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Showing metabocard for Iron (HMDB0015531)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (6) Show 6 proteinsXML
enzymes (6) Show 6 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-06 15:16:52 UTC
Update Date2022-03-07 02:52:01 UTC
HMDB IDHMDB0015531
Secondary Accession Numbers
  • HMDB0012943
  • HMDB12943
  • HMDB15531
Metabolite Identification
Common NameIron
DescriptionIron is a metallic element found in certain minerals, in nearly all soils, and in mineral waters. Iron is required for life. It exists in all living species, ranging from bacteria to humans. It can be found primarily in blood and it is an essential constituent of hemoglobin, cytochrome, and other components of respiratory enzyme systems. Its chief functions are in the transport of oxygen to tissue (hemoglobin) and in cellular oxidation mechanisms. Depletion of iron stores may result in iron-deficiency anemia. Iron is used to build up the blood in anemia. In humans, iron is involved in several metabolic pathways, some of which include the rofecoxib pathway, magnesium salicylate action pathway, etodolac pathway, and diclofenac pathway. Iron is also involved in several metabolic disorders, some of which include adenine phosphoribosyltransferase deficiency (APRT), porphyria variegata (PV), adenylosuccinate lyase deficiency, and AICA-ribosiduria. The major activity of supplemental iron is in the prevention and treatment of iron-deficiency anemia. Iron has putative immune-enhancing, anticarcinogenic, and cognition-enhancing activities. Iron can be found in a number of food items such as chinese water chestnut, hyssop, daikon radish, and peppermint, which makes it a potential biomarker for the consumption of these food products.
Structure
Data?1588787905
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0015531 (Iron)


  Mrv1652309042000362D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Fe  0  1  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   3
M  END
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3D MOL for HMDB0015531 (Iron)

HMDB0015531
     RDKit          3D
Iron
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   3
M  END
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3D SDF for HMDB0015531 (Iron)


  Mrv1652309042000362D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 Fe  0  1  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   3
M  END
> <DATABASE_ID>
HMDB0015531

> <DATABASE_NAME>
hmdb

> <SMILES>
[Fe+3]

> <INCHI_IDENTIFIER>
InChI=1S/Fe/q+3

> <INCHI_KEY>
VTLYFUHAOXGGBS-UHFFFAOYSA-N

> <FORMULA>
Fe

> <MOLECULAR_WEIGHT>
55.845

> <EXACT_MASS>
55.934942133

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
iron(3+) ion

> <JCHEM_LOGP>
-0.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA>
5.46

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.58

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
0.0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
iron(3+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0015531 (Iron)

HMDB0015531
     RDKit          3D
Iron
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   3
M  END
Download

PDB for HMDB0015531 (Iron)

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 Fe   UNK     0       0.000   0.000   0.000  0.00  0.00          Fe+3
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0015531 (Iron)

COMPND    HMDB0015531
HETATM    1 FE1  UNL     1       0.000   0.000   0.000  1.00  0.00          FE3+
END
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SMILES for HMDB0015531 (Iron)

[Fe+3]
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INCHI for HMDB0015531 (Iron)

InChI=1S/Fe/q+3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
FE (III) ionChEBI
Fe(III)ChEBI
Fe(3+)ChEBI
Ferric ionChEBI
Ferric ironChEBI
Iron, ion (fe(3+))ChEBI
Iron(3+)Kegg
Chemical FormulaFe
Average Molecular Weight55.845
Monoisotopic Molecular Weight55.934942133
IUPAC Nameiron(3+) ion
Traditional Nameiron(3+) ion
CAS Registry Number7439-89-6
SMILES
[Fe+3]
InChI Identifier
InChI=1S/Fe/q+3
InChI KeyVTLYFUHAOXGGBS-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

