Porphobilinogen (YMDB00401)

Identification

YMDB ID

YMDB00401

Name

Porphobilinogen

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Porphobilinogen is an intermediate in tetrapyrrole biosynthesis pathway. Uroporphyrinogen-III, the final product in this pathway, is a major branch point that leads to biosynthesis of different tetrapyrrole compounds (e.g. porphyrins). Tetrapyrroles usually function as a metal-binding cofactor in many important enzymes, proteins and pigments, such as heme, chlorophyll, cobalamine, siroheme, and cofator F430. [Biocyc PWY-5189]

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

CAS number

487-90-1

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)

IUPAC Name

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

Traditional IUPAC Name

porphobilinogen

Chemical Formula

C₁₀H₁₄N₂O₄

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.

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

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

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

Organoleptic Properties

Not Available

SMPDB Pathways

Porphyrin Metabolism

PW002462

KEGG Pathways

Porphyrin and chlorophyll metabolism

ec00860

SMPDB Reactions

5-Aminolevulinic acid → Porphobilinogen + water

Porphobilinogen + water → Hydroxymethylbilane + Ammonia

KEGG Reactions

Porphobilinogen + water → Ammonium + Hydroxymethylbilane

5-Aminolevulinic acid → water + Porphobilinogen + hydron

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

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

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:

Resource	Link
CHEBI ID	17381
HMDB ID	HMDB00245
Pubchem Compound ID	1021
Kegg ID	C00931
ChemSpider ID	995
FOODB ID	FDB021916
Wikipedia	Porphobilinogen
BioCyc ID	PORPHOBILINOGEN

Enzymes

Protein Details

1. Delta-aminolevulinic acid dehydratase

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.

Protein Details

2. 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:: HEM3
Uniprot ID:: P28789
Molecular weight:: 36674.19922

Reactions

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

Structure for #<Compound:0xa8fba114>

Enzymes

Reactions

Reactions