Hmdb loader

Showing metabocard for Zinc (HMDB0015532)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (83) Show 83 proteinsXML
enzymes (83) Show 83 proteins
Show more...Show more...Show more...Show more...Show more...
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
Thumb
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
Download

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
Download

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

$$$$
Download

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
Download

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
Download

3D PDB for HMDB0015532 (Zinc)

COMPND    HMDB0015532
HETATM    1 ZN1  UNL     1       0.000   0.000   0.000  1.00  0.00          ZN2+
END
Download

SMILES for HMDB0015532 (Zinc)

[Zn++]
Download

INCHI for HMDB0015532 (Zinc)

InChI=1S/Zn/q+2
Download
View in JSmolView Stereo Labels
Synonyms
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
Process
Naturally occurring process
Role
Industrial applicationEnvironmental roleBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point419.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.16ChemAxon
pKa (Strongest Acidic)3.09ChemAxon
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
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zinc 10V, Positive-QTOFsplash10-03di-9000000000-0cd08967c771fb6453292015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zinc 20V, Positive-QTOFsplash10-03di-9000000000-0cd08967c771fb6453292015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zinc 40V, Positive-QTOFsplash10-03di-9000000000-0cd08967c771fb6453292015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zinc 10V, Negative-QTOFsplash10-03di-9000000000-29976d3ebd17b2d11a4b2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zinc 20V, Negative-QTOFsplash10-03di-9000000000-29976d3ebd17b2d11a4b2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Zinc 40V, Negative-QTOFsplash10-03di-9000000000-29976d3ebd17b2d11a4b2015-09-15Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Kidney disease
  1. Paniagua R, Claure R, Amato D, Flores E, Perez A, Exaire E: Effects of oral administration of zinc and diiodohydroxyquinolein on plasma zinc levels of uremic patients. Nephron. 1995;69(2):147-50. [PubMed:7723896 ]
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 ]
Chronic renal failure
  1. McGregor DO, Dellow WJ, Lever M, George PM, Robson RA, Chambers ST: Dimethylglycine accumulates in uremia and predicts elevated plasma homocysteine concentrations. Kidney Int. 2001 Jun;59(6):2267-72. [PubMed:11380830 ]
Continuous ambulatory peritoneal dialysis
  1. McGregor DO, Dellow WJ, Lever M, George PM, Robson RA, Chambers ST: Dimethylglycine accumulates in uremia and predicts elevated plasma homocysteine concentrations. Kidney Int. 2001 Jun;59(6):2267-72. [PubMed:11380830 ]
Hemodialysis
  1. McGregor DO, Dellow WJ, Lever M, George PM, Robson RA, Chambers ST: Dimethylglycine accumulates in uremia and predicts elevated plasma homocysteine concentrations. Kidney Int. 2001 Jun;59(6):2267-72. [PubMed:11380830 ]
Hypertension
  1. Wang S, Ma A, Song S, Quan Q, Zhao X, Zheng X: Fasting serum free fatty acid composition, waist/hip ratio and insulin activity in essential hypertensive patients. Hypertens Res. 2008 Apr;31(4):623-32. doi: 10.1291/hypres.31.623. [PubMed:18633173 ]
Hyperzincaemia and hypercalprotectinaemia
  1. Isidor B, Poignant S, Corradini N, Fouassier M, Quartier P, Roth J, Picherot G: Hyperzincemia and hypercalprotectinemia: unsuccessful treatment with tacrolimus. Acta Paediatr. 2009 Feb;98(2):410-2. doi: 10.1111/j.1651-2227.2008.01092.x. Epub 2008 Nov 4. [PubMed:18983438 ]
Alzheimer's disease
  1. Molina JA, Jimenez-Jimenez FJ, Aguilar MV, Meseguer I, Mateos-Vega CJ, Gonzalez-Munoz MJ, de Bustos F, Porta J, Orti-Pareja M, Zurdo M, Barrios E, Martinez-Para MC: Cerebrospinal fluid levels of transition metals in patients with Alzheimer's disease. J Neural Transm (Vienna). 1998;105(4-5):479-88. [PubMed:9720975 ]
  2. 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 ]
Acrodermatitis enteropathica
  1. Nistor N, Ciontu L, Frasinariu OE, Lupu VV, Ignat A, Streanga V: Acrodermatitis Enteropathica: A Case Report. Medicine (Baltimore). 2016 May;95(20):e3553. doi: 10.1097/MD.0000000000003553. [PubMed:27196457 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB031256
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC00038
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound32051
PDB IDNot Available
ChEBI ID29105
Food Biomarker OntologyNot Available
VMH IDZN2
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References

