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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
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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
Description
Structure
Thumb
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

$$$$
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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
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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
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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++]
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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
Abnormal Concentrations
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)Not Available
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