ECMDB: Protoporphyrin IX (ECMDB00241) (M2MDB000101)

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

Proteins (731)

Record Information

Version

2.0

Creation Date

2012-05-31 10:24:38 -0600

Update Date

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

Secondary Accession Numbers

ECMDB00241

Identification

Name:

Protoporphyrin IX

Description

Protoporphyrins are tetrapyrroles containing 4 methyl, 2 propionic and 2 vinyl side chains. Protopophyrin is produced by oxidation of the methylene bridge of protoporphyrinogen. Protoporphyrin IX is the only naturally occurring isomer; it is an intermediate in heme biosynthesis, combining with ferrous iron to form protoheme IX, the heme prosthetic group of hemoglobin. Protoporphyrin IX is created by the enzyme protoporphyrinogen oxidase. The enzyme ferrochelatase converts it into heme. Protoporphyrin IX naturally occurs in small amounts in feces. It is accumulated and excreted excessively in the feces in protoporphyria and variegate porphyria. Protoporphyrin IX is also responsible for the brown pigment (Ooporphyrin) of birds' eggs Protoporphyrin IX is used as a branch point in the biosynthetic pathway leading to Heme (by insertion of iron) and chlorophylls (by insertion of Mg and further side-chain transformation).

Structure

MOL SDF PDB SMILES InChI

Synonyms:

3,3'-(3,7,12,17-Tetramethyl-8,13-divinyl-21H,23H-porphine-2,18-diyl)-bis-propionate
3,3'-(3,7,12,17-Tetramethyl-8,13-divinyl-21H,23H-porphine-2,18-diyl)-bis-propionic acid
3,3'-(3,7,12,17-Tetramethyl-8,13-divinylporphine-2,18-diyl)di
Kammerer'S prophyrin
Ooporphyrin
Por IX
Porphyrinogen IX
PpIX
Protoporphyrin
Protoporphyrin IX
Protoporphyrin-"IX"
Protoporphyrin-IX

Chemical Formula:

C₃₄H₃₄N₄O₄

Weight:

Average: 562.6582
Monoisotopic: 562.258005596

InChI Key:

KSFOVUSSGSKXFI-UJJXFSCMSA-N

InChI:

InChI=1S/C34H34N4O4/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25/h7-8,13-16,35,38H,1-2,9-12H2,3-6H3,(H,39,40)(H,41,42)/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-

CAS number:

553-12-8

IUPAC Name:

3-[20-(2-carboxyethyl)-9,14-diethenyl-5,10,15,19-tetramethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(21),2,4,6,8(23),9,11,13,15,17,19-undecaen-4-yl]propanoic acid

Traditional IUPAC Name:

3-[20-(2-carboxyethyl)-9,14-diethenyl-5,10,15,19-tetramethyl-21,22,23,24-tetraazapentacyclo[16.2.1.1^{3,6}.1^{8,11}.1^{13,16}]tetracosa-1(21),2,4,6,8(23),9,11,13,15,17,19-undecaen-4-yl]propanoic acid

SMILES:

CC1=C(CCC(O)=O)/C2=C/C3=N/C(=C\C4=C(C)C(C=C)=C(N4)/C=C4\N=C(\C=C\1/N\2)C(C=C)=C4C)/C(C)=C3CCC(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as porphyrins. Porphyrins are compounds containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Porphyrins

Direct Parent

Porphyrins

Alternative Parents

Not Available

Substituents

Not Available

Molecular Framework

Not Available

External Descriptors

Not Available

Physical Properties

State:

Solid

Charge:

-2

Melting point:

300 °C

Experimental Properties:

Property	Value	Source
Water Solubility:	0.169 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	0.022 g/L	ALOGPS
logP	4.4	ALOGPS
logP	6.78	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	3.68	ChemAxon
pKa (Strongest Basic)	4.96	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	131.96 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	163.81 m³·mol⁻¹	ChemAxon
Polarizability	66.03 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Membrane

Reactions:

SMPDB Pathways:

Porphyrin metabolism

PW000936

KEGG Pathways:

