Protoporphyrinogen IX (T3D4439)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationXML
Record Information
Version2.0
Creation Date2014-08-29 06:51:17 UTC
Update Date2018-03-21 17:46:22 UTC
Accession NumberT3D4439
Identification
Common NameProtoporphyrinogen IX
ClassSmall Molecule
DescriptionProtoporphyrinogen IX is an intermediate in heme biosynthesis. It is a porphyrinogen in which two pyrrole rings each have one methyl and one propionate side chain, and the other two pyrrole rings each have one methyl and one vinyl side chain. Fifteen isomers are possible but only one, type IX, occurs naturally. Protoporphyrinogen is produced by oxidative decarboxylation of coproporphyrinogen. Under certain conditions, protoporphyrinogen IX 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). In particular, protoporphyrinogen IX is accumulated and excreted excessively in the feces in acute intermittent porphyria, protoporphyria, and variegate porphyria. 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
  • Animal Toxin
  • Food Toxin
  • Metabolite
  • Natural Compound
  • Organic Compound
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Synonym
5,10,15,20,22,24-Hexahydro protoporphyrin IX deriv.
7,12-Diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoate
7,12-Diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoic acid
7,12-Diethenyl-5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21h,23h-porphine-2,18-dipropanoate
7,12-Diethenyl-5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21h,23h-porphine-2,18-dipropanoic acid
Protoporphyrinogen
Protoporphyrinogen-IX
Chemical FormulaC34H40N4O4
Average Molecular Mass568.706 g/mol
Monoisotopic Mass568.305 g/mol
CAS Registry Number7412-77-3
IUPAC Name3-[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(20),3,5,8,10,13,15,18-octaen-4-yl]propanoic acid
Traditional Name3-[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(20),3,5,8,10,13,15,18-octaen-4-yl]propanoic acid
SMILESCC1=C2CC3=C(C)C(C=C)=C(CC4=C(C)C(C=C)=C(CC5=C(C)C(CCC(O)=O)=C(CC(N2)=C1CCC(O)=O)N5)N4)N3
InChI IdentifierInChI=1S/C34H40N4O4/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/h7-8,35-38H,1-2,9-16H2,3-6H3,(H,39,40)(H,41,42)
InChI KeyInChIKey=UHSGPDMIQQYNAX-UHFFFAOYSA-N
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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassPorphyrins
Direct ParentPorphyrins
Alternative Parents
Substituents
  • Porphyrin
  • Dicarboxylic acid or derivatives
  • Substituted pyrrole
  • Pyrrole
  • Heteroaromatic compound
  • Azacycle
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carbonyl group
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginEndogenous
Cellular Locations
  • Cytoplasm
  • Membrane
  • Mitochondria
Biofluid LocationsNot Available
Tissue Locations
  • Liver
  • Placenta
Pathways
NameSMPDB LinkKEGG Link
Porphyrin MetabolismSMP00024 map00860
Porphyria Variegata (PV)SMP00346 Not Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
LogPNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.0055 g/LALOGPS
logP3.44ALOGPS
logP6.2ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)4.07ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area137.76 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity169.42 m³·mol⁻¹ChemAxon
Polarizability64.52 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0pi3-1000190000-2785151d048ffcfdafc12017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00bc-9000053000-45009d4bbcc7a57d2e8b2017-10-06View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ("Protoporphyrinogen IX,1TMS,#1" TMS) - 70eV, PositiveNot Available2021-10-14View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0000190000-7c4ce83e3be73bfccdf62015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0pi0-0000490000-affa2d20d85ce7a5a2a12015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dj-0020900000-a1714c4d96457c66da572015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0000090000-4148fa37b5b91e3b5a922015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-05tb-1000090000-27a9f5ba745bc29e2b222015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9000260000-392765703d0911aa98fc2015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0gb9-0000090000-9a1be7ce809937d549382021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ldi-0000190000-1a53eff6b6eaea2bd1a82021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-0000790000-030a68500ee48fd68e342021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014j-0000090000-4f79e644c71d1a64565b2021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014j-0000090000-8599f24133cbc58316eb2021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-1000950000-a5525829d1d51b8650b02021-09-22View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Not Available2022-08-20View Spectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityNot Available
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesThis is an endogenously produced metabolite found in the human body. It is used in metabolic reactions, catabolic reactions or waste generation.
Minimum Risk LevelNot Available
Health EffectsChronically high levels of porophyrins are associated with porphyrias such as Porphyria variegate, Acute Intermittent Porphyria and Hereditary Coproporphyria (HCP).
SymptomsNot Available
TreatmentNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDNot Available
HMDB IDHMDB01097
PubChem Compound ID121893
ChEMBL IDNot Available
ChemSpider ID108741
KEGG IDC01079
UniProt IDNot Available
OMIM ID
ChEBI ID15435
BioCyc IDPROTOPORPHYRINOGEN
CTD IDNot Available
Stitch IDNot Available
PDB IDNot Available
ACToR IDNot Available
Wikipedia LinkProtoporphyrinogen IX
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
  1. Wan J, Zhang L, Yang G, Zhan CG: Quantitative structure-activity relationship for cyclic imide derivatives of protoporphyrinogen oxidase inhibitors: a study of quantum chemical descriptors from density functional theory. J Chem Inf Comput Sci. 2004 Nov-Dec;44(6):2099-105. [15554680 ]
  2. Herrick AL, Moore MR, Thompson GG, Ford GP, McColl KE: Cholelithiasis in patients with variegate porphyria. J Hepatol. 1991 Jan;12(1):50-3. [2007776 ]
  3. Krijt J, Stranska P, Maruna P, Vokurka M, Sanitrak J: Herbicide-induced experimental variegate porphyria in mice: tissue porphyrinogen accumulation and response to porphyrogenic drugs. Can J Physiol Pharmacol. 1997 Oct-Nov;75(10-11):1181-7. [9431441 ]
  4. Bloomer JR: Enzyme defects in the porphyrias and their relevance to the biochemical abnormalities in these disorders. J Invest Dermatol. 1981 Jul;77(1):102-6. [7252240 ]
  5. de Villiers JN, Kotze MJ, van Heerden CJ, Sadie A, Gardner HF, Liebenberg J, van Zyl R, du Plessis L, Kimberg M, Frank J, Warnich L: Overrepresentation of the founder PPOX gene mutation R59W in a South African patient with severe clinical manifestation of porphyria. Exp Dermatol. 2005 Jan;14(1):50-5. [15660919 ]
  6. Corrigall AV, Hift RJ, Adams PA, Kirsch RE: Inhibition of mammalian protoporphyrinogen oxidase by acifluorfen. Biochem Mol Biol Int. 1994 Dec;34(6):1283-9. [7697001 ]
  7. Cox TM, Jack N, Lofthouse S, Watling J, Haines J, Warren MJ: King George III and porphyria: an elemental hypothesis and investigation. Lancet. 2005 Jul 23-29;366(9482):332-5. [16039338 ]
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available