ECMDB: Porphobilinogen (ECMDB00245) (M2MDB000104)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (2)XML

Proteins (712)

Record Information

Version

2.0

Creation Date

2012-05-31 10:24:48 -0600

Update Date

2015-09-13 12:56:07 -0600

Secondary Accession Numbers

ECMDB00245

Identification

Name:

Porphobilinogen

Description

Porphobilinogen is a pyrrole involved in porphyrin metabolism. -- Wikipedia; It consists of a pyrrole ring with acetyl, propionyl, and aminomethyl side chains; It is a key monopyrrolic intermediate in porphyrin, chlorophyll and vitamin B12 biosynthesis. Porphobilinogen is generated by the enzyme ALA dehydratase by combining two molecules of dALA together, and converted into hydroxymethyl bilane by the enzyme porphobilinogen deaminase. 4 molecules of porphobilinogen are condensed to form one molecule of uroporphyrinogen I, which is then converted successively to coproporphyrinogen I, protoporphyrin IX, and heme.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms:

5-(Aminomethyl)-4-(carboxymethyl)-Pyrrole-3-propionate
5-(Aminomethyl)-4-(carboxymethyl)-Pyrrole-3-propionic acid
PBG
Porphobilinogen

Chemical Formula:

C₁₀H₁₄N₂O₄

Weight:

Average: 226.2292
Monoisotopic: 226.095356946

InChI Key:

QSHWIQZFGQKFMA-UHFFFAOYSA-N

InChI:

InChI=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)

CAS number:

487-90-1

IUPAC Name:

3-[5-(aminomethyl)-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid

Traditional IUPAC Name:

porphobilinogen

SMILES:

NCC1=C(CC(O)=O)C(CCC(O)=O)=CN1

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.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

Aralkylamines

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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

dicarboxylic acid (CHEBI:17381 )
pyrroles (CHEBI:17381 )
aralkylamino compound (CHEBI:17381 )

Physical Properties

State:

Solid

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	2.72 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-2.7	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	3.66	ChemAxon
pKa (Strongest Basic)	8.78	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.41 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	56.38 m³·mol⁻¹	ChemAxon
Polarizability	22.56 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

2 5-Aminolevulinic acid <> Hydrogen ion +2 Water + Porphobilinogen
Water + 4 Porphobilinogen > Hydroxymethylbilane +4 Ammonium
2 5-Aminolevulinic acid <> Porphobilinogen +2 Water
4 Porphobilinogen + Water <> Hydroxymethylbilane +4 Ammonia
Water + Porphobilinogen <> Hydrogen ion + Ammonia + Hydroxymethylbilane
5-Aminolevulinic acid <> Hydrogen ion + Water + Porphobilinogen
2 5-Aminolevulinic acid > Porphobilinogen +2 Water
4 Porphobilinogen + Water > Hydroxymethylbilane +4 Ammonia
8 5-Aminolevulinic acid >4 Hydrogen ion +8 Water +4 Porphobilinogen
2 5-Aminolevulinic acid <> Hydrogen ion +2 Water + Porphobilinogen
2 5-Aminolevulinic acid <> Porphobilinogen +2 Water
4 Porphobilinogen + Water <> Hydroxymethylbilane +4 Ammonia
2 5-Aminolevulinic acid <> Hydrogen ion +2 Water + Porphobilinogen
4 Porphobilinogen + Water <> Hydroxymethylbilane +4 Ammonia

SMPDB Pathways:

Porphyrin metabolism

PW000936

KEGG Pathways:

Metabolic pathways eco01100
Porphyrin and chlorophyll metabolism ec00860

EcoCyc Pathways:

