Hmdb loader

Showing metabocard for Tin (HMDB0001960)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:29 UTC
Update Date2020-10-09 21:02:11 UTC
HMDB IDHMDB0001960
Secondary Accession Numbers
  • HMDB01960
Metabolite Identification
Common NameTin
DescriptionTin is a trace element that is required in bone formation. It has the atomic symbol Sn, atomic number 50, and atomic weight 118.71. (PubChem). Experimental studies over the last decade have suggested an association between thymus immune and homeostatic function and exogenous tin. It has been hypothesized that the thymus gland synthesizes and secretes one or more tin bearing factors that enhance immune defenses against malignancy and retard the gradual loss of immune capacity with senescence. (PMID 2195720 ). Physiologically, it exists as an ion in the body. Inorganic tin salts are poorly absorbed and rapidly excreted in the faeces; as a result they have a low toxicity. Only about 5 per cent is absorbed from the gastrointestinal tract, widely distributed in the body, then excreted by the kidney. Some tin is deposited in lung and bone. Some tin salts can cause renal necrosis after parenteral doses. Mutagenic studies on metallic tin and its compounds have been negative. Long-term animal carcinogenic studies have shown fewer malignant tumors in animals exposed to tin than in controls. Human volunteers developed mild signs of toxicity with tin, given in fruit juices, at a concentration of 1400 mg per litre. The WHO 1973 permissible limit for tin in tinned food is 250 micrograms per kg. The adult daily intake of tin was about 17 mg per day in 1940, but it has now decreased to about 3.5 mg, due to improvements in technique of tinning with enamel overcoat and crimped lids to minimize exposure to tin and lead solder. (PMID 3291572 ).
Structure
Data?1582752219
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001960 (Tin)


  Mrv0541 02231219172D          

  1  0  0  0  0  0            999 V2000
   26.8480  -16.2080    0.0000 Sn  0  0  0  0  0  4  0  0  0  0  0  0
M  CHG  1   1   4
M  END
Download

3D MOL for HMDB0001960 (Tin)

HMDB0001960
     RDKit          3D
Tin
  5  4  0  0  0  0  0  0  0  0999 V2000
   -0.0004    0.0029    0.0084 Sn  0  0  0  0  0  4  0  0  0  0  0  0
    1.3102   -1.1519   -0.1208 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6526    1.6257   -0.0735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1130   -0.2342   -1.3169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8493   -0.2425    1.5028 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
M  CHG  1   1   4
M  RAD  1   1   3
M  END
Download

3D SDF for HMDB0001960 (Tin)


  Mrv0541 02231219172D          

  1  0  0  0  0  0            999 V2000
   26.8480  -16.2080    0.0000 Sn  0  0  0  0  0  4  0  0  0  0  0  0
M  CHG  1   1   4
M  END
> <DATABASE_ID>
HMDB0001960

> <DATABASE_NAME>
hmdb

> <SMILES>
[SnH4+4]

> <INCHI_IDENTIFIER>
InChI=1S/Sn.4H/q+4;;;;

> <INCHI_KEY>
PXQLTWWGPFDWNT-UHFFFAOYSA-N

> <FORMULA>
H4Sn

> <MOLECULAR_WEIGHT>
122.74

> <EXACT_MASS>
123.933496699

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
4.69787638762204

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
λ⁸-tin(4+) ion

> <JCHEM_LOGP>
-1.8039999999999998

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
3.2

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
λ⁸-tin(4+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0001960 (Tin)

HMDB0001960
     RDKit          3D
Tin
  5  4  0  0  0  0  0  0  0  0999 V2000
   -0.0004    0.0029    0.0084 Sn  0  0  0  0  0  4  0  0  0  0  0  0
    1.3102   -1.1519   -0.1208 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6526    1.6257   -0.0735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1130   -0.2342   -1.3169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8493   -0.2425    1.5028 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
M  CHG  1   1   4
M  RAD  1   1   3
M  END
Download

PDB for HMDB0001960 (Tin)

