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Showing metabocard for Cadmium (HMDB0003638)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (13) Show 13 proteinsXML
enzymes (13) Show 13 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-13 02:21:40 UTC
Update Date2022-03-07 02:49:19 UTC
HMDB IDHMDB0003638
Secondary Accession Numbers
  • HMDB03638
Metabolite Identification
Common NameCadmium
DescriptionCadmium (group IIB of the periodic table of elements) is a heavy metal. It is not a naturally occurring metal in biological systems. Cadmium poses severe risks to human health. Physiologically, it exists as an ion in the body. Up to this day, it has not been shown that cadmium has any physiological function within the human body. Interest has therefore risen in its biohazardous potential. As first described by Friedrich Stromeyer (Gottingen, Germany) in 1817, cadmium intoxication can lead to kidney, bone, and pulmonary damage. Cadmium is widely used in industrial processes, e.g as an anticorrosive agent, as a stabilizer in PVC products, as a colour pigment, a neutron absorber in nuclear power plants, and in the fabrication of nickel cadmium batteries. Phosphate fertilizers also show a big cadmium load. Although some cadmium containing products can be recycled, a large share of the general cadmium pollution is caused by dumping and incinerating cadmium polluted waste. In Scandinavia for example, cadmium concentration in agricultural soil increases by 0.2 percent per year. Total global emission of cadmium amounts to 7000 t/year. The maximum permissible value for workers according to German law is 15 ug/l. For comparison: Non-smokers show an average cadmium blood concentration of 0.5 ug/l. Basically there are three possible ways of cadmium resorption: Gastrointestinal, pulmonary and dermal. The uptake through the human gastrointestinal is approximately 5 percent of an ingested amount of cadmium, depending on the exact dose and nutritional composition. The major source of inhalative cadmium intoxication is cigarette smoke. The human lung resorbes 40 to 60 percent of the cadmium in tobacco smoke. Little research has been done on dermal absorption of cadmium. Two mechanisms facilitate cadmium absorption by the skin: binding of a free cadmium ion to sulfhydryl radicals of cysteine in epidermal keratins, or an induction and complexing with metallothionein. Once taken up by the blood, the majority of cadmium is transported bound to proteins, such as Albumin and Metallothionein. The first organ reached after cadmium uptake into the GI-blood is the liver. Here cadmium induces the production of Metallothionein. After consecutive hepatocyte necrosis and apoptosis, Cd-Metallothionein complexes are washed into sinusoidal blood. From here, parts of the absorbed cadmium enter the entero-hepatical cycle via secretion into the biliary tract in form of Cadmium-glutathione conjugates. Enzymatically degraded to cadmium-cysteine complexes in the biliary tree, cadmium reenters the small intestines. The main organ for long-term cadmium accumulation is the kidney. Here the half life period for cadmium is approximately 10 years. A life long intake can therefore lead to a cadmium accumulation in the kidney, consequently resulting in tubulus cell necrosis. The blood concentration of cadmium serves as a reliable indicator for a recent exposition, while the urinary concentration reflects past exposure, body burden and renal accumulation. Excretion of Cadmium takes place via faeces and urine. (PMID: 16961932 ).
Structure
Data?1599761532
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003638 (Cadmium)


  Mrv0541 02231219462D          

  1  0  0  0  0  0            999 V2000
   19.1108  -14.5667    0.0000 Cd  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 HMDB0003638 (Cadmium)

HMDB0003638
     RDKit          3D
Cadmium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Cd  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 HMDB0003638 (Cadmium)


  Mrv0541 02231219462D          

  1  0  0  0  0  0            999 V2000
   19.1108  -14.5667    0.0000 Cd  0  2  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   2
M  END
> <DATABASE_ID>
HMDB0003638

> <DATABASE_NAME>
hmdb

> <SMILES>
[Cd++]

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

> <INCHI_KEY>
WLZRMCYVCSSEQC-UHFFFAOYSA-N

> <FORMULA>
Cd

> <MOLECULAR_WEIGHT>
112.411

> <EXACT_MASS>
113.903358121

> <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>
cadmium(2+) ion

> <JCHEM_LOGP>
-0.07

> <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>
cadmium(2+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0003638 (Cadmium)

