Showing metabocard for Copper (MMDBc0000133)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:37:05 UTC
Update Date2022-08-30 23:58:23 UTC
MiMeDB IDMMDBc0000133
Metabolite Identification
Common NameCopper
DescriptionCopper is an essential nutrient to all higher plants and animals. Physiologically, it exists as an ion in the body. In animals, it is found primarily in the bloodstream, as a cofactor in various enzymes, and in copper-based pigments. In the body, copper shifts between the cuprous (Cu1+) and cupric (Cu2+) forms, though the majority of the body's copper is in the Cu2+ form. The ability of copper to easily accept and donate electrons explains its important role in oxidation-reduction (redox) reactions and in scavenging free radicals. Copper is a critical functional component of a number of essential enzymes known as cuproenzymes. For instance, the copper-dependent enzyme, cytochrome c oxidase, plays a critical role in cellular energy production. By catalyzing the reduction of molecular oxygen (O2) to water (H2O), cytochrome c oxidase generates an electrical gradient used by the mitochondria to create the vital energy-storing molecule, ATP. Another cuproenzyme, lysyl oxidase, is required for the cross-linking of collagen and elastin, which are essential for the formation of strong and flexible connective tissue. Another cuproeznyme, Monoamine oxidase (MAO), plays a role in the metabolism of the neurotransmitters norepinephrine, epinephrine, and dopamine. MAO also functions in the degradation of the neurotransmitter serotonin, which is the basis for the use of MAO inhibitors as antidepressants. One of the most important cuproenzymes is Superoxide dismutase (SOD). SOD functions as an antioxidant by catalyzing the conversion of superoxide radicals (free radicals or ROS) to hydrogen peroxide, which can subsequently be reduced to water by other antioxidant enzymes. Two forms of SOD contain copper: 1) copper/zinc SOD is found within most cells of the body, including red blood cells, and 2) extracellular SOD is a copper-containing enzyme found at high levels in the lungs and low levels in blood plasma. In sufficient amounts, copper can be poisonous or even fatal to organisms. Copper is normally bound to cuproenzymes (such as SOD, MOA) and is thus only toxic when unsequestered and unmediated. It is believed that zinc and copper compete for absorption in the digestive tract so that a diet that is excessive in one of these minerals may result in a deficiency in the other. An imbalance of zinc and copper status might be involved in human hypertension. Furthermore, copper is found to be associated with hyperzincaemia and hypercalprotectinaemia and Wilson's disease, which are inborn errors of metabolism.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000564abfa19d38>


  Mrv1652309042000052D          

  1  0  0  0  0  0            999 V2000
   12.7775  -16.3242    0.0000 Cu  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 #<Metabolite:0x0000564abfa19d38>

HMDB0000657
     RDKit          3D
Copper
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Cu  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 #<Metabolite:0x0000564abfa19d38>


  Mrv1652309042000052D          

  1  0  0  0  0  0            999 V2000
   12.7775  -16.3242    0.0000 Cu  0  2  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   2
M  END
> <DATABASE_ID>
MMDBc0000133

> <DATABASE_NAME>
MIME

> <SMILES>
[Cu++]

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

> <INCHI_KEY>
JPVYNHNXODAKFH-UHFFFAOYSA-N

> <FORMULA>
Cu

> <MOLECULAR_WEIGHT>
63.546

> <EXACT_MASS>
62.929601079

> <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>
copper(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>
copper(2+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for #<Metabolite:0x0000564abfa19d38>

HMDB0000657
     RDKit          3D
Copper
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Cu  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 #<Metabolite:0x0000564abfa19d38>

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 Cu   UNK     0      23.851 -30.472   0.000  0.00  0.00          Cu+2
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for #<Metabolite:0x0000564abfa19d38>

COMPND    HMDB0000657
HETATM    1 CU1  UNL     1       0.000   0.000   0.000  1.00  0.00          CU2+
END
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SMILES for #<Metabolite:0x0000564abfa19d38>

[Cu++]
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INCHI for #<Metabolite:0x0000564abfa19d38>

InChI=1S/Cu/q+2
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Synonyms
ValueSource
COPPER (II) ionChEBI
Copper(II) cationChEBI
Copper, ion (cu2+)ChEBI
Cu(II)ChEBI
Cu2+ChEBI
Cu(2+)ChEBI
Cupric ionChEBI
CuHMDB
Chemical FormulaCu
Average Molecular Weight63.546
Monoisotopic Molecular Weight62.929601079
IUPAC Namecopper(2+) ion
Traditional Namecopper(2+) ion
CAS Registry Number7440-50-8
SMILES
[Cu++]
InChI Identifier
InChI=1S/Cu/q+2
InChI KeyJPVYNHNXODAKFH-UHFFFAOYSA-N