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protoporphyrin IX

PubChem CID
4971
Structure
protoporphyrin IX_small.png
protoporphyrin IX_3D_Structure.png
Molecular Formula
Synonyms
  • protoporphyrin IX
  • protoporphyrin
  • 553-12-8
  • Ooporphyrin
  • Protoporpyrin IX
Molecular Weight
562.7 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2004-09-16
  • Modify:
    2025-01-18
Description
Protoporphyrin is a cyclic tetrapyrrole that consists of porphyrin bearing four methyl substituents at positions 3, 8, 13 and 17, two vinyl substituents at positions 7 and 12 and two 2-carboxyethyl substituents at positions 2 and 18. The parent of the class of protoporphyrins. It has a role as a photosensitizing agent, a metabolite, an Escherichia coli metabolite and a mouse metabolite. It is a conjugate acid of a protoporphyrinate and a protoporphyrin(2-).
Protoporphyrin IX is a metabolite found in or produced by Escherichia coli (strain K12, MG1655).
protoporphyrin IX has been reported in Homo sapiens and Turdus merula with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
protoporphyrin IX.png

1.2 3D Conformer

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

3-[18-(2-carboxyethyl)-8,13-bis(ethenyl)-3,7,12,17-tetramethyl-22,23-dihydroporphyrin-2-yl]propanoic acid
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

2.1.2 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/h7-8,13-16,35-36H,1-2,9-12H2,3-6H3,(H,39,40)(H,41,42)
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

ZCFFYALKHPIRKJ-UHFFFAOYSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

CC1=C(C2=CC3=NC(=CC4=NC(=CC5=C(C(=C(N5)C=C1N2)C=C)C)C(=C4CCC(=O)O)C)C(=C3C)CCC(=O)O)C=C
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C34H34N4O4
Computed by PubChem 2.2 (PubChem release 2021.10.14)

2.3 Other Identifiers

2.3.1 CAS

553-12-8

2.3.3 Deprecated CAS

1005309-17-0, 1018811-74-9, 1057726-94-9, 1185235-79-3, 1564276-52-3, 1650010-82-4, 1818-68-4, 2234266-25-0, 227475-00-5, 263148-77-2, 37188-04-8, 392312-74-2, 42183-71-1, 50312-31-7, 562103-89-3, 61320-51-2, 63872-77-5, 673437-82-6, 68034-48-0, 720672-66-2, 75440-82-3, 75460-41-2, 75599-49-4, 75750-98-0, 880014-89-1, 885267-29-8, 942418-20-4
1005309-17-0, 1057726-94-9, 1818-68-4, 227475-00-5, 263148-77-2, 37188-04-8, 392312-74-2, 42183-71-1, 50312-31-7, 562103-89-3, 61320-51-2, 63872-77-5, 673437-82-6, 68034-48-0, 720672-66-2, 75440-82-3, 75460-41-2, 75599-49-4, 75750-98-0, 885267-29-8, 942418-20-4

2.3.4 European Community (EC) Number

2.3.5 UNII

2.3.6 ChEBI ID

2.3.7 ChEMBL ID

2.3.8 DrugBank ID

2.3.9 DSSTox Substance ID

2.3.10 KEGG ID

2.3.11 Metabolomics Workbench ID

2.3.12 NCI Thesaurus Code

2.3.13 Nikkaji Number

2.3.14 NSC Number

2.3.15 Wikidata

2.3.16 Wikipedia

2.4 Synonyms

2.4.1 MeSH Entry Terms

  • PPIX
  • protoporphyrin
  • protoporphyrin IX
  • protoporphyrin IX dihydride
  • protoporphyrin IX, disodium salt

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
562.7 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
4.6
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
4
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
8
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
562.25800558 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
562.25800558 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
132 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
42
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
1010
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Covalently-Bonded Unit Count
Property Value
1
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2021.10.14)

