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Identification
YMDB IDYMDB00401
NamePorphobilinogen
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionPorphobilinogen belongs to the class of organic compounds known as aralkylamines. These are alkylamines in which the alkyl group is substituted at one carbon atom by an aromatic hydrocarbyl group. Porphobilinogen is a very strong basic compound (based on its pKa). Porphobilinogen exists in all living species, ranging from bacteria to humans. Within yeast, porphobilinogen participates in a number of enzymatic reactions. In particular, porphobilinogen can be biosynthesized from 5-aminolevulinic acid; which is catalyzed by the enzyme Delta-aminolevulinic acid dehydratase. In addition, porphobilinogen can be converted into hydroxymethylbilane; which is mediated by the enzyme porphobilinogen deaminase. In yeast, porphobilinogen is involved in the metabolic pathway called the porphyrin metabolism pathway. Porphobilinogen is a potentially toxic compound.
Structure
Thumb
Synonyms
  • 5-(aminomethyl)-4-(carboxymethyl)-Pyrrole-3-propionate
  • 5-(aminomethyl)-4-(carboxymethyl)-Pyrrole-3-propionic acid
  • PBG
  • Porphobilinogen
CAS number487-90-1
WeightAverage: 226.2292
Monoisotopic: 226.095356946
InChI KeyQSHWIQZFGQKFMA-UHFFFAOYSA-N
InChIInChI=1S/C10H14N2O4/c11-4-8-7(3-10(15)16)6(5-12-8)1-2-9(13)14/h5,12H,1-4,11H2,(H,13,14)(H,15,16)
IUPAC Name3-[5-(aminomethyl)-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid
Traditional IUPAC Nameporphobilinogen
Chemical FormulaC10H14N2O4
SMILES[H]OC(=O)C([H])([H])C1=C(N([H])C([H])=C1C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])N([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as aralkylamines. These are alkylamines in which the alkyl group is substituted at one carbon atom by an aromatic hydrocarbyl group.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentAralkylamines
Alternative Parents
Substituents
  • Aralkylamine
  • Dicarboxylic acid or derivatives
  • Substituted pyrrole
  • Heteroaromatic compound
  • Pyrrole
  • Amino acid
  • Amino acid or derivatives
  • Carboxylic acid derivative
  • Azacycle
  • Carboxylic acid
  • Organoheterocyclic compound
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility2.72 g/LALOGPS
logP-2.4ALOGPS
logP-2.7ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)3.66ChemAxon
pKa (Strongest Basic)8.78ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area116.41 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity56.38 m³·mol⁻¹ChemAxon
Polarizability22.56 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Porphyrin MetabolismPW002462 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Porphyrin and chlorophyll metabolismec00860 Map00860
SMPDB Reactions
5-Aminolevulinic acidPorphobilinogen + water
Porphobilinogen + waterHydroxymethylbilane + Ammonia
KEGG Reactions
Porphobilinogen + waterAmmonium + Hydroxymethylbilane
5-Aminolevulinic acidwater + Porphobilinogen + hydron
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-001j-1923000000-70c31b91868484322655JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001j-1923000000-70c31b91868484322655JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-3920000000-d4006159f28f6672d3a5JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0080-9071000000-ad88926555e7416fedb3JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0a4i-0090000000-912aa953bdd13d6d18caJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00dl-1900000000-8a87960bb63c4915db22JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-006x-9500000000-c934217374e64d6edee3JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4l-0980000000-423d28b762ba4c07586bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-0910000000-31575764ba8bd8d50279JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-074r-0900000000-9d96bd59f1a4371a8df4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0059-0790000000-2cc911a67c1aa8e35d99JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-06ur-0940000000-2c3da60da6ab9523fbf3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bt9-4900000000-cf52dffb4284f9eeaa5dJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Synthesis Reference:Frydman, Benjamin; Despuy, Maria E.; Rapoport, Henry. Pyrroles from azaindoles. A synthesis of porphobilinogen. Journal of the American Chemical Society (1965), 87(15), 3530-1.
External Links:
ResourceLink
CHEBI ID17381
HMDB IDHMDB00245
Pubchem Compound ID1021
Kegg IDC00931
ChemSpider ID995
FOODB IDFDB021916
WikipediaPorphobilinogen
BioCyc IDPORPHOBILINOGEN

Enzymes

General function:
Involved in porphobilinogen synthase activity
Specific function:
Catalyzes an early step in the biosynthesis of tetrapyrroles. Binds two molecules of 5-aminolevulinate per subunit, each at a distinct site, and catalyzes their condensation to form porphobilinogen
Gene Name:
HEM2
Uniprot ID:
P05373
Molecular weight:
37739.69922
Reactions
2 5-aminolevulinate → porphobilinogen + 2 H(2)O.
General function:
Involved in hydroxymethylbilane synthase activity
Specific function:
Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps
Gene Name:
HEM3
Uniprot ID:
P28789
Molecular weight:
36674.19922
Reactions
4 porphobilinogen + H(2)O → hydroxymethylbilane + 4 NH(3).