Protoporphyrin IX (PAMDB000101)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000101
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
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🔍MOLSDFPDBSMILESInChIView Structure
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
Average Molecular Weight: 562.6582
Monoisotopic Molecular Weight: 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?,??1????.1??,???tetracosa-1(21),2,4,6,8(23),9,11,13,15,17,19-undecaen-4-yl]propanoic acid
Traditional IUPAC Name: protoporphyrin
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
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as porphyrins. These 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 ClassOrganoheterocyclic compounds
Class Tetrapyrroles and derivatives
Sub ClassPorphyrins
Direct Parent Porphyrins
Alternative Parents
Substituents
  • Porphyrin
  • Substituted pyrrole
  • Dicarboxylic acid or derivatives
  • Heteroaromatic compound
  • Pyrrole
  • Azacycle
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: 300 °C
Experimental Properties:
PropertyValueSource
Water Solubility:0.169 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.0217 mg/mLALOGPS
logP4.4ALOGPS
logP6.78ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)3.68ChemAxon
pKa (Strongest Basic)4.96ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area131.96 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity163.81 m3·mol-1ChemAxon
Polarizability65.97 Å3ChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Membrane
Reactions:
Oxygen + Protoporphyrinogen IX >3 Water + Protoporphyrin IX
3 Fumaric acid + Protoporphyrinogen IX > Protoporphyrin IX +3 Succinic acid
Protoporphyrin IX + Fe2+ <> Heme +2 Hydrogen ion + Fe2+
Protoporphyrinogen IX + 3 Menaquinone + 3 Menaquinone <> Protoporphyrin IX +3 Menaquinol 6
Iron + Protoporphyrin IX > Heme + Hydrogen ion
Protoporphyrinogen IX + Oxygen > Protoporphyrin IX + Hydrogen peroxide
Protoporphyrinogen IX + a menaquinone > Protoporphyrin IX + a menaquinol
Protoporphyrinogen IX + 3 Menaquinone > Protoporphyrin IX +3 Menaquinol 6
Protoporphyrinogen IX + menaquinone-8 > Protoporphyrin IX + Menaquinol 6
Protoporphyrin IX + Iron >2 Hydrogen ion + ferroheme b
Pathways:
Spectra
Spectra:
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) Download (PDF)
External Links:
ResourceLink
CHEBI ID15430
HMDB IDHMDB00241
Pubchem Compound ID4971
Kegg IDC02191
ChemSpider ID10469486
WikipediaProtoporphyrin IX
BioCyc IDPROTOPORPHYRIN_IX
EcoCyc IDPROTOPORPHYRIN_IX