Record Information
Version2.0
Creation Date2012-05-31 14:50:53 -0600
Update Date2015-10-02 02:25:52 -0600
Secondary Accession Numbers
  • ECMDB20564
Identification
Name:Heme D
DescriptionHeme D is a member of the chemical class known as tetrapyrroles and Derivatives. These are polycyclic aromatic compounds containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. (inferred from compound structure). A heme (American English) or haem (British English) is a prosthetic group that consists of an iron atom contained in the center of a large heterocyclic organic ring called a porphyrin. Heme D is a derivative of heme B, but in which the propionic acid side chain at the carbon of position 6, which is also hydroxylated, forms a γ-spirolactone. Ring III is also hydroxylated at position 5, in a conformation trans to the new lactone group. Heme D is the site for oxygen reduction to water of many types of bacteria at low oxygen tension. In E coli, heme D is formed from protoheme in the interior of the catalase hydroperoxidase II (HPII) molecule through a self-catalyzed reaction. [PMID: 8621527]
Structure
Thumb
Synonyms:Not Available
Chemical Formula:C34H34N4O10
Weight:Average: 658.6546
Monoisotopic: 658.227493328
InChI Key:ZAKGXCNMJBQQNZ-CXJCYTKDSA-N
InChI:InChI=1S/C34H34N4O10/c1-15-17(5-7-27(39)40)21-10-22-18(6-8-28(41)42)16(2)20(36-22)11-25-33(3,13-29(43)44)32(48)24(38-25)12-26-34(4,14-30(45)46)31(47)23(37-26)9-19(15)35-21/h9-12,35-36H,5-8,13-14H2,1-4H3,(H,39,40)(H,41,42)(H,43,44)(H,45,46)/b19-9-,20-11-,21-10-,22-10-,23-9-,24-12-,25-11-,26-12-
CAS number:60318-31-2
IUPAC Name:3-[20-(2-carboxyethyl)-10,15-bis(carboxymethyl)-5,10,15,19-tetramethyl-9,14-dioxo-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),2,4,6,8(23),11,13(22),16,18-nonaen-4-yl]propanoic acid
Traditional IUPAC Name:3-[20-(2-carboxyethyl)-10,15-bis(carboxymethyl)-5,10,15,19-tetramethyl-9,14-dioxo-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),2,4,6,8(23),11,13(22),16,18-nonaen-4-yl]propanoic acid
SMILES:CC1=C(CCC(O)=O)/C2=C/C3=C(CCC(O)=O)C(C)=C(N3)\C=C3/N=C(/C=C4\N=C(\C=C\1/N\2)C(=O)C4(C)CC(O)=O)C(=O)C3(C)CC(O)=O
Chemical Taxonomy
ClassificationNot classified
Physical Properties
State:Not Available
Charge:-4
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.011 g/LALOGPS
logP2.25ALOGPS
logP4.44ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)3.25ChemAxon
pKa (Strongest Basic)1.82ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area240.7 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity167.65 m³·mol⁻¹ChemAxon
Polarizability68.88 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
SMPDB Pathways:
Oxidative phosphorylationPW000919 ThumbThumb?image type=greyscaleThumb?image type=simple
Porphyrin metabolismPW000936 ThumbThumb?image type=greyscaleThumb?image type=simple
pyruvate to cytochrome bd terminal oxidase electron transferPW002087 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-006x-0000049000-d8522732d667d82e6c5eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-006t-0000093000-017f14665c351db4de30View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0uxs-0000090000-9929b674dff943dc2a7cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-06rj-0000039000-5ce0f872f6e20759c21cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000b-0000097000-e6291c1bdcc69dc05ca2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-6000093000-70baccb3d19c3204b22eView in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • 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
  • Murshudov, G. N., Grebenko, A. I., Barynin, V., Dauter, Z., Wilson, K. S., Vainshtein, B. K., Melik-Adamyan, W., Bravo, J., Ferran, J. M., Ferrer, J. C., Switala, J., Loewen, P. C., Fita, I. (1996). "Structure of the heme d of Penicillium vitale and Escherichia coli catalases." J Biol Chem 271:8863-8868. Pubmed: 8621527
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID3582
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDHeme
BioCyc IDHEME_D
EcoCyc IDHEME_D

Enzymes

General function:
Involved in catalase activity
Specific function:
Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide
Gene Name:
katE
Uniprot ID:
P21179
Molecular weight:
84162
Reactions
2 H(2)O(2) = O(2) + 2 H(2)O.