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Showing metabocard for Silicon (HMDB0002175)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:39 UTC
Update Date2020-10-09 21:10:36 UTC
HMDB IDHMDB0002175
Secondary Accession Numbers
  • HMDB02175
Metabolite Identification
Common NameSilicon
DescriptionSilicon (Si) is the second most abundant element in the Earth's crust and although there has been interest in the biological role of Si since the beginning of the century, it is only in the last three decades that it has been suggested as an essential trace element. Si may have a role in a number of areas of human physiology and metabolism, especially bone and connective tissue formation, but possibly also gene expression and cardiovascular health. Si is rarely found in its elemental form as it readily reacts with atmospheric O2 and water to produce silicates. Physiologically, it exists as an ion in the body. These vary in composition from simple soluble orthosilicic acid and oligomers through to less soluble colloids and gels, and insoluble solid-phase silicates. The latter constitute the vast majority of environmental silicates (for example, soil minerals), although natural waters contain soluble silicates (mostly orthosilicic acid) generally at 1 to 20 mg/l. Orthosilicic acid is the most readily absorbed form of Si and silicate in man. Silicon plays an important role in bone mineralization and formation and is therefore incorporated into a wide variety of medical implants and bone grafts used today. Low bone mass (osteoporosis) is a silent epidemic of the 21st century, which presently in the UK results in over 200,000 fractures annually at a cost of over one billion pounds. Figures are set to increase worldwide. Understanding the factors which affect bone metabolism is thus of primary importance in order to establish preventative measures or treatments for this condition. Nutrition is an important determinant of bone health, but the effects of the individual nutrients and minerals, other than calcium, is little understood. Accumulating evidence over the last 30 years strongly suggest that dietary silicon is beneficial to bone and connective tissue health and we recently reported strong positive associations between dietary Si intake and bone mineral density in US and UK cohorts. The exact biological role(s) of silicon in bone health is still not clear, although a number of possible mechanisms have been suggested, including the synthesis of collagen and/or its stabilization, and matrix mineralization. The field of bioorganosilicon chemistry, which sprung up in the 1970s to exploit the opportunities of silicon for drug design, is currently being developed into a practical and commercial enterprise. Some of the fundamental differences between carbon and silicon can lead to marked alterations in the physicochemical and biological properties of the silicon-containing analogues and the resulting benefits can be exploited in the drug design process. Recent evidence confirms the fundamental involvement of the human immune system in the reaction to implantation of silicone based medical devices. An as yet to be particularized epitope of many complex substances sharing siloxane structures is presented through the MHC-II apparatus with development and retention of T cell memory. This memory can be tested for in practical terms using one or more forms of silica, which links the immuno-histopathology and autoimmune attributes of 'silicosis' with those of 'siliconosis'. The lesions of siliconosis are typical of those for persistent antigens and delayed, cell mediated hypersensitivity. The basic descriptive pathology of the reaction to silicone has been known since soon after introduction of silicones in medical procedures, with the exception of some details related to the more recent discoveries on the role of cytokines in the immunopathic process. The clinical consequences of siliconosis are common and can be severe in some individuals implanted with silicone devices. (PMID: 16277785 , 16632368 , 17435952 , 12821303 , 12951816 , 9951648 ).
Structure
Data?1582752233
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002175 (Silicon)


  Mrv0541 02231219242D          

  1  0  0  0  0  0            999 V2000
   27.9751  -16.5461    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   4
M  END
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3D MOL for HMDB0002175 (Silicon)

HMDB0002175
     RDKit          3D
Silicon
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Si  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   4
M  END
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3D SDF for HMDB0002175 (Silicon)


  Mrv0541 02231219242D          

  1  0  0  0  0  0            999 V2000
   27.9751  -16.5461    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   4
M  END
> <DATABASE_ID>
HMDB0002175

> <DATABASE_NAME>
hmdb

> <SMILES>
[Si+4]

> <INCHI_IDENTIFIER>
InChI=1S/Si/q+4

> <INCHI_KEY>
RWMKKWXZFRMVPB-UHFFFAOYSA-N

> <FORMULA>
Si

> <MOLECULAR_WEIGHT>
28.0855

> <EXACT_MASS>
27.976926533

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
silicon(4+) ion

> <JCHEM_LOGP>
0.045

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
silicon(4+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0002175 (Silicon)

HMDB0002175
     RDKit          3D
Silicon
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Si  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   4
M  END
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PDB for HMDB0002175 (Silicon)

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 Si   UNK     0      52.220 -30.886   0.000  0.00  0.00          Si+4
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0002175 (Silicon)

