 40V, Positive-QTOFsplash10-0a4i-9000000000-5ec55e9e276ff34b918f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cobalt 10V, Negative-QTOFsplash10-0a4i-9000000000-c4eed668d3af388c4a952016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cobalt 20V, Negative-QTOFsplash10-0a4i-9000000000-c4eed668d3af388c4a952016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cobalt 40V, Negative-QTOFsplash10-0a4i-9000000000-c4eed668d3af388c4a952016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue Locations
  • Epidermis
  • Kidney
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0031 +/- 0.0017 uMElderly (>65 years old)BothNormal details
BloodDetected and Quantified0.00183 (0.00067 - 0.00460) uMAdult (>18 years old)Both
Normal
    • Geigy Scientific ...
 details
BloodDetected and Quantified0.00067 - 0.0080 uMAdult (>18 years old)Both
Normal		 details
Cerebrospinal Fluid (CSF)Detected and Quantified0.01+/-0.005 (0.001-0.04) uMAdult (>18 years old)BothNormal details
SalivaDetected and Quantified0.006 +/- 0.002 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
SalivaDetected and Quantified0.509 +/- 0.509 uMAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified0.339 +/- 0.509 uMAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified0.119 +/- 0.0339 uMAdult (>18 years old)Not SpecifiedNormal
    • Natheer H. Al-Raw...
 details
UrineDetected and Quantified0.0014 (0.0001-0.014) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.00081 +/- 0.00053 umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
    • West Cadwell, N.J...
    • Basel, Switzerlan...
 details
UrineDetected and Quantified0.000712 (0.000671-0.000756) umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
UrineDetected and Quantified0.00111 (0.00103-0.00119) umol/mmol creatinineChildren (1-13 years old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0037 +/- 0.0017 uMAdult (>18 years old)BothMultiple sclerosis details
BloodDetected and Quantified0.0019 +/- 0.0085 uMAdult (>18 years old)BothParkinson's disease details
BloodDetected and Quantified0.0019 +/- 0.0010 uMAdult (>18 years old)BothAlzheimer's disease details
SalivaDetected and Quantified2.545 +/- 0.170 uMAdult (>18 years old)Not SpecifiedOral squamous cell carcinoma
    • Natheer H. Al-Raw...
 details
SalivaDetected and Quantified2.715 +/- 0.848 uMAdult (>18 years old)Not Specified
Oral squamous cell carcinoma
    • Natheer H. Al-Raw...
 details
SalivaDetected and Quantified2.0362 +/- 0.509 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 IDFDB003581
KNApSAcK IDNot Available
Chemspider ID94546
KEGG Compound IDC00175
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCobalt
METLIN IDNot Available
PubChem Compound104729
PDB IDNot Available
ChEBI ID48828
Food Biomarker OntologyNot Available
VMH IDCOBALT2
MarkerDB IDMDB00000200
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Liden C, Skare L, Lind B, Nise G, Vahter M: Assessment of skin exposure to nickel, chromium and cobalt by acid wipe sampling and ICP-MS. Contact Dermatitis. 2006 May;54(5):233-8. [PubMed:16689805 ]
  2. Larese Filon F, Maina G, Adami G, Venier M, Coceani N, Bussani R, Massiccio M, Barbieri P, Spinelli P: In vitro percutaneous absorption of cobalt. Int Arch Occup Environ Health. 2004 Feb;77(2):85-9. Epub 2003 Jun 19. [PubMed:12819972 ]
  3. Fisher JW: A quest for erythropoietin over nine decades. Annu Rev Pharmacol Toxicol. 1998;38:1-20. [PubMed:9597146 ]
  4. Morales Concepcion JC, Cordies Jackson E, Sandin Hernandez N, Reno Cespedes J, Moreno Diaz ME: [Metachronous bilateral Wilms' tumor]. Arch Esp Urol. 2000 Apr;53(3):245-7. [PubMed:10851730 ]
  5. De Boeck M, Kirsch-Volders M, Lison D: Cobalt and antimony: genotoxicity and carcinogenicity. Mutat Res. 2003 Dec 10;533(1-2):135-52. [PubMed:14643417 ]