Adverse health effect

Disposition

Biological location

Source

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point1538 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.77ChemAxon
pKa (Strongest Acidic)4.58ChemAxon
Physiological Charge3ChemAxon
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
Iron[Fe+3]696.0Standard polar33892256
Iron[Fe+3]230.1Standard non polar33892256
Iron[Fe+3]46.4Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iron 10V, Positive-QTOFsplash10-0a4i-9000000000-af3e7aec4f5bd96686832015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iron 20V, Positive-QTOFsplash10-0a4i-9000000000-af3e7aec4f5bd96686832015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iron 40V, Positive-QTOFsplash10-0a4i-9000000000-af3e7aec4f5bd96686832015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iron 10V, Negative-QTOFsplash10-0udi-9000000000-3335fec4c3184739b75e2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iron 20V, Negative-QTOFsplash10-0udi-9000000000-3335fec4c3184739b75e2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iron 40V, Negative-QTOFsplash10-0udi-9000000000-3335fec4c3184739b75e2015-09-15Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified16.7 +/- 6.0 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified10.744-26.860 uMAdult (>18 years old)Not SpecifiedNormal details
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01592 details
BloodDetected and Quantified2.87-22.92 uMChildren (0 - <14 years old)Both
Normal
    • CALIPER Paediatri...
 details
BloodDetected and Quantified3.58-29.009 uMAdolescent (14 - <19 years oldFemale
Normal
    • CALIPER Paediatri...
 details
BloodDetected and Quantified5.55-30.083 uMAdolescent (14 - <19 years oldMale
Normal
    • CALIPER Paediatri...
 details
BloodDetected and Quantified9.00-30.0 uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified12.0-32.0 uMAdult (>18 years old)Male
Normal		 details
BloodDetected and Quantified16.653 (2.686-40.290) uMAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified19.339 (3.760-41.364) uMAdult (>18 years old)Male
Normal		 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01592 details
UrineDetected and Quantified0.36 (0.018-0.83) umol/mmol creatinineNewborn (0-30 days old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified15.1 +/- 6.6 uMAdult (>18 years old)BothErythropoietic protoporphyria details
BloodDetected and Quantified5.551-6.625 uMAdult (>18 years old)Female
Aceruloplasminemia		 details
BloodDetected and Quantified25.4 uMAdult (>18 years old)FemaleLecithin:cholesterol Acyltransferase Deficiency details
BloodDetected and Quantified22.204 (7.521-44.0505) uMAdult (>18 years old)Male
Hemochromatosis, type 1		 details
BloodDetected and Quantified18.444 (1.0744-42.976) uMAdult (>18 years old)Female
Hemochromatosis, type 1		 details
Associated Disorders and Diseases
Disease References
Aceruloplasminemia
  1. Roberti Mdo R, Borges Filho HM, Goncalves CH, Lima FL: Aceruloplasminemia: a rare disease - diagnosis and treatment of two cases. Rev Bras Hematol Hemoter. 2011;33(5):389-92. doi: 10.5581/1516-8484.20110104. [PubMed:23049345 ]
Hemochromatosis, type 1
  1. Bulaj ZJ, Griffen LM, Jorde LB, Edwards CQ, Kushner JP: Clinical and biochemical abnormalities in people heterozygous for hemochromatosis. N Engl J Med. 1996 Dec 12;335(24):1799-805. doi: 10.1056/NEJM199612123352403. [PubMed:8943161 ]
Erythropoietic protoporphyria
  1. Cole DE, Farag S, Dooley KC: Ethanolaminuria: a non-specific laboratory finding in the seriously ill infant. Clin Biochem. 1988 Oct;21(5):297-300. [PubMed:3233740 ]
Lecithin:cholesterol Acyltransferase Deficiency
  1. Idzior-Walus B, Sieradzki J, Kostner G, Malecki MT, Klupa T, Wesolowska T, Rostworowski W, Hartwich J, Walus M, Kiec AD, Naruszewicz M: Familial lecithin-cholesterol acyltransferase deficiency: biochemical characteristics and molecular analysis of a new LCAT mutation in a Polish family. Atherosclerosis. 2006 Apr;185(2):413-20. Epub 2005 Jul 26. [PubMed:16051254 ]
Associated OMIM IDs
  • 604290 (Aceruloplasminemia)
  • 235200 (Hemochromatosis, type 1)
  • 177000 (Erythropoietic protoporphyria)
  • 245900 (Lecithin:cholesterol Acyltransferase Deficiency)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB029221
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC14819
BioCyc IDFE%2b3
BiGG IDNot Available
Wikipedia LinkIron(III)
METLIN IDNot Available
PubChem Compound29936
PDB IDNot Available
ChEBI ID29034
Food Biomarker OntologyNot Available
VMH IDFE3
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General ReferencesNot Available