3.2 Experimental Properties

3.2.1 Solubility

169 mg/L (at 25 °C)
YALKOWSKY,SH & DANNENFELSER,RM (1992)

3.2.2 Collision Cross Section

241.4 Ų [M+H]+ [CCS Type: DT; Method: single field calibrated with Agilent tune mix (Agilent)]

245.23 Ų [M-H]- [CCS Type: DT; Method: single field calibrated with Agilent tune mix (Agilent)]

241.3 Ų [M+H]+ [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]
238.8 Ų [M+H]+ [CCS Type: TW; Method: calibrated with polyalanine and drug standards]

4 Spectral Information

4.1 Mass Spectrometry

4.1.1 MS-MS

1 of 2
NIST Number
1052746
Instrument Type
IT/ion trap
Collision Energy
0
Spectrum Type
MS2
Precursor Type
[M+H]+
Precursor m/z
563.2653
Total Peaks
53
m/z Top Peak
504.3
m/z 2nd Highest
545.3
m/z 3rd Highest
505.3
Thumbnail
Thumbnail
2 of 2
NIST Number
1052747
Instrument Type
IT/ion trap
Collision Energy
0
Spectrum Type
MS2
Precursor Type
[M-H]-
Precursor m/z
561.2507
Total Peaks
16
m/z Top Peak
473.3
m/z 2nd Highest
474.3
m/z 3rd Highest
499.3
Thumbnail
Thumbnail

4.1.2 LC-MS

1 of 7
View All
MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
563.27
Instrument
qTof
Ionization Mode
positive
Top 5 Peaks

563.265686 100

431.223053 50.87

445.238464 50.77

504.250671 36.48

564.268311 35.61

Thumbnail
Thumbnail
2 of 7
View All
MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
M-H
Precursor m/z
601.1105753580729
Instrument
Thermo Finnigan LTQ
Instrument Type
Linear Ion Trap
Ionization Mode
positive
Collision Energy
35
Top 5 Peaks

557.19 100

529.15 86.21

539.12 11.16

511.16 7.87

483.19 1.98

Thumbnail
Thumbnail

6 Chemical Vendors

7 Pharmacology and Biochemistry

7.1 MeSH Pharmacological Classification

Photosensitizing Agents
Drugs that are pharmacologically inactive but when exposed to ultraviolet radiation or sunlight are converted to their active metabolite to produce a beneficial reaction affecting the diseased tissue. These compounds can be administered topically or systemically and have been used therapeutically to treat psoriasis and various types of neoplasms. (See all compounds classified as Photosensitizing Agents.)

7.2 Biochemical Reactions

8 Use and Manufacturing

8.1 General Manufacturing Information

EPA TSCA Commercial Activity Status
21H,23H-Porphine-2,18-dipropanoic acid, 7,12-diethenyl-3,8,13,17-tetramethyl-: INACTIVE

9 Safety and Hazards

9.1 Hazards Identification

9.1.1 GHS Classification

Pictogram(s)
Irritant
Signal
Warning
GHS Hazard Statements

H315 (100%): Causes skin irritation [Warning Skin corrosion/irritation]

H319 (100%): Causes serious eye irritation [Warning Serious eye damage/eye irritation]

H335 (100%): May cause respiratory irritation [Warning Specific target organ toxicity, single exposure; Respiratory tract irritation]

Precautionary Statement Codes

P261, P264, P264+P265, P271, P280, P302+P352, P304+P340, P305+P351+P338, P319, P321, P332+P317, P337+P317, P362+P364, P403+P233, P405, and P501

(The corresponding statement to each P-code can be found at the GHS Classification page.)

ECHA C&L Notifications Summary

Aggregated GHS information provided per 66 reports by companies from 2 notifications to the ECHA C&L Inventory. Each notification may be associated with multiple companies.

Information may vary between notifications depending on impurities, additives, and other factors. The percentage value in parenthesis indicates the notified classification ratio from companies that provide hazard codes. Only hazard codes with percentage values above 10% are shown.