Metabolic pathways eco01100
Porphyrin and chlorophyll metabolism ec00860

EcoCyc Pathways:

heme biosynthesis from uroporphyrinogen-III I HEME-BIOSYNTHESIS-II
heme biosynthesis from uroporphyrinogen-III II HEMESYN2-PWY
superpathway of heme biosynthesis from uroporphyrinogen-III PWY0-1415

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0uxu-1000290000-e22236fe3cca8eed1ecf	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00di-6000094000-b9c12952e100c5144cab	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("Protoporphyrin IX,1TMS,#1" TMS) - 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_1) - 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 (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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0000090000-5d5be53410134c5719ab	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00kb-1000590000-2d4157b9f73534d95a9c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-1000910000-07524a9291a1921dfafc	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0000090000-5df26c1cfb9a0b16a91a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0296-1000190000-2d4bcb49201fc10adc09	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000230000-064fb944a966d08c06bf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0000090000-87c1740ecd1a28f4a2d9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03xu-0000590000-99160b987bb7e62ab362	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-0000900000-f2d9118441a9c8c47d79	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03dj-0000090000-d428ac6dc2fc4794cc41	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0j4j-0000090000-2b065966ec57bb97d511	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0uk9-1000970000-b435817e4dc349e65ab3	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:

Bailey GG, Needham LL: Simultaneous quantification of erythrocyte zinc protoporphyrin and protoporphyrin IX by liquid chromatography. Clin Chem. 1986 Dec;32(12):2137-42. Pubmed: 3779978
Bartosova J, Hrkal Z: Accumulation of protoporphyrin-IX (PpIX) in leukemic cell lines following induction by 5-aminolevulinic acid (ALA). Comp Biochem Physiol C Toxicol Pharmacol. 2000 Jul;126(3):245-52. Pubmed: 11048674
Bissonnette R, Zeng H, McLean DI, Korbelik M, Lui H: Oral aminolevulinic acid induces protoporphyrin IX fluorescence in psoriatic plaques and peripheral blood cells. Photochem Photobiol. 2001 Aug;74(2):339-45. Pubmed: 11547574
Casas A, Batlle AM, Butler AR, Robertson D, Brown EH, MacRobert A, Riley PA: Comparative effect of ALA derivatives on protoporphyrin IX production in human and rat skin organ cultures. Br J Cancer. 1999 Jul;80(10):1525-32. Pubmed: 10408393
Chisolm J Jr, Brown DH: Micro-scale photofluorometric determination of "free erythrocyte pophyrin" (protoporphyrin IX). Clin Chem. 1975 Oct;21(11):1669-82. Pubmed: 1164799
De Rosa FS, Marchetti JM, Thomazini JA, Tedesco AC, Bentley MV: A vehicle for photodynamic therapy of skin cancer: influence of dimethylsulphoxide on 5-aminolevulinic acid in vitro cutaneous permeation and in vivo protoporphyrin IX accumulation determined by confocal microscopy. J Control Release. 2000 Apr 3;65(3):359-66. Pubmed: 10699294
Gottsch JD, Graham CR Jr, Hairston RJ, Chen CH, Green WR, Stark WJ: Protoporphyrin IX photosensitization of corneal endothelium. Arch Ophthalmol. 1989 Oct;107(10):1497-500. Pubmed: 2803100
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
Krieg RC, Fickweiler S, Wolfbeis OS, Knuechel R: Cell-type specific protoporphyrin IX metabolism in human bladder cancer in vitro. Photochem Photobiol. 2000 Aug;72(2):226-33. Pubmed: 10946577
Kufner G, Schlegel H, Jager R: A spectrophotometric micromethod for determining erythrocyte protoporphyrin-IX in whole blood or erythrocytes. Clin Chem Lab Med. 2005;43(2):183-91. Pubmed: 15843214
Messmann H, Knuchel R, Baumler W, Holstege A, Scholmerich J: Endoscopic fluorescence detection of dysplasia in patients with Barrett's esophagus, ulcerative colitis, or adenomatous polyps after 5-aminolevulinic acid-induced protoporphyrin IX sensitization. Gastrointest Endosc. 1999 Jan;49(1):97-101. Pubmed: 9869731
Rick K, Sroka R, Stepp H, Kriegmair M, Huber RM, Jacob K, Baumgartner R: Pharmacokinetics of 5-aminolevulinic acid-induced protoporphyrin IX in skin and blood. J Photochem Photobiol B. 1997 Oct;40(3):313-9. Pubmed: 9372622
Sakai T, Takeuchi Y, Ikeya Y, Araki T, Ushio K: [Automated HPLC method for determining zinc protoporphyrin IX and protoporphyrin IX in erythrocytes of workers exposed to lead] Sangyo Igaku. 1988 Nov;30(6):467-74. Pubmed: 3221502
Smits T, Robles CA, van Erp PE, van de Kerkhof PC, Gerritsen MJ: Correlation between macroscopic fluorescence and protoporphyrin IX content in psoriasis and actinic keratosis following application of aminolevulinic acid. J Invest Dermatol. 2005 Oct;125(4):833-9. Pubmed: 16185285
Stankiewicz A, Lutz W, Krajewska B, Szulc B: [Plasma indicators of iron metabolism in persons occupationally exposed to organic solvents with normal and increased levels of protoporphyrin IX in erythrocytes] Pol Tyg Lek. 1986 Jul 7;41(27):851-4. Pubmed: 3763462
Stankiewicz A, Lutz W, Szeszko A: [Protoporphyrin IX level in erythrocytes of persons with alcoholic liver cirrhosis] Pol Tyg Lek. 1985 Jul 15;40(28):787-9. Pubmed: 4059100
Stankiewicz A: The concentration of protoporphyrin IX in workers occupationally exposed to lead. Mater Med Pol. 1989 Apr-Jun;21(2):100-2. Pubmed: 2488459
Stankiewicz A: [Erythrocyte protoporphyrin IX in occupational exposure to asbestos] Med Pr. 1984;35(5):351-4. Pubmed: 6530952
Star WM, Aalders MC, Sac A, Sterenborg HJ: Quantitative model calculation of the time-dependent protoporphyrin IX concentration in normal human epidermis after delivery of ALA by passive topical application or lontophoresis. Photochem Photobiol. 2002 Apr;75(4):424-32. Pubmed: 12003134
Sudworth CD, Stringer MR, Cruse-Sawyer JE, Brown SB: Fluorescence microspectroscopy technique for the study of intracellular protoporphyrin IX dynamics. Appl Spectrosc. 2003 Jun;57(6):682-8. Pubmed: 14658702
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
von Beckerath M, Juzenas P, Ma LW, Iani V, Lofgren L, Moan J: The influence of UV exposure on 5-aminolevulinic acid-induced protoporphyrin IX production in skin. Photochem Photobiol. 2001 Dec;74(6):825-8. Pubmed: 11783939
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:

