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Showing metabocard for Zinc (HMDB0015532)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-06 15:16:52 UTC
Update Date2022-03-07 02:52:01 UTC
HMDB IDHMDB0015532
Secondary Accession Numbers
  • HMDB0001303
  • HMDB01303
  • HMDB15532
Metabolite Identification
Common NameZinc
DescriptionZinc is an essential element, necessary for sustaining all life. It is a trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Physiologically, it exists as an ion in the body. It is estimated that 3000 of the hundreds of thousands of proteins in the human body contain zinc prosthetic groups. In addition, there are over a dozen cell types in the human body that secrete zinc ions, and the roles of these secreted zinc signals in medicine and health are now being actively studied. Intriguingly, brain cells in the mammalian forebrain are one type of cell that secretes zinc, along with its other neuronal messenger substances. Cells in the salivary gland, prostate, immune system, and intestine are other types that secrete zinc. Obtaining a sufficient zinc intake during pregnancy and in young children is a problem, especially among those who cannot afford a good and varied diet. Zinc deficiency is associated with anemia, short stature, hypogonadism, impaired wound healing, and geophagia. Brain development is stunted by zinc deficiency in utero and in youth. Zinc is an activator of certain enzymes, such as carbonic anhydrase. Carbonic anhydrase is important in the transport of carbon dioxide in vertebrate blood. Even though zinc is an essential requirement for a healthy body, too much zinc can be harmful. Excessive absorption of zinc can also suppress copper and iron absorption. The free zinc ion in solution is highly toxic to plants, invertebrates, and even vertebrate fish. The Free Ion Activity Model (FIAM) is well-established in the literature and shows that just micromolar amounts of the free ion kill some organisms.
Structure
Data?1582753307
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0015532 (Zinc)


  Mrv1652309042000362D          

  1  0  0  0  0  0            999 V2000
   26.2844  -17.0871    0.0000 Zn  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 HMDB0015532 (Zinc)

HMDB0015532
     RDKit          3D
Zinc
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Zn  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 HMDB0015532 (Zinc)


  Mrv1652309042000362D          

  1  0  0  0  0  0            999 V2000
   26.2844  -17.0871    0.0000 Zn  0  2  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   2
M  END
> <DATABASE_ID>
HMDB0015532

> <DATABASE_NAME>
hmdb

> <SMILES>
[Zn++]

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

> <INCHI_KEY>
PTFCDOFLOPIGGS-UHFFFAOYSA-N

> <FORMULA>
Zn

> <MOLECULAR_WEIGHT>
65.409

> <EXACT_MASS>
63.929146578

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
zinc(2+) ion

> <JCHEM_LOGP>
0.156

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
3.55

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.09

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
0.0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
zinc(2+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0015532 (Zinc)

HMDB0015532
     RDKit          3D
Zinc
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Zn  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 HMDB0015532 (Zinc)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1 Zn   UNK     0      49.064 -31.896   0.000  0.00  0.00          Zn+2
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0015532 (Zinc)

COMPND    HMDB0015532
HETATM    1 ZN1  UNL     1       0.000   0.000   0.000  1.00  0.00          ZN2+
END
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SMILES for HMDB0015532 (Zinc)

[Zn++]
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INCHI for HMDB0015532 (Zinc)

InChI=1S/Zn/q+2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Dietary zincChEBI
Zinc cationChEBI
ZINC ionChEBI
Zinc, ion (ZN2+)ChEBI
ZN(II)ChEBI
ZN(2+)ChEBI
ZN2+ChEBI
Mannosidase b, alphaMeSH
alpha Mannosidase bMeSH
alpha-D-Mannoside mannohydrolaseMeSH
Neutral alpha-mannosidaseMeSH
alpha D MannosidaseMeSH
alpha-D-MannosidaseMeSH
Lysosomal alpha-mannosidaseMeSH
Mannohydrolase, alpha-D-mannosideMeSH
alpha MannosidaseMeSH
alpha-MannosidaseMeSH
LAMANMeSH
Lysosomal alpha mannosidaseMeSH
Neutral alpha mannosidaseMeSH
alpha D Mannoside mannohydrolaseMeSH
alpha-Mannosidase, lysosomalMeSH
alpha-Mannosidase, neutralMeSH
Topostin bMeSH
Chemical FormulaZn
Average Molecular Weight65.409
Monoisotopic Molecular Weight63.929146578
IUPAC Namezinc(2+) ion
Traditional Namezinc(2+) ion
CAS Registry Number7440-66-6
SMILES
[Zn++]
InChI Identifier
InChI=1S/Zn/q+2
InChI KeyPTFCDOFLOPIGGS-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 effect
Health effect
Disposition
Biological locationRoute of exposureSource