Zinc beryllium silicate (T3D1376)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationTargets (4)XML
Targets (4)
Record Information
Version2.0
Creation Date2009-06-19 21:58:42 UTC
Update Date2014-12-24 20:23:48 UTC
Accession NumberT3D1376
Identification
Common NameZinc beryllium silicate
ClassSmall Molecule
DescriptionZinc beryllium silicate is a chemical compound of zinc, beryllium, and silicon. Zinc is a metallic element with the atomic number 30. It is found in nature most often as the mineral sphalerite. Though excess zinc in harmful, in smaller amounts it is an essential element for life, as it is a cofactor for over 300 enzymes and is found in just as many transcription factors. Beryllium is a lightweight alkaline earth metal with the atomic number 4. It is a relatively rare element found naturally only combined with other elements in minerals. (4, 6, 7)
Compound Type
  • Beryllium Compound
  • Industrial/Workplace Toxin
  • Inorganic Compound
  • Pollutant
  • Synthetic Compound
  • Zinc Compound
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Synonym
Zinc-beryllium silicate
Chemical FormulaBeO4SiZn
Average Molecular Mass166.504 g/mol
Monoisotopic Mass164.898 g/mol
CAS Registry Number39413-47-3
IUPAC Nameberyllium(2+) ion zinc(2+) ion silicate
Traditional Nameberyllium(2+) ion zinc(2+) ion orthosilicate
SMILES[Be++].[Zn++].[O-][Si]([O-])([O-])[O-]
InChI IdentifierInChI=1S/Be.O4Si.Zn/c;1-5(2,3)4;/q+2;-4;+2
InChI KeyInChIKey=HVCJNUXSXRYNNS-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of inorganic compounds known as alkaline earth metal silicates. These are inorganic compounds in which the largest oxoanion is silicate, and in which the heaviest atom not in an oxoanion is an alkaline earth metal.
KingdomInorganic compounds
Super ClassMixed metal/non-metal compounds
ClassAlkaline earth metal oxoanionic compounds
Sub ClassAlkaline earth metal silicates
Direct ParentAlkaline earth metal silicates
Alternative Parents
Substituents
  • Silicate
  • Alkaline earth metal silicate
  • Inorganic beryllium salt
  • Inorganic oxide
  • Inorganic salt
  • Inorganic metalloid salt
Molecular FrameworkNot Available
External DescriptorsNot Available
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
LogPNot Available
Predicted Properties
PropertyValueSource
logP-2.6ChemAxon
pKa (Strongest Acidic)9.82ChemAxon
pKa (Strongest Basic)-4.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area92.24 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity5.77 m³·mol⁻¹ChemAxon
Polarizability5.14 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Toxicity Profile
Route of ExposureOral (7) ; inhalation (7) ; dermal (7)
Mechanism of ToxicityAnaemia results from the excessive absorption of zinc suppressing copper and iron absorption, most likely through competitive binding of intestinal mucosal cells. Unbalanced levels of copper and zinc binding to Cu,Zn-superoxide dismutase has been linked to amyotrophic lateral sclerosis (ALS). Stomach acid dissolves metallic zinc to give corrosive zinc chloride, which can cause damage to the stomach lining. Metal fume fever is thought to be an immune response to inhaled zinc. Once in the body, beryllium acts as a hapten and interacts with human leucocyte antigen (HLA) DP presenting cells in the lungs, becoming physically associated with a major histocompatability (MHC) class II molecule. This MHC class II-beryllium-peptide complex is recognized by the T lymphocyte receptor, triggering CD4+ T lymphocyte activation and proliferation. The resulting inflammatory response is a cell-mediated process orchestrated by cytokines and results in the formation of (usually pulmonary) granulomas. Beryllium's toxicity may be controlled by the iron-storage protein ferritin, which sequesters beryllium by binding it and preventing it from interacting with other enzymes. (5, 1, 6, 7, 2, 3)
MetabolismZinc can enter the body through the lungs, skin, and gastrointestinal tract. Intestinal absorption of zinc is controlled by zinc carrier protein CRIP. Zinc also binds to metallothioneins, which help prevent absorption of excess zinc. Zinc is widely distributed and found in all tissues and tissues fluids, concentrating in the liver, gastrointestinal tract, kidney, skin, lung, brain, heart, and pancreas. In the bloodstream zinc is found bound to carbonic anhydrase in erythrocytes, as well as bound to albumin, _2-macroglobulin, and amino acids in the the plasma. Albumin and amino acid bound zinc can diffuse across tissue membranes. Zinc is excreted in the urine and faeces. Beryllium is absorbed mainly through the lungs, where it enters the bloodstream and is transported throughout the body by binding to prealbumins and _-globulins. Beryllium accumulates in lung tissue and the skeleton. It is excreted mainly in the urine. (5, 7)