Only showing the first 10 proteins. There are 83 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Pyruvate carboxylase, mitochondrial
General function:
Involved in catalytic activity
Specific function:
Pyruvate carboxylase catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second. Catalyzes in a tissue specific manner, the initial reactions of glucose (liver, kidney) and lipid (adipose tissue, liver, brain) synthesis from pyruvate.
Gene Name:
PC
Uniprot ID:
P11498
Molecular weight:
129632.565
Enzyme Details
2. Phospholipase D2
General function:
Involved in protein binding
Specific function:
May have a role in signal-induced cytoskeletal regulation and/or endocytosis (By similarity).
Gene Name:
PLD2
Uniprot ID:
O14939
Molecular weight:
104656.485
Enzyme Details
3. Methionine synthase
General function:
Involved in cobalamin binding
Specific function:
Catalyzes the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate (By similarity).
Gene Name:
MTR
Uniprot ID:
Q99707
Molecular weight:
140525.91
Enzyme Details
4. Aminopeptidase N
General function:
Involved in proteolysis
Specific function:
Broad specificity aminopeptidase. Plays a role in the final digestion of peptides generated from hydrolysis of proteins by gastric and pancreatic proteases. May play a critical role in the pathogenesis of cholesterol gallstone disease. May be involved in the metabolism of regulatory peptides of diverse cell types, responsible for the processing of peptide hormones, such as angiotensin III and IV, neuropeptides, and chemokines. Found to cleave antigen peptides bound to major histocompatibility complex class II molecules of presenting cells and to degrade neurotransmitters at synaptic junctions. Is also implicated as a regulator of IL-8 bioavailability in the endometrium, and therefore may contribute to the regulation of angiogenesis. Is used as a marker for acute myeloid leukemia and plays a role in tumor invasion. In case of human coronavirus 229E (HCoV-229E) infection, serves as receptor for HCoV-229E spike glycoprotein. Mediates as well human cytomegalovirus (HCMV) infection.
Gene Name:
ANPEP
Uniprot ID:
P15144
Molecular weight:
Not Available
Enzyme Details
5. Alcohol dehydrogenase [NADP(+)]
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the NADPH-dependent reduction of a variety of aromatic and aliphatic aldehydes to their corresponding alcohols. Catalyzes the reduction of mevaldate to mevalonic acid and of glyceraldehyde to glycerol. Has broad substrate specificity. In vitro substrates include succinic semialdehyde, 4-nitrobenzaldehyde, 1,2-naphthoquinone, methylglyoxal, and D-glucuronic acid. Plays a role in the activation of procarcinogens, such as polycyclic aromatic hydrocarbon trans-dihydrodiols, and in the metabolism of various xenobiotics and drugs, including the anthracyclines doxorubicin (DOX) and daunorubicin (DAUN).
Gene Name:
AKR1A1
Uniprot ID:
P14550
Molecular weight:
36572.71
Enzyme Details
6. Alcohol dehydrogenase class-3
General function:
Involved in zinc ion binding
Specific function:
Class-III ADH is remarkably ineffective in oxidizing ethanol, but it readily catalyzes the oxidation of long-chain primary alcohols and the oxidation of S-(hydroxymethyl) glutathione.
Gene Name:
ADH5
Uniprot ID:
P11766
Molecular weight:
39723.945
Enzyme Details
7. Alcohol dehydrogenase 1B
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
ADH1B
Uniprot ID:
P00325
Molecular weight:
39835.17
Enzyme Details
8. Alcohol dehydrogenase class 4 mu/sigma chain
General function:
Involved in zinc ion binding
Specific function:
Could function in retinol oxidation for the synthesis of retinoic acid, a hormone important for cellular differentiation. Medium-chain (octanol) and aromatic (m-nitrobenzaldehyde) compounds are the best substrates. Ethanol is not a good substrate but at the high ethanol concentrations reached in the digestive tract, it plays a role in the ethanol oxidation and contributes to the first pass ethanol metabolism.
Gene Name:
ADH7
Uniprot ID:
P40394
Molecular weight:
41480.985
Enzyme Details
9. Alcohol dehydrogenase 1A
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
ADH1A
Uniprot ID:
P07327
Molecular weight:
39858.37
Enzyme Details
10. Alcohol dehydrogenase 6
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
ADH6
Uniprot ID:
P28332
Molecular weight:
39072.275

Only showing the first 10 proteins. There are 83 proteins in total.

Show all enzymes and transporters