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Identification
YMDB IDYMDB00156
NameProtoporphyrinogen IX
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionProtoporphyrinogen IX is an intermediate in the heme biosynthesis from uroporphyrinogen-III pathway. In this pathway, protoporphyrinogen IX is obtained from coproporphyrinogen III and converted to protoporphyrin IX. Protoheme IX is the final product in this pathway but different derivatives of protoheme can actually be formed that differ in modifications to the porphyrin ring, including how it is bound to the protein (e.g. heme o, heme a, heme c, and heme d). [Biocyc HEME-BIOSYNTHESIS-II]
Structure
Thumb
Synonyms
  • 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
  • 5,10,15,20,22,24-Hexahydro protoporphyrin IX deriv.
CAS number7412-77-3
WeightAverage: 568.7058
Monoisotopic: 568.304955788
InChI KeyUHSGPDMIQQYNAX-UHFFFAOYSA-N
InChIInChI=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)
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 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
Chemical FormulaC34H40N4O4
SMILES[H]OC(=O)C([H])([H])C([H])([H])C1=C2N([H])C(=C1C([H])([H])[H])C([H])([H])C1=C(C([H])=C([H])[H])C(=C(N1[H])C([H])([H])C1=C(C([H])=C([H])[H])C(=C(N1[H])C([H])([H])C1=C(C(=C(N1[H])C2([H])[H])C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]
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
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
Biological Properties
Cellular Locations
  • mitochondrion
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Porphyrin MetabolismPW002462 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Porphyrin and chlorophyll metabolismec00860 Map00860
SMPDB Reactions
Coproporphyrinogen III + oxygen + HydrogenProtoporphyrinogen IX + Carbon dioxide + water
Protoporphyrinogen IX + oxygenProtoporphyrin IX + Hydrogen peroxide
KEGG Reactions
Coproporphyrinogen III + oxygen + hydronwater + Carbon dioxide + Protoporphyrinogen IX
oxygen + Protoporphyrinogen IXwater + Protoporphyrin IX
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
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
  • Chelstowska, A., Rytka, J. (1993). "[Biosynthesis of heme in yeast Saccharomyces cerevisiae]." Postepy Biochem 39:173-185.8234090
  • Hoffman, M., Gora, M., Rytka, J. (2003). "Identification of rate-limiting steps in yeast heme biosynthesis." Biochem Biophys Res Commun 310:1247-1253.14559249
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID15435
HMDB IDHMDB01097
Pubchem Compound ID121893
Kegg IDC01079
ChemSpider ID108741
FOODB IDFDB022425
WikipediaProtoporphyrinogen_IX
BioCyc IDPROTOPORPHYRINOGEN

Enzymes

General function:
Involved in oxygen-dependent protoporphyrinogen oxidase activity
Specific function:
Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX
Gene Name:
HEM14
Uniprot ID:
P40012
Molecular weight:
59702.39844
Reactions
Protoporphyrinogen-IX + 3 O(2) → protoporphyrin-IX + 3 H(2)O(2).
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:
HEM13
Uniprot ID:
P11353
Molecular weight:
37711.30078
Reactions
Coproporphyrinogen-III + O(2) + 2 H(+) → protoporphyrinogen-IX + 2 CO(2) + 2 H(2)O.