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)1, carcinogenic to humans. (10)
Uses/SourcesNot Available
Minimum Risk LevelIntermediate Oral: 0.3 mg/kg/day (Zinc) (9) Chronic Oral: 0.3 mg/kg/day (Zinc) (9) Chronic Oral: 0.002 mg/kg/day (Beryllium) (9)
Health EffectsChronic exposure to zinc causes anemia, atazia, lethargy, and decreases the level of good cholesterol in the body. It is also believed to cause pancreatic and reproductive damage. Acute inhalation of a high level of beryllium can results in a pneumonia-like condition called acute beryllium disease. Chronic inhalation of beryllium can caused an inflammatory reaction in the respiratory system called chronic beryllium disease. Chronic beryllium disease may result in anorexia and weight loss, as well as right side heart enlargement and heart disease in advanced cases. Chronic exposure can also increase the risk of lung cancer. Skin contact with beryllium results in contact dermatitus. (4, 5, 7)
SymptomsIngestion of large doses of zinc causes stomach cramps, nausea, and vomiting. Acute inhalation of large amounts of zinc causes metal fume fever, which is characterized by chills, fever, headache, weakness, dryness of the nose and throat, chest pain, and coughing. Dermal contact with zinc results in skin irritation. Chronic beryllium disease causes fatigue, weakness, difficulty breathing, and a persistent dry cough. (4, 5, 7)
TreatmentZinc poisoning is treated symptomatically, often by administering fluids such as water or milk, or with gastric lavage. Chronic beryllium disease is treated with immunosuppressive medicines, usually of the glucocorticoid class. (4, 7)
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDNot Available
HMDB IDNot Available
PubChem Compound ID22748686
ChEMBL IDNot Available
ChemSpider ID15350486
KEGG IDNot Available
UniProt IDNot Available
OMIM ID
ChEBI IDNot Available
BioCyc IDNot Available
CTD IDNot Available
Stitch IDZinc beryllium silicate
PDB IDNot Available
ACToR IDNot Available
Wikipedia LinkNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
  1. Amicosante M, Berretta F, Dweik R, Saltini C: Role of high-affinity HLA-DP specific CLIP-derived peptides in beryllium binding to the HLA-DPGlu69 berylliosis-associated molecules and presentation to beryllium-sensitized T cells. Immunology. 2009 Sep;128(1 Suppl):e462-70. doi: 10.1111/j.1365-2567.2008.03000.x. Epub 2008 Dec 23. [19191908 ]
  2. Vonk WI, Klomp LW: Role of transition metals in the pathogenesis of amyotrophic lateral sclerosis. Biochem Soc Trans. 2008 Dec;36(Pt 6):1322-8. doi: 10.1042/BST0361322. [19021549 ]
  3. Lindenschmidt RC, Sendelbach LE, Witschi HP, Price DJ, Fleming J, Joshi JG: Ferritin and in vivo beryllium toxicity. Toxicol Appl Pharmacol. 1986 Feb;82(2):344-50. [3945960 ]
  4. Wikipedia. Beryllium. Last Updated 17 March 2009. [Link]
  5. ATSDR - Agency for Toxic Substances and Disease Registry (2002). Toxicological profile for beryllium. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
  6. Wikipedia. Zinc. Last Updated 24 March 2009. [Link]
  7. ATSDR - Agency for Toxic Substances and Disease Registry (2005). Toxicological profile for zinc. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
  8. Wikipedia. Metallothionein. Last Updated 20 December 2008. [Link]
  9. ATSDR - Agency for Toxic Substances and Disease Registry (2001). Minimal Risk Levels (MRLs) for Hazardous Substances. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
  10. International Agency for Research on Cancer (2014). IARC Monographs on the Evaluation of Carcinogenic Risks to Humans. [Link]
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available

Targets

Target Details
1. HLA class II histocompatibility antigen, DP alpha 1 chain
General Function:
Peptide antigen binding
Specific Function:
Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation of proteins that access the endocytic route, where they are processed by lysosomal proteases and other hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous. As membrane proteins on their way to degradation in lysosomes as part of their normal turn-over are also contained in the endosomal/lysosomal compartments, exogenous antigens must compete with those derived from endogenous components. Autophagy is also a source of endogenous peptides, autophagosomes constitutively fuse with MHC class II loading compartments. In addition to APCs, other cells of the gastrointestinal tract, such as epithelial cells, express MHC class II molecules and CD74 and act as APCs, which is an unusual trait of the GI tract. To produce a MHC class II molecule that presents an antigen, three MHC class II molecules (heterodimers of an alpha and a beta chain) associate with a CD74 trimer in the ER to form a heterononamer. Soon after the entry of this complex into the endosomal/lysosomal system where antigen processing occurs, CD74 undergoes a sequential degradation by various proteases, including CTSS and CTSL, leaving a small fragment termed CLIP (class-II-associated invariant chain peptide). The removal of CLIP is facilitated by HLA-DM via direct binding to the alpha-beta-CLIP complex so that CLIP is released. HLA-DM stabilizes MHC class II molecules until primary high affinity antigenic peptides are bound. The MHC II molecule bound to a peptide is then transported to the cell membrane surface. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO. Primary dendritic cells (DCs) also to express HLA-DO. Lysosomal microenvironment has been implicated in the regulation of antigen loading into MHC II molecules, increased acidification produces increased proteolysis and efficient peptide loading.
Gene Name:
HLA-DPA1
Uniprot ID:
P20036
Molecular Weight:
29380.345 Da
References
  1. Amicosante M, Berretta F, Dweik R, Saltini C: Role of high-affinity HLA-DP specific CLIP-derived peptides in beryllium binding to the HLA-DPGlu69 berylliosis-associated molecules and presentation to beryllium-sensitized T cells. Immunology. 2009 Sep;128(1 Suppl):e462-70. doi: 10.1111/j.1365-2567.2008.03000.x. Epub 2008 Dec 23. [19191908 ]
  2. ATSDR - Agency for Toxic Substances and Disease Registry (2002). Toxicological profile for beryllium. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
Target Details
2. HLA class II histocompatibility antigen, DP beta 1 chain
General Function:
Peptide antigen binding
Specific Function:
Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation of proteins that access the endocytic route, where they are processed by lysosomal proteases and other hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous. As membrane proteins on their way to degradation in lysosomes as part of their normal turn-over are also contained in the endosomal/lysosomal compartments, exogenous antigens must compete with those derived from endogenous components. Autophagy is also a source of endogenous peptides, autophagosomes constitutively fuse with MHC class II loading compartments. In addition to APCs, other cells of the gastrointestinal tract, such as epithelial cells, express MHC class II molecules and CD74 and act as APCs, which is an unusual trait of the GI tract. To produce a MHC class II molecule that presents an antigen, three MHC class II molecules (heterodimers of an alpha and a beta chain) associate with a CD74 trimer in the ER to form a heterononamer. Soon after the entry of this complex into the endosomal/lysosomal system where antigen processing occurs, CD74 undergoes a sequential degradation by various proteases, including CTSS and CTSL, leaving a small fragment termed CLIP (class-II-associated invariant chain peptide). The removal of CLIP is facilitated by HLA-DM via direct binding to the alpha-beta-CLIP complex so that CLIP is released. HLA-DM stabilizes MHC class II molecules until primary high affinity antigenic peptides are bound. The MHC II molecule bound to a peptide is then transported to the cell membrane surface. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO. Primary dendritic cells (DCs) also to express HLA-DO. Lysosomal microenvironment has been implicated in the regulation of antigen loading into MHC II molecules, increased acidification produces increased proteolysis and efficient peptide loading.