tetrapyrrole biosynthesis I PWY-5188

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-001j-1923000000-70c31b91868484322655	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-001j-1923000000-70c31b91868484322655	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-3920000000-d4006159f28f6672d3a5	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0080-9071000000-ad88926555e7416fedb3	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0a4i-0090000000-912aa953bdd13d6d18ca	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00dl-1900000000-8a87960bb63c4915db22	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-006x-9500000000-c934217374e64d6edee3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-0udi-1910000000-4a59655d524261d288a0	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, negative	splash10-0a4i-9000000000-5a7fed67c4a8909b6d89	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 15V, negative	splash10-00xr-0910000000-79d39f97cef0385e0978	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 0V, negative	splash10-0fb9-0790000000-a3976589df77175b4e7b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-0fb9-0890000000-8659c76eb4cd3bbc050a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-0ui0-0970000000-ace836f5bc7c40d838f3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, negative	splash10-0ufr-0970000000-34b54c13783e56f913ed	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 6V, negative	splash10-0udi-0920000000-ab742bdbcc6ad44ca7ad	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 8V, negative	splash10-0udi-0900000000-d9086599996dff3ecc2b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 9V, negative	splash10-0udi-1900000000-ca027f0ab39ba0260c42	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 10V, negative	splash10-0zfr-4900000000-c5f999c0aa9c0e985528	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 13V, negative	splash10-0a4i-9700000000-c39abc4f07f6ba584489	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 14V, negative	splash10-0a4i-9400000000-6eece2186d7d8e426696	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 18V, negative	splash10-0a4i-9200000000-4b1d1515941d17b58cd8	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 15V, negative	splash10-0udi-0900000000-4211fc4d53d78720f632	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 15V, negative	splash10-0a4i-0900000000-3b3b751b5b26d5ba4273	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4l-0980000000-423d28b762ba4c07586b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-0910000000-31575764ba8bd8d50279	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-074r-0900000000-9d96bd59f1a4371a8df4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0059-0790000000-2cc911a67c1aa8e35d99	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06ur-0940000000-2c3da60da6ab9523fbf3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bt9-4900000000-cf52dffb4284f9eeaa5d	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Buchet JP, Lauwerys R, Hassoun A, Dratwa M, Wens R, Collart F, Tielemans C: Effect of aluminum on porphyrin metabolism in hemodialyzed patients. Nephron. 1987;46(4):360-3. Pubmed: 3658064
Dhar GJ, Bossenmaier I, Petryka ZJ, Cardinal R, Watson CJ: Effects of hematin in hepatic porphyria. Further studies. Ann Intern Med. 1975 Jul;83(1):20-30. Pubmed: 1147435
Ellencweig N, Schoenfeld N, Zemishlany Z: Acute intermittent porphyria: psychosis as the only clinical manifestation. Isr J Psychiatry Relat Sci. 2006;43(1):52-6. Pubmed: 16910386
Evans J, Lefkowitch J, Lim CK, Billing B: Fecal porphyrin abnormalities in a patient with features of Rotor's syndrome. Gastroenterology. 1981 Dec;81(6):1125-30. Pubmed: 7286590
Ford RE, Ou CN, Ellefson RD: Assay for erythrocyte uroporphyrinogen I synthase activity, with porphobilinogen as substrate. Clin Chem. 1980 Jul;26(8):1182-5. Pubmed: 7389090
Hsiao KJ, Lee FY, Wu SJ, Chang WJ: Determination of erythrocyte porphobilinogen deaminase activity using porphobilinogen as substrate. Clin Chim Acta. 1987 Sep 30;168(2):257-8. Pubmed: 3677422
Ivanov E, Pisanets M: Studies on the biosynthesis of porphyrins in erythrocytes after incubation with delta-aminolevulinic acid: an attempt to investigate the pathogenesis of nephrogenic anemia. Acta Biol Med Ger. 1982;41(4):307-13. Pubmed: 7124248
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Mustajoki P: Normal erythrocyte uroporphyrinogen I synthase in a kindred with acute intermittent porphyria. Ann Intern Med. 1981 Aug;95(2):162-6. Pubmed: 7258864
Sassa S, Solish G, Levere RD, Kappas A: Studies in porphyria. IV. Expression of the gene defect of acute intermittent porphyria in cultured human skin fibroblasts and amniotic cells: prenatal diagnosis of the porphyric trait. J Exp Med. 1975 Sep 1;142(3):722-31. Pubmed: 1165472
Shiue JW, Lee FY, Hsiao KJ, Tsai YT, Lee SD, Wu SJ: Abnormal thyroid function and hypercholesterolemia in a case of acute intermittent porphyria. Taiwan Yi Xue Hui Za Zhi. 1989 Jul;88(7):729-31. Pubmed: 2809566
Tishler PV, Woodward B, O'Connor J, Holbrook DA, Seidman LJ, Hallett M, Knighton DJ: High prevalence of intermittent acute porphyria in a psychiatric patient population. Am J Psychiatry. 1985 Dec;142(12):1430-6. Pubmed: 4073306
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

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.

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CHEBI ID	17381
HMDB ID	HMDB00245
Pubchem Compound ID	1021
Kegg ID	C00931
ChemSpider ID	995
Wikipedia	Porphobilinogen
BioCyc ID	PORPHOBILINOGEN
EcoCyc ID	PORPHOBILINOGEN
Ligand Expo	PBG

Enzymes

Protein Details

1. Porphobilinogen deaminase

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:: hemC
Uniprot ID:: P06983
Molecular weight:: 33851

Reactions

4 porphobilinogen + H(2)O = hydroxymethylbilane + 4 NH(3).

Protein Details

2. Delta-aminolevulinic acid dehydratase

General function:: Involved in catalytic 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:: hemB
Uniprot ID:: P0ACB2
Molecular weight:: 35624

Reactions

2 5-aminolevulinate = porphobilinogen + 2 H(2)O.

Porphobilinogen (ECMDB00245) (M2MDB000104)

Structure for #<Compound:0xa56e3c3c>

Enzymes

Reactions

Reactions