HMDB0003638
     RDKit          3D
Cadmium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Cd  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 HMDB0003638 (Cadmium)

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 Cd   UNK     0      35.673 -27.191   0.000  0.00  0.00          Cd+2
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0003638 (Cadmium)

COMPND    HMDB0003638
HETATM    1 CD1  UNL     1       0.000   0.000   0.000  1.00  0.00          CD2+
END
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SMILES for HMDB0003638 (Cadmium)

[Cd++]
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INCHI for HMDB0003638 (Cadmium)

InChI=1S/Cd/q+2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
CADMIUM ionChEBI
Cadmium, ion (CD2+)ChEBI
CD(2+)ChEBI
CD2+ChEBI
Cadmium atomHMDB
Cadmium elementalHMDB
Cadmium metallicumHMDB
CdHMDB
Colloidal cadmiumHMDB
KadmiumHMDB
Chemical FormulaCd
Average Molecular Weight112.411
Monoisotopic Molecular Weight113.903358121
IUPAC Namecadmium(2+) ion
Traditional Namecadmium(2+) ion
CAS Registry Number7440-43-9
SMILES
[Cd++]
InChI Identifier
InChI=1S/Cd/q+2
InChI KeyWLZRMCYVCSSEQC-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 Point321 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.07ChemAxon
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 Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+128.432859911
AllCCS[M+H-H2O]+124.832859911
AllCCS[M+NH4]+131.732859911
AllCCS[M+Na]+132.732859911
AllCCS[M-H]-152.932859911
AllCCS[M+Na-2H]-164.632859911
AllCCS[M+HCOO]-177.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Cadmium[Cd++]700.5Standard polar33892256
Cadmium[Cd++]269.9Standard non polar33892256
Cadmium[Cd++]55.3Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cadmium 10V, Positive-QTOFsplash10-03di-0900000000-f8713a66369086ec0ad52016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cadmium 20V, Positive-QTOFsplash10-03di-0900000000-f8713a66369086ec0ad52016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cadmium 40V, Positive-QTOFsplash10-03di-0900000000-f8713a66369086ec0ad52016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cadmium 10V, Negative-QTOFsplash10-03di-0900000000-c6c3e3d7e513c880c7f42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cadmium 20V, Negative-QTOFsplash10-03di-0900000000-c6c3e3d7e513c880c7f42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cadmium 40V, Negative-QTOFsplash10-03di-0900000000-c6c3e3d7e513c880c7f42016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.00088 +/- 0.00044 uMElderly (>65 years old)BothNormal details
BloodDetected and Quantified0.0049 (0.0018-0.011) uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
BloodDetected and Quantified0.019 (0.004-0.068) uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
BloodDetected and Quantified0.00318 (0.00309-0.00329) uMAdult (>18 years old)Not SpecifiedNormal details
BloodDetected and Quantified0.00269 (0.00261-0.00277) uMChildren (1-13 years old)Not SpecifiedNormal details
BloodDetected and Quantified0.00202(0.00088-0.00465) uMNot AvailableBothNormal
    • Report on Human B...
 details
BloodDetected and Quantified0.00746(0.00553-0.00992) uMAdult (>18 years old)BothNormal
    • Report on Human B...
 details
Cerebrospinal Fluid (CSF)Detected and Quantified0.015 +/- 0.007 uMAdult (>18 years old)BothNormal details
SalivaDetected and Quantified0.000205 +/- 0.000133 uMAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified0.000142 +/- 0.000142 uMAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified0.000187 +/- 0.000107 uMAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified0.000187 +/- 0.000133 uMAdult (>18 years old)Male
Normal		 details
UrineDetected and Quantified0.0004 (0.0002-0.0010) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.0012 +/- 0.0013 umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
    • West Cadwell, N.J...
    • Basel, Switzerlan...
 details
UrineDetected and Quantified0.000243 (0.000233-0.000255) umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
UrineDetected and Quantified0.0000774 (0.00007-0.0000855) umol/mmol creatinineChildren (1-13 years old)Not SpecifiedNormal details
UrineDetected and Quantified0.00021 (0.000027-0.00112) umol/mmol creatinineNewborn (0-30 days old)Both
Normal		 details
UrineDetected and Quantified0.00035(0.00024-0.00051) umol/mmol creatinineNot AvailableBothNormal
    • Report on Human B...
 details
UrineDetected and Quantified0.00060 (0.00035-0.00100) umol/mmol creatinineAdult (>18 years old)BothNormal
    • Report on Human B...
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0097 +/- 0.0049 uMAdult (>18 years old)BothMultiple sclerosis details
BloodDetected and Quantified0.00061 +/- 0.00023 uMAdult (>18 years old)BothParkinson's disease details
BloodDetected and Quantified4.4 +/- 2.5 uMAdult (>18 years old)Both
Macular degeneration		 details
BloodDetected and Quantified0.00120 +/- 0.00053 uMElderly (>65 years old)BothAlzheimer's disease details
Associated Disorders and Diseases
Disease References
Macular degeneration
  1. Erie JC, Good JA, Butz JA, Hodge DO, Pulido JS: Urinary cadmium and age-related macular degeneration. Am J Ophthalmol. 2007 Sep;144(3):414-418. Epub 2007 Jul 13. [PubMed:17631267 ]
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 IDFDB030717
KNApSAcK IDNot Available
Chemspider ID28935
KEGG Compound IDC01413
BioCyc IDCD%2b2
BiGG IDNot Available
Wikipedia LinkCadmium
METLIN IDNot Available
PubChem Compound31193
PDB IDNot Available
ChEBI ID48775
Food Biomarker OntologyNot Available
VMH IDCD2
MarkerDB IDMDB00000430
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Godt J, Scheidig F, Grosse-Siestrup C, Esche V, Brandenburg P, Reich A, Groneberg DA: The toxicity of cadmium and resulting hazards for human health. J Occup Med Toxicol. 2006 Sep 10;1:22. [PubMed:16961932 ]