Gene Name:
HLA-DPB1
Uniprot ID:
P04440
Molecular Weight:
29159.195 Da
References
  1. Amicosante M, Berretta F, Dweik R, Saltini C: Role of high-affinity HLA-DP specific CLIP-derived peptides in beryllium binding to the HLA-DPGlu69 berylliosis-associated molecules and presentation to beryllium-sensitized T cells. Immunology. 2009 Sep;128(1 Suppl):e462-70. doi: 10.1111/j.1365-2567.2008.03000.x. Epub 2008 Dec 23. [19191908 ]
  2. ATSDR - Agency for Toxic Substances and Disease Registry (2002). Toxicological profile for beryllium. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
Target Details
3. HLA class II histocompatibility antigen, DP beta 1 chain
General Function:
Peptide antigen binding
Specific Function:
Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation of proteins that access the endocytic route, where they are processed by lysosomal proteases and other hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous. As membrane proteins on their way to degradation in lysosomes as part of their normal turn-over are also contained in the endosomal/lysosomal compartments, exogenous antigens must compete with those derived from endogenous components. Autophagy is also a source of endogenous peptides, autophagosomes constitutively fuse with MHC class II loading compartments. In addition to APCs, other cells of the gastrointestinal tract, such as epithelial cells, express MHC class II molecules and CD74 and act as APCs, which is an unusual trait of the GI tract. To produce a MHC class II molecule that presents an antigen, three MHC class II molecules (heterodimers of an alpha and a beta chain) associate with a CD74 trimer in the ER to form a heterononamer. Soon after the entry of this complex into the endosomal/lysosomal system where antigen processing occurs, CD74 undergoes a sequential degradation by various proteases, including CTSS and CTSL, leaving a small fragment termed CLIP (class-II-associated invariant chain peptide). The removal of CLIP is facilitated by HLA-DM via direct binding to the alpha-beta-CLIP complex so that CLIP is released. HLA-DM stabilizes MHC class II molecules until primary high affinity antigenic peptides are bound. The MHC II molecule bound to a peptide is then transported to the cell membrane surface. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO. Primary dendritic cells (DCs) also to express HLA-DO. Lysosomal microenvironment has been implicated in the regulation of antigen loading into MHC II molecules, increased acidification produces increased proteolysis and efficient peptide loading.
Gene Name:
HLA-DPB1
Uniprot ID:
P04440
Molecular Weight:
29159.195 Da
References
  1. Amicosante M, Berretta F, Dweik R, Saltini C: Role of high-affinity HLA-DP specific CLIP-derived peptides in beryllium binding to the HLA-DPGlu69 berylliosis-associated molecules and presentation to beryllium-sensitized T cells. Immunology. 2009 Sep;128(1 Suppl):e462-70. doi: 10.1111/j.1365-2567.2008.03000.x. Epub 2008 Dec 23. [19191908 ]
  2. ATSDR - Agency for Toxic Substances and Disease Registry (2002). Toxicological profile for beryllium. U.S. Public Health Service in collaboration with U.S. Environmental Protection Agency (EPA). [Link]
Target Details
4. Superoxide dismutase [Cu-Zn]
General Function:
Zinc ion binding
Specific Function:
Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
Gene Name:
SOD1
Uniprot ID:
P00441
Molecular Weight:
15935.685 Da
References
  1. Vonk WI, Klomp LW: Role of transition metals in the pathogenesis of amyotrophic lateral sclerosis. Biochem Soc Trans. 2008 Dec;36(Pt 6):1322-8. doi: 10.1042/BST0361322. [19021549 ]