T3DB: Porphobilinogen

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References Gene Regulation Targets (1)XML

Targets (1)

Record Information

Version

2.0

Creation Date

2014-08-29 06:11:46 UTC

Update Date

2018-03-21 17:46:22 UTC

Accession Number

T3D4274

Identification

Common Name

Porphobilinogen

Class

Small Molecule

Description

Porphobilinogen (PBG) is a pyrrole-containing intermediate in the biosynthesis of porphyrins. It is generated from aminolevulinate (ALA) by the enzyme ALA dehydratase. Porphobilinogen is then converted into hydroxymethylbilane by the enzyme porphobilinogen deaminase (also known as hydroxymethylbilane synthase). Under certain conditions, porphobilinogen can act as a phototoxin, a neurotoxin, and a metabotoxin. A phototoxin leads to cell damage upon exposure to light. A neurotoxin causes damage to nerve cells and nerve tissues. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of porphyrins are associated with porphyrias such as porphyria variegate, acute intermittent porphyria, and hereditary coproporphyria (HCP). There are several types of porphyrias (most are inherited). Hepatic porphyrias are characterized by acute neurological attacks (seizures, psychosis, extreme back and abdominal pain, and an acute polyneuropathy), while the erythropoietic forms present with skin problems (usually a light-sensitive blistering rash and increased hair growth). The neurotoxicity of porphyrins may be due to their selective interactions with tubulin, which disrupt microtubule formation and cause neural malformations (PMID: 3441503).

Compound Type

Amine
Animal Toxin
Food Toxin
Metabolite
Natural Compound
Organic Compound

Chemical Structure

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

Synonyms

Synonym
2-aminomethylpyrrol-3-acetic acid 4-propionic acid
5-(Aminomethyl)-4-(carboxymethyl)-1H-pyrrole-3-propionic acid
5-(Aminomethyl)-4-(carboxymethyl)-Pyrrole-3-propionate
5-(Aminomethyl)-4-(carboxymethyl)-Pyrrole-3-propionic acid
PBG

Chemical Formula

C₁₀H₁₄N₂O₄

Average Molecular Mass

226.229 g/mol

Monoisotopic Mass

226.095 g/mol

CAS Registry Number

487-90-1

IUPAC Name

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

Traditional Name

porphobilinogen

SMILES

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

InChI Identifier

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)

InChI Key

InChIKey=QSHWIQZFGQKFMA-UHFFFAOYSA-N

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 )

Biological Properties

Status

Detected and Not Quantified

Origin

Endogenous

Cellular Locations

Cytoplasm
Membrane

Biofluid Locations

Not Available

Tissue Locations

Erythrocyte
Liver

Pathways

Name	SMPDB Link	KEGG Link
Porphyrin Metabolism	SMP00024	map00860
Acute Intermittent Porphyria	SMP00344	Not Available
Hereditary Coproporphyria (HCP)	SMP00342	Not Available
Porphyria Variegata (PV)	SMP00346	Not Available

Applications

Not Available

Biological Roles

metabolite

Chemical Roles

Not Available

Physical Properties

State

Solid

Appearance

White powder.

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available
LogP	Not Available

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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-001j-1923000000-70c31b91868484322655	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-001j-1923000000-70c31b91868484322655	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-3920000000-d4006159f28f6672d3a5	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0080-9071000000-ad88926555e7416fedb3	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0a4i-0090000000-912aa953bdd13d6d18ca	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00dl-1900000000-8a87960bb63c4915db22	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-006x-9500000000-c934217374e64d6edee3	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , negative	splash10-0udi-1910000000-4a59655d524261d288a0	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, negative	splash10-0a4i-9000000000-5a7fed67c4a8909b6d89	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 15V, negative	splash10-00xr-0910000000-79d39f97cef0385e0978	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 0V, negative	splash10-0fb9-0790000000-a3976589df77175b4e7b	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-0fb9-0890000000-8659c76eb4cd3bbc050a	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-0ui0-0970000000-ace836f5bc7c40d838f3	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, negative	splash10-0ufr-0970000000-34b54c13783e56f913ed	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 6V, negative	splash10-0udi-0920000000-ab742bdbcc6ad44ca7ad	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 8V, negative	splash10-0udi-0900000000-d9086599996dff3ecc2b	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 9V, negative	splash10-0udi-1900000000-ca027f0ab39ba0260c42	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 10V, negative	splash10-0zfr-4900000000-c5f999c0aa9c0e985528	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 13V, negative	splash10-0a4i-9700000000-c39abc4f07f6ba584489	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 14V, negative	splash10-0a4i-9400000000-6eece2186d7d8e426696	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 18V, negative	splash10-0a4i-9200000000-4b1d1515941d17b58cd8	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 15V, negative	splash10-0udi-0900000000-4211fc4d53d78720f632	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 15V, negative	splash10-0a4i-0900000000-3b3b751b5b26d5ba4273	2020-07-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4l-0980000000-423d28b762ba4c07586b	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-0910000000-31575764ba8bd8d50279	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-074r-0900000000-9d96bd59f1a4371a8df4	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0059-0790000000-2cc911a67c1aa8e35d99	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06ur-0940000000-2c3da60da6ab9523fbf3	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bt9-4900000000-cf52dffb4284f9eeaa5d	2015-05-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum

Toxicity Profile

Route of Exposure

Not Available

Mechanism of Toxicity

Not Available

Metabolism

Not Available

Toxicity Values

Not Available

Lethal Dose

Not Available

Carcinogenicity (IARC Classification)

No indication of carcinogenicity to humans (not listed by IARC).

Uses/Sources

This is an endogenously produced metabolite found in the human body. It is used in metabolic reactions, catabolic reactions or waste generation.

Minimum Risk Level

Not Available

Health Effects

Chronically high levels of porophyrins are associated with porphyrias such as Porphyria variegate, Acute Intermittent Porphyria and Hereditary Coproporphyria (HCP).

Symptoms

Not Available

Treatment

Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

External Links

DrugBank ID

DB02272

HMDB ID

HMDB00245

PubChem Compound ID

1021

ChEMBL ID

Not Available

ChemSpider ID

995

KEGG ID

C00931

UniProt ID

Not Available

OMIM ID

ChEBI ID

17381

BioCyc ID

PORPHOBILINOGEN

CTD ID

Not Available

Stitch ID

Not Available

PDB ID

PBG

ACToR ID

Not Available

Wikipedia Link

Porphobilinogen

References

Synthesis Reference

Not Available

MSDS

Link

General References

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. [1147435 ]
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. [7124248 ]
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. [16910386 ]
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. [3658064 ]
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. [4073306 ]
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. [3677422 ]
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. [7286590 ]
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. [1165472 ]
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. [7389090 ]
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. [2809566 ]
Mustajoki P: Normal erythrocyte uroporphyrinogen I synthase in a kindred with acute intermittent porphyria. Ann Intern Med. 1981 Aug;95(2):162-6. [7258864 ]

Gene Regulation

Up-Regulated Genes

Not Available

Down-Regulated Genes

Not Available

Targets

Target Details

1. Delta-aminolevulinic acid dehydratase

General Function:: Zinc ion binding
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:: ALAD
Uniprot ID:: P13716
Molecular Weight:: 36294.485 Da

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [17139284 ]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [17016423 ]
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [10592235 ]

Porphobilinogen (T3D4274)

Structure for T3D4274: Porphobilinogen

Targets

References