Enzymes

Enzyme Details
1. Heme oxygenase 2
General function:
Involved in heme oxygenase (decyclizing) activity
Specific function:
Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed. Heme oxygenase 2 could be implicated in the production of carbon monoxide in brain where it could act as a neurotransmitter.
Gene Name:
HMOX2
Uniprot ID:
P30519
Molecular weight:
36032.615
Reactions
Hemoglobin + FADH + Oxygen → Globin + Biliverdin + Carbon monoxide + Iron + FAD + Waterdetails
Enzyme Details
2. Heme oxygenase 1
General function:
Involved in heme oxygenase (decyclizing) activity
Specific function:
Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.
Gene Name:
HMOX1
Uniprot ID:
P09601
Molecular weight:
32818.345
Reactions
Hemoglobin + FADH + Oxygen → Globin + Biliverdin + Carbon monoxide + Iron + FAD + Waterdetails
Enzyme Details
3. Ferritin, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis. Has ferroxidase activity. Iron is taken up in the ferrous form and deposited as ferric hydroxides after oxidation.
Gene Name:
FTMT
Uniprot ID:
Q8N4E7
Molecular weight:
27537.885
Reactions
Fe2+ + Hydrogen Ion + Oxygen → Iron + Waterdetails
Enzyme Details
4. Ceruloplasmin
General function:
Involved in oxidoreductase activity
Specific function:
Ceruloplasmin is a blue, copper-binding (6-7 atoms per molecule) glycoprotein. It has ferroxidase activity oxidizing Fe(2+) to Fe(3+) without releasing radical oxygen species. It is involved in iron transport across the cell membrane. Provides Cu(2+) ions for the ascorbate-mediated deaminase degradation of the heparan sulfate chains of GPC1. May also play a role in fetal lung development or pulmonary antioxidant defense (By similarity).
Gene Name:
CP
Uniprot ID:
P00450
Molecular weight:
122204.45
Reactions
Fe2+ + Hydrogen Ion + Oxygen → Iron + Waterdetails
Enzyme Details
5. Frataxin, mitochondrial
General function:
Involved in cellular iron ion homeostasis
Specific function:
Promotes the biosynthesis of heme and assembly and repair of iron-sulfur clusters by delivering Fe(2+) to proteins involved in these pathways. May play a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe(2+) to Fe(3+); the oligomeric form but not the monomeric form has in vitro ferroxidase activity. May be able to store large amounts of iron in the form of a ferrihydrite mineral by oligomerization; however, the physiological relevance is unsure as reports are conflicting and the function has only been shown using heterologous overexpression systems. Modulates the RNA-binding activity of ACO1.
Gene Name:
FXN
Uniprot ID:
Q16595
Molecular weight:
23134.895
Reactions
Fe2+ + Hydrogen Ion + Oxygen → Iron + Waterdetails
Enzyme Details
6. Ferritin heavy chain
General function:
Involved in oxidoreductase activity
Specific function:
Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis. Has ferroxidase activity. Iron is taken up in the ferrous form and deposited as ferric hydroxides after oxidation. Also plays a role in delivery of iron to cells. Mediates iron uptake in capsule cells of the developing kidney (By similarity).
Gene Name:
FTH1
Uniprot ID:
P02794
Molecular weight:
21225.47
Reactions
Fe2+ + Hydrogen Ion + Oxygen → Iron + Waterdetails