| Creation Date |
Date the MetaboCard entry was created |
| Last Update |
Date the MetaboCard was last updated |
| Accession No |
HMDB Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the metabolite's name |
| Common Name |
Common name of metabolite |
| Description |
Description of the metabolite describing its chemical properties, metabolic role, general function, medical relevance or other useful data |
| Synonyms |
Common synonyms for the metabolite gathered from various sources and languages |
| Chemical IUPAC Name |
IUPAC or standard chemical name for the metabolite |
| Chemical Formula |
Chemical formula describing atomic or elemental composition |
| Chemical Structure |
Thumbnail image (GIF) of the metabolite structure |
| Chemical Taxonomy |
Listing of the chemical classification to which the compound belongs. Similar to biological taxonomy, HMDB uses 1) Chemical Kingdom (organic, inorganic, radical); 2) Chemical Class (amine, organic acid, amino acid, nucleoside, etc.); 3) Chemical species (as determined by Chekmol); 4) Biofunction (biological function of the metabolite) and 5) Application (potential industrial or medical application of the metabolite) |
| Molecular Weight |
Molecular weight in g/mol, determined from molecular formula. Both monoisotopic and average molecular weight are provided |
| Smiles (Isomeric) |
SMILES string corresponding to the isomeric (chiral) metabolite structure |
| Smiles (Canonical) |
SMILES string corresponding to the non-chiral metabolite structure |
| KEGG Compound ID |
Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG) |
| BioCyc ID |
BioCyc database compound identification number (if molecule is in BioCyc) |
| PubChem Compound ID |
NCBI's PubChem database compound identification number (if molecule is in PubChem) |
| PubChem Substance ID(s) |
NCBI's PubChem database substance identification number (if molecule is in PubChem) |
| ChEBI ID |
EBI's Chemicals of Biological Interest identification number (if molecule is in CHEBI) |
| CAS Registry Number |
Chemical Abstract Service identification number |
| InChI Identifier |
IUPAC approved InChI identifier |
| Synthesis Reference |
Reference or patent number to description of compound's synthesis |
| Melting Point |
Melting point (if solid) or boiling point (if liquid) in degrees Celsius |
| H2O Solubility Experimental |
Water solubility in mg/mL as determined using experimental methods |
| H2O Solubility Predicted |
Water solubility in mg/mL using either ACD solubility predictor and/or local software |
| State |
Physical state (solid, liquid, gas) |
| LogP/Hphobicity |
Water/octanol partition coefficient |
| Material Safety Data Sheet (MSDS) |
MSDS is the Material Safety Data Sheet as supplied by either the supplier or manufacturer |
| MOL File Image |
Image of structure in Mol file format |
| MOL File Text |
Text version of metabolite structure in Mol file format |
| SDF File [Text] |
Text version of structure in SDF file format |
| PDB File Calculated Image |
Image of metabolite's 3D structure in PDB format, calculated using MolConvert (if small molecule) |
| PDB File Calculated Text |
Image of metabolite's 3D structure in PDB format, calculated using MolConvert (if small molecule) |
| PDB ID |
PDB identification number of protein structure bound to the metabolite if it exists in PDB |
| PDB File Experimental Text |
PDB text file of structure of metabolite if it exists in PDB |
| PDB File Experimental Image |
Image of metabolite's 3D structure in PDB format |
| Experimental 1H NMR Spectrum |
Image of experimentally measured 1H NMR spectrum (with peak labels and assignments) of metabolite - if collected |
| Experimental 13C NMR Spectrum |
Image of experimentally measured 13C HSQC NMR spectrum (with peak labels and assignments) of metabolite - if collected |
| Predicted 1H NMR Spectrum |
Image of ACD predicted 1H NMR spectrum (with peak labels and assignments) of metabolite |
| Experimental 13C NMR Spectrum |
Image of ACD predicted 13C NMR spectrum (with peak labels and assignments) of metabolite |
| Mass Spectrum |
Image of Ion Trap MS/MS Spectrum of metabolite (if it exists) |
| Cellular Location |
Likely or observed location of the metabolite inside the cell (Cytoplasm, Nucleus, Membrane, Extracellular, etc.) |
| Biofluid Location |
Observed location of the metabolite in different biofluids (Urine, Blood, CSF, Saliva, Bile, Seminal, etc.) |
| Tissue Location |
Observed location of the metabolite in different tissues |
| Concentration [Normal Urine] |
Literature and/or experimentally measured normal concentration of the metabolite in urine, reported as umol/mmol Creatinine with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Concentration [Normal Plasma] |
Literature and/or experimentally measured normal concentration of the metabolite in blood plasma, reported as micromolar (uM) with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Concentration [Normal CSF] |
Literature and/or experimentally measured normal concentration of the metabolite in cerebrospinal fluid (CSF), reported as micromolar (uM) with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Concentration [Normal Cellular] |
Literature and/or experimentally measured normal concentration of the metabolite within cells, reported as micromolar (uM) with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Concentration [Normal Other Biofluids] |
Literature and/or experimentally measured normal concentration of the metabolite in other biofluids or tissues, reported as micromolar (uM) with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Associated Disorders |