Games, David E.; Jackson, Anthony H.; Jackson, J. Richard; Belcher, Roderick V.; Smith, Sydney G. Biosynthesis of protoporphyrin-IX from coproporphyrinogen-III. Journal of the Chemical Society, Chemical Communications (1976), (6), 187-8.

Material Safety Data Sheet (MSDS)

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Links

External Links:

Resource	Link
CHEBI ID	15430
HMDB ID	HMDB00241
Pubchem Compound ID	4971
Kegg ID	C02191
ChemSpider ID	10469486
Wikipedia	Protoporphyrin IX
BioCyc ID	PROTOPORPHYRIN_IX
EcoCyc ID	PROTOPORPHYRIN_IX

Enzymes

Protein Details

1. Protoporphyrinogen oxidase

General function:: Involved in FMN binding
Specific function:: Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX. Does not use oxygen directly. Is coupled to the respiratory chain
Gene Name:: hemG
Uniprot ID:: P0ACB4
Molecular weight:: 21226

Reactions

Protoporphyrinogen IX + 3 menaquinone = protoporphyrin IX + 3 menaquinol.

Protein Details

2. Ferrochelatase

General function:: Involved in ferrochelatase activity
Specific function:: Catalyzes the ferrous insertion into protoporphyrin IX
Gene Name:: hemH
Uniprot ID:: P23871
Molecular weight:: 35884

Reactions

Protoheme + 2 H(+) = protoporphyrin + Fe(2+).

Protoporphyrin IX (ECMDB00241) (M2MDB000101)

Structure for #<Compound:0xa6394f1c>

Enzymes

Reactions

Reactions