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 Sn   UNK     0      50.116 -30.255   0.000  0.00  0.00          Sn+4
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
Download

3D PDB for HMDB0001960 (Tin)

COMPND    HMDB0001960
HETATM    1 SN1  UNL     1      -0.000   0.003   0.008  1.00  0.00          SN4+
HETATM    2  H1  UNL     1       1.310  -1.152  -0.121  1.00  0.00           H  
HETATM    3  H2  UNL     1       0.653   1.626  -0.074  1.00  0.00           H  
HETATM    4  H3  UNL     1      -1.113  -0.234  -1.317  1.00  0.00           H  
HETATM    5  H4  UNL     1      -0.849  -0.242   1.503  1.00  0.00           H  
CONECT    1    2    3    4    5
END
Download

SMILES for HMDB0001960 (Tin)

[SnH4+4]
Download

INCHI for HMDB0001960 (Tin)

InChI=1S/Sn.4H/q+4;;;;
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
CI pigment metal 5HMDB
Haro mix ZT-514HMDB
InnohepHMDB
Metallic tinHMDB
Silver matt powderHMDB
SNHMDB
StanumHMDB
Tin flakeHMDB
Tin powderHMDB
TindamaxHMDB
ZINNHMDB
Chemical FormulaH4Sn
Average Molecular Weight122.74
Monoisotopic Molecular Weight123.933496699
IUPAC Nameλ⁸-tin(4+) ion
Traditional Nameλ⁸-tin(4+) ion
CAS Registry Number7440-31-5
SMILES
[SnH4+4]
InChI Identifier
InChI=1S/Sn.4H/q+4;;;;
InChI KeyPXQLTWWGPFDWNT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as miscellaneous mixed metal/non-metals. These are inorganic compounds containing non-metal as well as metal atoms but not belonging to afore mentioned classes.
KingdomInorganic compounds
Super ClassMixed metal/non-metal compounds
ClassMiscellaneous mixed metal/non-metals
Sub ClassNot Available
Direct ParentMiscellaneous mixed metal/non-metals
Alternative ParentsNot Available
Substituents
  • Miscellaneous mixed metal/non-metal
Molecular FrameworkNot Available
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point231.93 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.8ChemAxon
Physiological Charge4ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity3.2 m³·mol⁻¹ChemAxon
Polarizability4.7 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]+153.3732859911
AllCCS[M-H]-367.2532859911
AllCCS[M+H]+153.432859911
AllCCS[M+H-H2O]+149.232859911
AllCCS[M+NH4]+157.332859911
AllCCS[M+Na]+158.432859911
AllCCS[M-H]-367.232859911
AllCCS[M+Na-2H]-379.432859911
AllCCS[M+HCOO]-392.532859911

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0024-0.0212 uMAdult (>18 years old)Both
Normal		 details
BloodDetected and Quantified0.013 +/- 0.0051 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.0065 +/- 0.0039 uMElderly (>65 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.05 (0.03-0.18) uMAdult (>18 years old)BothNormal details
SalivaDetected and Quantified0.020 +/- 0.02 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
UrineDetected and Quantified0.0011 (0.00016-0.0069) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified<0.00552 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
UrineDetected and Quantified< 0.00552 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.004 +/- 0.0018 uMAdult (>18 years old)BothParkinson's disease details
BloodDetected and Quantified0.016 +/- 0.009 uMAdult (>18 years old)BothMultiple sclerosis details
BloodDetected and Quantified0.011 +/- 0.0056 uMAdult (>18 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 IDFDB003722
KNApSAcK IDC00000001
Chemspider ID10620886
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkTin
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID32990
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000358
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Cardarelli N: Tin and the thymus gland: a review. Thymus. 1990 Jun;15(4):223-31. [PubMed:2195720 ]
  2. Winship KA: Toxicity of tin and its compounds. Adverse Drug React Acute Poisoning Rev. 1988 Spring;7(1):19-38. [PubMed:3291572 ]