Only showing the first 10 proteins. There are 13 proteins in total.

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Enzymes

Enzyme Details
1. Beta-Ala-His dipeptidase
General function:
Involved in metallopeptidase activity
Specific function:
Preferential hydrolysis of the beta-Ala-|-His dipeptide (carnosine), and also anserine, Xaa-|-His dipeptides and other dipeptides including homocarnosine
Gene Name:
CNDP1
Uniprot ID:
Q96KN2
Molecular weight:
56691.6
Enzyme Details
2. 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
3. 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
4. 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
Enzyme Details
5. Metallothionein-1E
General function:
Involved in metal ion binding
Specific function:
Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids
Gene Name:
MT1E
Uniprot ID:
P04732
Molecular weight:
6014.1
Enzyme Details
6. Metallothionein-1F
General function:
Involved in metal ion binding
Specific function:
Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids
Gene Name:
MT1F
Uniprot ID:
P04733
Molecular weight:
6086.1
Enzyme Details
7. Metallothionein-1G
General function:
Involved in metal ion binding
Specific function:
Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids
Gene Name:
MT1G
Uniprot ID:
P13640
Molecular weight:
6141.2
Enzyme Details
8. Metallothionein-1H
General function:
Involved in metal ion binding
Specific function:
Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids
Gene Name:
MT1H
Uniprot ID:
P80294
Molecular weight:
6039.1
Enzyme Details
9. Metallothionein-1X
General function:
Involved in metal ion binding
Specific function:
Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids
Gene Name:
MT1X
Uniprot ID:
P80297
Molecular weight:
6068.1
Enzyme Details
10. Metallothionein-1L
General function:
Involved in metal ion binding
Specific function:
Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids
Gene Name:
MT1L
Uniprot ID:
Q93083
Molecular weight:
6062.1

Only showing the first 10 proteins. There are 13 proteins in total.

Show all enzymes and transporters