Literature and/or experimentally measured abnormal concentration of the metabolite in urine, reported as umol/mmol Creatinine with associated range or SD error. Measurements made by the HMP team are reported with *** |
| OMIM ID |
Online Mendellian Inheritance of Man (OMIM) disease identification number(s). This includes disease that are associated with defects in the compounds metabolism |
| MetaGene ID |
Disease identification number for Metagene Online Knowledge base for inborn errors of metabolism. This includes disease that are associated with defects in the compounds metabolism |
| Concentration [Abnormal Urine] |
Literature and/or experimentally measured abnormal concentration of the metabolite in urine, reported as umol/mmol Creatinine with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Concentration [Abnormal Plasma] |
Literature and/or experimentally measured abnormal concentration of the metabolite in blood plasma, reported as micromolar (uM) with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Concentration [Abnormal CSF] |
Literature and/or experimentally measured abnormal concentration of the metabolite in cerebrospinal fluid (CSF), reported as micromolar (uM) with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Concentration [Abnormal Cellular] |
Literature and/or experimentally measured abnormal concentration of the metabolite within cells, reported as micromolar (uM) with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Concentration [Normal Other Biofluids] |
Literature and/or experimentally measured abnormal concentration of the metabolite in other biofluids or tissues, reported as micromolar (uM) with associated range or SD error. Measurements made by the HMP team are reported with *** |
| Concentration References |
PubMed ID's or textbook references to reported metabolite concentrations given in above fields. |
| Pathway Names |
Names of metabolic pathways associated with the metabolite |
| KEGG Images |
Images of the KEGG-rendered metabolic pathways or pathway maps |
| SimCell Pathway Images |
Images of manually drawn metabolic pathways rendered using a metabolic modeling package called SimCell |
| SimCell Pathway Graphs |
Images of metabolic simulations (enzyme progress curves) generated via SimCell |
| SimCell Pathway SBMLs |
Systems Biology Markup Language (SBML) description for association pathway that allows that metabolic simulation to be run on SimCell |
| Metabolite's Protein Targets |
A list of all known proteins that are believed to bind, metabolize or transport the metabolite (these are presented below the field break) |
| Name |
Name of metabolite's protein target (this may include a receptor, enzyme, transporter or any other protein that acts on the metabolite) |
| Gene Name |
Gene name of metabolite's protein target (this may include a receptor, enzyme, transporter or any other protein that acts on the metabolite) |
| Synonyms |
Alternate names (protein names, abbreviations, etc.) of the metabolite's protein target |
| Protein Sequence |
Protein sequence of the metabolite's protein target |
| Number of Residues |
Number of amino acid's in the metabolite's protein target |
| Molecular Weight |
Molecular weight of the metabolite's protein target given in Daltons or g/mol |
| Theoretical pI |
Theoretical isoelectric point (the pH at which the protein has 0 charge) of the metabolite's protein target |
| GO Classification |
Gene ontology classification of the metabolite's protein target including function, cellular process and location |
| General function |
Short 3-4 word summary of the function(s) of the metabolite's protein target |
| Specific Function |
Detailed 30-40 word summary of the function(s) of the metabolite's protein target |
| Pathway |
List of KEGG pathways that the enzyme/protein participates in |
| Reaction |
Reaction(s) in which the metabolite's protein target participates |
| Pfam Domain Function |
Names and ID numbers of PFAM domains found in the metabolite's protein target |
| Signals |
Location of signal peptide or other localization signals in the metabolite's protein target sequence |
| Transmembrane Regions |
Number and location of the protein target's transmembrane helices |
| Metabolic Importance |
Importance or essentialness of the metabolite's target in terms of the organism's ability to survive without it |
| EC Link |
Link to the Enzyme Classification (EC) number for the metabolite's protein target |
| GenBank ID Protein |
GenBank protein ID for the metabolite's protein target |
| SwissProt ID |
SwissProt ID for the metabolite's protein target |
| PDB ID |
PDB ID for the metabolite's target (if it exists) |
| 3D Structure Image |
Image of the metabolites' target protein as rendered using WebMol |
| 3D Structure Text |
PDB text of the metabolite's protein target |
| Cellular Location |
Location of the enzyme inside or around the cell (cytoplasm, nucleus, membrane, etc.) |
| Gene Sequence |
cDNA sequence of the metabolite's protein target |
| GenBank ID Gene |
GenBank gene ID for the metabolite's target |
| Chromosome Location |
Location of the metabolite's protein/gene target on any of the 23 human chromosomes |
| Locus |
More detailed location of the chromosomal position of the enzyme |
| SNPs |
List of Single Nucleotide Polymorphisms found in the metabolite's protein target. This multicolumn table provides a hyperlink to the refSNP ID, the type of SNP (synonymous or non-synonymous), level of validation, base changes, position of the SNP, the consequent amino acid changes (if applicable), the amino acid position (if applicable) and the allele frequencies in different populations. |
| References |
PubMed references to the metabolite's protein target and its interactions with the metabolite |