COMPND    HMDB0002175
HETATM    1 SI1  UNL     1       0.000   0.000   0.000  1.00  0.00          SI4+
END
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SMILES for HMDB0002175 (Silicon)

[Si+4]
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INCHI for HMDB0002175 (Silicon)

InChI=1S/Si/q+4
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Si(4+)ChEBI
SiHMDB
SilicaHMDB
SilicateHMDB
Silicic acidHMDB
Chemical FormulaSi
Average Molecular Weight28.0855
Monoisotopic Molecular Weight27.976926533
IUPAC Namesilicon(4+) ion
Traditional Namesilicon(4+) ion
CAS Registry Number7440-21-3
SMILES
[Si+4]
InChI Identifier
InChI=1S/Si/q+4
InChI KeyRWMKKWXZFRMVPB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous metalloid compounds. These are inorganic compounds containing only metal atoms,with the largest atom being a metalloid atom.
KingdomInorganic compounds
Super ClassHomogeneous metal compounds
ClassHomogeneous metalloid compounds
Sub ClassNot Available
Direct ParentHomogeneous metalloid compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous metalloid
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point1414 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.045ChemAxon
Physiological Charge4ChemAxon
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
Silicon[Si+4]687.9Standard polar33892256
Silicon[Si+4]230.0Standard non polar33892256
Silicon[Si+4]51.1Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified5.98 +/- 2.56 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified5.48 +/- 2.24 uMElderly (>65 years old)BothNormal details
BloodDetected and Quantified3.95 +/- 1.96 uMElderly (>65 years old)BothNormal details
BloodDetected and Quantified3.97 +/- 1.97 uMElderly (>65 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified3.4 +/- 1.35 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified7.83 +/- 5.05 uMAdult (>18 years old)BothMultiple sclerosis details
BloodDetected and Quantified10.54 +/- 3.72 uMAdult (>18 years old)BothParkinson's disease details
BloodDetected and Quantified8.58 +/- 5.91 uMElderly (>65 years old)Both
Parkinson's disease		 details
BloodDetected and Quantified10.50 +/- 3.70 uMElderly (>65 years old)Both
Parkinson's disease		 details
BloodDetected and Quantified7.97 +/- 3.79 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 ]
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 IDFDB003713
KNApSAcK IDNot Available
Chemspider ID3296906
KEGG Compound IDC06263
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSilicon
METLIN IDNot Available
PubChem Compound4082203
PDB IDNot Available
ChEBI ID30584
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00030000
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Nielsen FH: How should dietary guidance be given for mineral elements with beneficial actions or suspected of being essential? J Nutr. 1996 Sep;126(9 Suppl):2377S-2385S. [PubMed:8811801 ]
  2. Epstein E: The anomaly of silicon in plant biology. Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):11-7. [PubMed:11607449 ]
  3. Uthus EO, Seaborn CD: Deliberations and evaluations of the approaches, endpoints and paradigms for dietary recommendations of the other trace elements. J Nutr. 1996 Sep;126(9 Suppl):2452S-2459S. [PubMed:8811811 ]
  4. Jones LH: Mineral components of plant cell walls. Am J Clin Nutr. 1978 Oct;31(10 Suppl):S94-S98. [PubMed:707400 ]
  5. Powell JJ, McNaughton SA, Jugdaohsingh R, Anderson SH, Dear J, Khot F, Mowatt L, Gleason KL, Sykes M, Thompson RP, Bolton-Smith C, Hodson MJ: A provisional database for the silicon content of foods in the United Kingdom. Br J Nutr. 2005 Nov;94(5):804-12. [PubMed:16277785 ]
  6. Porter AE: Nanoscale characterization of the interface between bone and hydroxyapatite implants and the effect of silicon on bone apposition. Micron. 2006;37(8):681-8. Epub 2006 Mar 31. [PubMed:16632368 ]
  7. Jugdaohsingh R: Silicon and bone health. J Nutr Health Aging. 2007 Mar-Apr;11(2):99-110. [PubMed:17435952 ]
  8. Showell GA, Mills JS: Chemistry challenges in lead optimization: silicon isosteres in drug discovery. Drug Discov Today. 2003 Jun 15;8(12):551-6. [PubMed:12821303 ]
  9. Bains W, Tacke R: Silicon chemistry as a novel source of chemical diversity in drug design. Curr Opin Drug Discov Devel. 2003 Jul;6(4):526-43. [PubMed:12951816 ]
  10. Shanklin DR, Smalley DL: The immunopathology of siliconosis. History, clinical presentation, and relation to silicosis and the chemistry of silicon and silicone. Immunol Res. 1998;18(3):125-73. [PubMed:9951648 ]