Hmdb loader

Showing metabocard for Beryllium (HMDB0002387)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:51 UTC
Update Date2022-03-07 02:49:15 UTC
HMDB IDHMDB0002387
Secondary Accession Numbers
  • HMDB02387
Metabolite Identification
Common NameBeryllium
DescriptionBeryllium is a light-weight metallic element, which was first recognized as a lung hazard in Europe in the 1930s, shortly after its first production in modern industry. People exposed to beryllium compounds are at increased risk of developing beryllium sensitization and chronic beryllium disease (CBD). The chronic lung disease was first described among workers exposed to beryllium-containing materials used in the manufacture of fluorescent lamps. In primary production of beryllium metal, which was used in nuclear weapons components, physicians recognized severe dermatitis, reversible pneumonitis, and chronic granulomatous lung disease. Physiologically, this metal/element exists as an ion in the body. It is now recognized that the physicochemical properties of beryllium compounds may account for the differing clinical presentations in different industries. In primary production of beryllium metal, soluble salts are present and cause rashes in approximately one fourth of exposed workers and reversible acute pneumonitis in a smaller portion of the workforce. After heavy inhalation exposures, radiographic abnormalities evolve at approximately three weeks; resolution of symptoms and radiologic abnormalities away from exposure occur only after months, but symptoms recur immediately upon reexposure. The granulomatous nature of chronic beryllium disease is now known to be caused by cell-mediated sensitization to beryllium. Chronic beryllium disease (CBD) is a granulomatous lung disorder characterized by the accumulation of beryllium-specific CD4(+) T cells. Depending on genetic susceptibility and the nature of the exposure, CBD occurs in up to 20% of exposed workers. Genetic susceptibility has been associated with particular HLA-DP alleles, especially those possessing a negatively charged glutamic acid residue at the 69th position of the beta-chain. The mechanism for this association lies in the ability of these HLA-DP molecules to bind and present beryllium to pathogenic CD4(+) T cells. Large numbers of effector memory, beryllium-specific CD4(+) T cells are recruited to the lung of these subjects and secrete Th1-type cytokines upon beryllium recognition. The presence of circulating beryllium-specific CD4(+) T cells directly correlates with the severity of lymphocytic alveolitis. Since 1987, this biomarker of sensitization has enabled medical surveillance of beryllium-exposed workforces. Beryllium lymphocyte proliferation tests have been used to screen workers to detect sensitization, to characterize epidemiologically workplace risks for beryllium sensitization, and to evaluate the effectiveness of interventions intended to prevent sensitization. The most compelling real-world example of genetic testing for susceptibility to a workplace exposure involves those industries that process or fabricate beryllium. Under reasonable assumptions, the longitudinal positive predictive value of the HLA-DPB1-Glu69 marker of susceptibility to beryllium disease is 12%. Interpretive challenges further limit the utility of the test and may inadvertently suggest a false sense of safety among workers. Reduction in inhalation exposure to beryllium has not resulted in a concomitant reduction in the occurrence of beryllium sensitization or CBD, suggesting that continued prevalence may be due, in part, to unchecked skin exposure to beryllium-containing particles. (PMID: 17094767 , 16697706 , 16231190 ).
Structure
Data?1582752247
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002387 (Beryllium)


  Mrv0541 02231219312D          

  1  0  0  0  0  0            999 V2000
   19.1583  -13.2683    0.0000 Be  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 HMDB0002387 (Beryllium)

HMDB0002387
     RDKit          3D
Beryllium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Be  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 HMDB0002387 (Beryllium)


  Mrv0541 02231219312D          

  1  0  0  0  0  0            999 V2000
   19.1583  -13.2683    0.0000 Be  0  2  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   2
M  END
> <DATABASE_ID>
HMDB0002387

> <DATABASE_NAME>
hmdb

> <SMILES>
[Be++]

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

> <INCHI_KEY>
PWOSZCQLSAMRQW-UHFFFAOYSA-N

> <FORMULA>
Be

> <MOLECULAR_WEIGHT>
9.0122

> <EXACT_MASS>
9.012182135

> <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>
beryllium(2+) ion

> <JCHEM_LOGP>
0

> <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>
beryllium(2+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0002387 (Beryllium)

HMDB0002387
     RDKit          3D
Beryllium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Be  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   2
M  END
Download

PDB for HMDB0002387 (Beryllium)

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 Be   UNK     0      35.762 -24.767   0.000  0.00  0.00          Be+2
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
Download

3D PDB for HMDB0002387 (Beryllium)

COMPND    HMDB0002387
HETATM    1 BE1  UNL     1       0.000   0.000   0.000  1.00  0.00          BE2+
END
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SMILES for HMDB0002387 (Beryllium)

[Be++]
Download

INCHI for HMDB0002387 (Beryllium)

InChI=1S/Be/q+2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Be(2+)ChEBI
BeHMDB
Beryllium atomHMDB
Beryllium elementHMDB
Beryllium metallicumHMDB
Beryllium-9HMDB
GluciniumHMDB
GlucinumHMDB
Chemical FormulaBe
Average Molecular Weight9.0122
Monoisotopic Molecular Weight9.012182135
IUPAC Nameberyllium(2+) ion
Traditional Nameberyllium(2+) ion
CAS Registry Number7440-41-7
SMILES
[Be++]
InChI Identifier
InChI=1S/Be/q+2
InChI KeyPWOSZCQLSAMRQW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous alkaline earth metal compounds. These are inorganic compounds containing only metal atoms,with the largest atom being a alkaline earth metal atom.
KingdomInorganic compounds
Super ClassHomogeneous metal compounds
ClassHomogeneous alkaline earth metal compounds
Sub ClassNot Available
Direct ParentHomogeneous alkaline earth metal compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous alkaline earth metal
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Indirect biological roleIndustrial applicationEnvironmental roleBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point1300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0ChemAxon
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
Beryllium[Be++]690.8Standard polar33892256
Beryllium[Be++]274.9Standard non polar33892256
Beryllium[Be++]59.9Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0266 +/- 0.0155 uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.045 +/- 0.019 uMAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.033 +/- 0.019 uMAdult (>18 years old)BothParkinson's disease details
BloodDetected and Quantified0.0344 +/- 0.0189 uMElderly (>65 years old)BothAlzheimer's disease 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 ]
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 IDFDB022990
KNApSAcK IDNot Available
Chemspider ID96830
KEGG Compound IDC16460
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkBeryllium
METLIN IDNot Available
PubChem Compound107649
PDB ID0BE
ChEBI ID30502
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Kreiss K, Day GA, Schuler CR: Beryllium: a modern industrial hazard. Annu Rev Public Health. 2007;28:259-77. [PubMed:17094767 ]
  2. Amicosante M, Fontenot AP: T cell recognition in chronic beryllium disease. Clin Immunol. 2006 Nov;121(2):134-43. Epub 2006 May 12. [PubMed:16697706 ]
  3. Day GA, Stefaniak AB, Weston A, Tinkle SS: Beryllium exposure: dermal and immunological considerations. Int Arch Occup Environ Health. 2006 Feb;79(2):161-4. Epub 2005 Oct 18. [PubMed:16231190 ]