9.1.2 Hazard Classes and Categories

Skin Irrit. 2 (100%)

Eye Irrit. 2 (100%)

STOT SE 3 (100%)

10 Associated Disorders and Diseases

11 Literature

11.1 Consolidated References

11.2 NLM Curated PubMed Citations

11.3 Springer Nature References

11.4 Thieme References

11.5 Wiley References

11.6 Chemical Co-Occurrences in Literature

11.7 Chemical-Gene Co-Occurrences in Literature

11.8 Chemical-Disease Co-Occurrences in Literature

12 Patents

12.1 Depositor-Supplied Patent Identifiers

12.2 Chemical Co-Occurrences in Patents

12.3 Chemical-Disease Co-Occurrences in Patents

12.4 Chemical-Gene Co-Occurrences in Patents

13 Interactions and Pathways

13.1 Protein Bound 3D Structures

13.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

13.2 Chemical-Target Interactions

13.3 Drug-Drug Interactions

13.4 Pathways

14 Biological Test Results

14.1 BioAssay Results

15 Taxonomy

The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata) | DOI:10.5281/zenodo.5794106

16 Classification

16.1 MeSH Tree

16.2 NCI Thesaurus Tree

16.3 ChEBI Ontology

16.4 ChemIDplus

16.5 ChEMBL Target Tree

16.6 UN GHS Classification

16.7 NORMAN Suspect List Exchange Classification

16.8 CCSBase Classification

16.9 EPA DSSTox Classification

16.10 EPA TSCA and CDR Classification

16.11 LOTUS Tree

16.12 MolGenie Organic Chemistry Ontology

17 Information Sources

  1. BindingDB
    LICENSE
    All data curated by BindingDB staff are provided under the Creative Commons Attribution 3.0 License (https://creativecommons.org/licenses/by/3.0/us/).
    https://www.bindingdb.org/rwd/bind/info.jsp
    3-[(1Z,4Z,9Z,15Z)-18-(2-Carboxy-ethyl)-3,7,12,17-tetramethyl-8,13-divinyl-porphyrin-2-yl]-propionic acid
    https://www.bindingdb.org/rwd/bind/chemsearch/marvin/MolStructure.jsp?monomerid=51757
  2. Comparative Toxicogenomics Database (CTD)
    LICENSE
    It is to be used only for research and educational purposes. Any reproduction or use for commercial purpose is prohibited without the prior express written permission of NC State University.
    http://ctdbase.org/about/legal.jsp
  3. Drug Gene Interaction database (DGIdb)
    LICENSE
    The data used in DGIdb is all open access and where possible made available as raw data dumps in the downloads section.
    http://www.dgidb.org/downloads
  4. DrugBank
    LICENSE
    Creative Common's Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/legalcode)
    https://www.drugbank.ca/legal/terms_of_use
  5. Therapeutic Target Database (TTD)
  6. CCSbase
    CCSbase Classification
    https://ccsbase.net/
  7. ChEBI
  8. E. coli Metabolome Database (ECMDB)
    LICENSE
    ECMDB is offered to the public as a freely available resource.
    https://ecmdb.ca/citations
  9. LOTUS - the natural products occurrence database
    LICENSE
    The code for LOTUS is released under the GNU General Public License v3.0.
    https://lotus.nprod.net/
  10. NCI Thesaurus (NCIt)
    LICENSE
    Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. Credit the National Cancer Institute as the source.
    https://www.cancer.gov/policies/copyright-reuse
  11. Yeast Metabolome Database (YMDB)
    LICENSE
    YMDB is offered to the public as a freely available resource.
    http://www.ymdb.ca/downloads
  12. ChEMBL
    LICENSE
    Access to the web interface of ChEMBL is made under the EBI's Terms of Use (http://www.ebi.ac.uk/Information/termsofuse.html). The ChEMBL data is made available on a Creative Commons Attribution-Share Alike 3.0 Unported License (http://creativecommons.org/licenses/by-sa/3.0/).
    http://www.ebi.ac.uk/Information/termsofuse.html
  13. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  14. DTP/NCI
    LICENSE
    Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. Credit the National Cancer Institute as the source.
    https://www.cancer.gov/policies/copyright-reuse
  15. EPA Chemicals under the TSCA
    21H,23H-Porphine-2,18-dipropanoic acid, 7,12-diethenyl-3,8,13,17-tetramethyl-
    https://www.epa.gov/chemicals-under-tsca
    EPA TSCA Classification
    https://www.epa.gov/tsca-inventory
  16. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  17. European Chemicals Agency (ECHA)
    LICENSE
    Use of the information, documents and data from the ECHA website is subject to the terms and conditions of this Legal Notice, and subject to other binding limitations provided for under applicable law, the information, documents and data made available on the ECHA website may be reproduced, distributed and/or used, totally or in part, for non-commercial purposes provided that ECHA is acknowledged as the source: "Source: European Chemicals Agency, http://echa.europa.eu/". Such acknowledgement must be included in each copy of the material. ECHA permits and encourages organisations and individuals to create links to the ECHA website under the following cumulative conditions: Links can only be made to webpages that provide a link to the Legal Notice page.
    https://echa.europa.eu/web/guest/legal-notice
    3,3'-(3,7,12,17-tetramethyl-8,13-divinylporphine-2,18-diyl)di(propionic acid)
    https://echa.europa.eu/substance-information/-/substanceinfo/100.008.213
    3,3'-(3,7,12,17-tetramethyl-8,13-divinylporphine-2,18-diyl)di(propionic acid) (EC: 209-033-7)
    https://echa.europa.eu/information-on-chemicals/cl-inventory-database/-/discli/details/24468
  18. FDA Global Substance Registration System (GSRS)
    LICENSE
    Unless otherwise noted, the contents of the FDA website (www.fda.gov), both text and graphics, are not copyrighted. They are in the public domain and may be republished, reprinted and otherwise used freely by anyone without the need to obtain permission from FDA. Credit to the U.S. Food and Drug Administration as the source is appreciated but not required.
    https://www.fda.gov/about-fda/about-website/website-policies#linking
  19. Japan Chemical Substance Dictionary (Nikkaji)
  20. KEGG
    LICENSE
    Academic users may freely use the KEGG website. Non-academic use of KEGG generally requires a commercial license
    https://www.kegg.jp/kegg/legal.html
  21. MassBank of North America (MoNA)
    LICENSE
    The content of the MoNA database is licensed under CC BY 4.0.
    https://mona.fiehnlab.ucdavis.edu/documentation/license
  22. Metabolomics Workbench
  23. NIST Mass Spectrometry Data Center
    LICENSE
    Data covered by the Standard Reference Data Act of 1968 as amended.
    https://www.nist.gov/srd/public-law
  24. Protein Data Bank in Europe (PDBe)
  25. Springer Nature
  26. Thieme Chemistry
    LICENSE
    The Thieme Chemistry contribution within PubChem is provided under a CC-BY-NC-ND 4.0 license, unless otherwise stated.
    https://creativecommons.org/licenses/by-nc-nd/4.0/
  27. Wikidata
  28. Wikipedia
  29. Wiley
  30. PubChem
  31. Medical Subject Headings (MeSH)
    LICENSE
    Works produced by the U.S. government are not subject to copyright protection in the United States. Any such works found on National Library of Medicine (NLM) Web sites may be freely used or reproduced without permission in the U.S.
    https://www.nlm.nih.gov/copyright.html
  32. GHS Classification (UNECE)
  33. NORMAN Suspect List Exchange
    LICENSE
    Data: CC-BY 4.0; Code (hosted by ECI, LCSB): Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  34. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  35. NCBI
CONTENTS