Only showing the first 10 proteins. There are 27 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Methionine synthase
General function:
Involved in cobalamin binding
Specific function:
Catalyzes the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate (By similarity).
Gene Name:
MTR
Uniprot ID:
Q99707
Molecular weight:
140525.91
Enzyme Details
2. Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
General function:
Involved in catalytic activity
Specific function:
Hydrolyzes lysophospholipids to produce lysophosphatidic acid (LPA) in extracellular fluids. Major substrate is lysophosphatidylcholine. Also can act on sphingosylphosphphorylcholine producing sphingosine-1-phosphate, a modulator of cell motility. Can hydrolyze, in vitro, bis-pNPP, to some extent pNP-TMP, and barely ATP. Involved in several motility-related processes such as angiogenesis and neurite outgrowth. Acts as an angiogenic factor by stimulating migration of smooth muscle cells and microtubule formation. Stimulates migration of melanoma cells, probably via a pertussis toxin-sensitive G protein. May have a role in induction of parturition. Possible involvement in cell proliferation and adipose tissue development. Tumor cell motility-stimulating factor.
Gene Name:
ENPP2
Uniprot ID:
Q13822
Molecular weight:
98992.78
Enzyme Details
3. Methylmalonyl-CoA mutase, mitochondrial
General function:
Involved in isomerase activity
Specific function:
Involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. MCM has different functions in other species.
Gene Name:
MUT
Uniprot ID:
P22033
Molecular weight:
83133.755
Enzyme Details
4. S-adenosylmethionine synthase isoform type-2
General function:
Involved in methionine adenosyltransferase activity
Specific function:
Catalyzes the formation of S-adenosylmethionine from methionine and ATP.
Gene Name:
MAT2A
Uniprot ID:
P31153
Molecular weight:
43660.37
Enzyme Details
5. S-adenosylmethionine synthase isoform type-1
General function:
Involved in methionine adenosyltransferase activity
Specific function:
Catalyzes the formation of S-adenosylmethionine from methionine and ATP.
Gene Name:
MAT1A
Uniprot ID:
Q00266
Molecular weight:
43647.6
Enzyme Details
6. 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
7. cGMP-specific 3',5'-cyclic phosphodiesterase
General function:
Involved in catalytic activity
Specific function:
Plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. This phosphodiesterase catalyzes the specific hydrolysis of cGMP to 5'-GMP.
Gene Name:
PDE5A
Uniprot ID:
O76074
Molecular weight:
99984.14
Enzyme Details
8. Chondroitin sulfate synthase 3
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Has both beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity. Transfers glucuronic acid (GlcUA) from UDP-GlcUA and N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of the elongating chondroitin polymer. Specific activity is much reduced compared to CHSY1.
Gene Name:
CHSY3
Uniprot ID:
Q70JA7
Molecular weight:
100283.535
Enzyme Details
9. Chondroitin sulfate synthase 2
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Has both beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity. Transfers glucuronic acid (GlcUA) from UDP-GlcUA and N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of the elongating chondroitin polymer.
Gene Name:
CHPF
Uniprot ID:
Q8IZ52
Molecular weight:
68367.94
Enzyme Details
10. Chondroitin sulfate synthase 1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Has both beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity. Transfers glucuronic acid (GlcUA) from UDP-GlcUA and N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of the elongating chondroitin polymer. Involved in the negative control of osteogenesis likely through the modulation of NOTCH signaling.
Gene Name:
CHSY1
Uniprot ID:
Q86X52
Molecular weight:
91783.785

Transporters

Enzyme Details
1. Transcobalamin-2
General function:
Involved in cobalamin binding
Specific function:
Primary vitamin B12-binding and transport protein. Delivers cobalamin to cells
Gene Name:
TCN2
Uniprot ID:
P20062
Molecular weight:
47534.5
Enzyme Details
2. Transcobalamin-1
General function:
Involved in cobalamin binding
Specific function:
Vitamin B12-binding protein. Transports cobalamin into cells
Gene Name:
TCN1
Uniprot ID:
P20061
Molecular weight:
48206.3
Enzyme Details
3. Gastric intrinsic factor
General function:
Involved in cobalamin binding
Specific function:
Promotes absorption of the essential vitamin cobalamin (Cbl) in the ileum by specific receptor-mediated endocytosis
Gene Name:
GIF
Uniprot ID:
P27352
Molecular weight:
45415.7
Enzyme Details
4. Cubilin
General function:
Involved in calcium ion binding
Specific function:
Cotransporter which plays a role in lipoprotein, vitamin and iron metabolism, by facilitating their uptake. Binds to ALB, MB, Kappa and lambda-light chains, TF, hemoglobin, GC, SCGB1A1, APOA1, high density lipoprotein, and the GIF-cobalamin complex. The binding of all ligands required calcium. Serves as important transporter in several absorptive epithelia, including intestine, renal proximal tubules and embryonic yolk sac. Interaction with LRP2 mediates its trafficking throughout vesicles and facilitates the uptake of specific ligands like GC, hemoglobin, ALB, TF and SCGB1A1. Interaction with AMN controls its trafficking to the plasma membrane and facilitates endocytosis of ligands. May play an important role in the development of the peri-implantation embryo through internalization of APOA1 and cholesterol. Binds to LGALS3 at the maternal-fetal interface
Gene Name:
CUBN
Uniprot ID:
O60494
Molecular weight:
398672.8

Only showing the first 10 proteins. There are 27 proteins in total.

Show all enzymes and transporters