ECMDB: Protoporphyrinogen IX (ECMDB01097) (M2MDB000254)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)XML

Proteins (985)

Record Information

Version

2.0

Creation Date

2012-05-31 13:45:13 -0600

Update Date

2015-06-03 15:53:44 -0600

Secondary Accession Numbers

ECMDB01097

Identification

Name:

Protoporphyrinogen IX

Description

Protoporphyrinogen IX is an intermediate in heme biosynthesis. It is a porphyrinogen in which 2 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. 15 isomers are possible but only one, type IX, occurs naturally. Protoporphyrinogen is produced by oxidative decarboxylation of coproporphyrinogen.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

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
Protoporphyrinogen-IX

Chemical Formula:

C₃₄H₄₀N₄O₄

Weight:

Average: 568.7058
Monoisotopic: 568.304955788

InChI Key:

UHSGPDMIQQYNAX-UHFFFAOYSA-N

InChI:

InChI=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)

CAS number:

7412-77-3

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(20),3,5,8,10,13,15,18-octaen-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(20),3,5,8,10,13,15,18-octaen-4-yl]propanoic acid

SMILES:

CC1=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

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

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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

porphyrinogens (CHEBI:15435 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	0.0055 g/L	ALOGPS
logP	3.44	ALOGPS
logP	6.2	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	4.07	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	137.76 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	169.42 m³·mol⁻¹	ChemAxon
Polarizability	64.52 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	splash10-0pi3-1000190000-2785151d048ffcfdafc1	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00bc-9000053000-45009d4bbcc7a57d2e8b	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("Protoporphyrinogen IX,1TMS,#1" TMS) - 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_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 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 (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0000190000-7c4ce83e3be73bfccdf6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0pi0-0000490000-affa2d20d85ce7a5a2a1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dj-0020900000-a1714c4d96457c66da57	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0000090000-4148fa37b5b91e3b5a92	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-05tb-1000090000-27a9f5ba745bc29e2b22	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000260000-392765703d0911aa98fc	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0gb9-0000090000-9a1be7ce809937d54938	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ldi-0000190000-1a53eff6b6eaea2bd1a8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-0000790000-030a68500ee48fd68e34	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014j-0000090000-4f79e644c71d1a64565b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014j-0000090000-8599f24133cbc58316eb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-1000950000-a5525829d1d51b8650b0	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:

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. Pubmed: 7252240
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. Pubmed: 7697001
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. Pubmed: 16039338
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. Pubmed: 15660919
Herrick AL, Moore MR, Thompson GG, Ford GP, McColl KE: Cholelithiasis in patients with variegate porphyria. J Hepatol. 1991 Jan;12(1):50-3. Pubmed: 2007776
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
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. Pubmed: 9431441
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
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. Pubmed: 15554680
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:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	15435
HMDB ID	HMDB01097
Pubchem Compound ID	121893
Kegg ID	C01079
ChemSpider ID	108741
Wikipedia	Protoporphyrinogen IX
BioCyc ID	PROTOPORPHYRINOGEN
EcoCyc ID	PROTOPORPHYRINOGEN

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. Oxygen-independent coproporphyrinogen-III oxidase

General function:: Involved in coproporphyrinogen oxidase activity
Specific function:: Anaerobic transformation of coproporphyrinogen-III into protoporphyrinogen-IX
Gene Name:: hemN
Uniprot ID:: P32131
Molecular weight:: 52729

Reactions

Coproporphyrinogen-III + 2 S-adenosyl-L-methionine = protoporphyrinogen-IX + 2 CO(2) + 2 L-methionine + 2 5'-deoxyadenosine.

Protein Details

3. Coproporphyrinogen-III oxidase, aerobic

General function:: Involved in coproporphyrinogen oxidase activity
Specific function:: Key enzyme in heme biosynthesis. Catalyzes the oxidative decarboxylation of propionic acid side chains of rings A and B of coproporphyrinogen III
Gene Name:: hemF
Uniprot ID:: P36553
Molecular weight:: 34322

Reactions

Coproporphyrinogen-III + O(2) + 2 H(+) = protoporphyrinogen-IX + 2 CO(2) + 2 H(2)O.

Protein Details

4. Oxygen-independent coproporphyrinogen-III oxidase-like protein yggW

General function:: Involved in coproporphyrinogen oxidase activity
Specific function:: Not Available
Gene Name:: yggW
Uniprot ID:: P52062
Molecular weight:: 42584

Protoporphyrinogen IX (ECMDB01097) (M2MDB000254)

Structure for #<Compound:0xad2c1980>

Enzymes

Reactions

Reactions

Reactions