NP-MRD: Showing NP-Card for Protoporphyrinogen IX (NP0054936)

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Record Information

Version

2.0

Created at

2022-04-28 01:08:11 UTC

Updated at

2022-04-28 01:08:11 UTC

NP-MRD ID

NP0054936

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Protoporphyrinogen IX

Description

Protoporphyrinogen IX 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. By the action of protoporphyrinogen oxidase, protoporphyrinogen IX is later converted into protoporphyrin IX, the first colored tetrapyrrole in the biosynthesis of hemes. Protoporphyrinogen IX is a weakly acidic compound (based on its pKa). In coproporphyrinogen III, the substituents on the pyrrole rings have the arrangement MP-MP-MP-PM, where M and P are methyl and propionic acid, respectively. Protoporphyrinogen IX exists in all living species, ranging from bacteria to humans. The compound is synthesized in most organisms from coproporphyrinogen III by the enzyme coproporphyrinogen oxidase:The process entails conversion of two of four propionic acid groups to vinyl groups. Like most porphyrinogens, it is colorless. In humans, protoporphyrinogen IX is involved in the metabolic disorder called the acute intermittent porphyria pathway. Outside of the human body, Protoporphyrinogen IX has been detected, but not quantified in, several different foods, such as okra, canada blueberries, sourdocks, spearmints, and grapefruits. This could make protoporphyrinogen IX a potential biomarker for the consumption of these foods. Protoporphyrinogen IX is a potentially toxic compound. It is a direct precursor of protoporphyrin IX.The compound is a porphyrinogen, meaning that it has a non-aromatic hexahydroporphine core, which will be oxidized to a porphine core in later stages of the heme synthesis. Protoporphyrinogen IX is an organic chemical compound which is produced along the synthesis of porphyrins, a class of critical biochemicals that include hemoglobin and chlorophyll. Protoporphyrinogen IX is found in Arabidopsis thaliana. Protoporphyrinogen IX was first documented in 1981 (PMID: 7252240). In protoporphyrinogen IX, the sequence becomes MV-MV-MP-PM, where V is vinyl (PMID: 15554680) (PMID: 2007776) (PMID: 9431441) (PMID: 15660919).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652303021823532D          

 42 46  0  0  0  0            999 V2000
   -1.6485    0.7079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0870   -0.0015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7305   -1.6712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0660   -0.0015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8556   -0.8572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0243    1.4592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1 42  1  0  0  0  0
 16  1  2  0  0  0  0
 12  1  1  0  0  0  0
  2  3  1  0  0  0  0
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  3  4  1  0  0  0  0
  4 13  1  0  0  0  0
 18  4  2  0  0  0  0
  5  6  1  0  0  0  0
 13  5  1  0  0  0  0
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  6  7  1  0  0  0  0
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 37 36  1  0  0  0  0
 37 38  2  0  0  0  0
 40 39  1  0  0  0  0
 40 41  2  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652303021823532D          

 42 46  0  0  0  0            999 V2000
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   -0.8347   -0.8572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0243    1.4592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8211    1.6727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4609    2.0435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6744    2.8404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0661   -1.4624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8629   -1.6759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0243   -1.4624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8211   -1.6759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4399    2.0435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6533    2.8404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4502    3.0539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0661    1.4592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8629    1.6727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0764    2.4696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4399   -2.0467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6533   -2.8436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4502   -3.0571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4609   -2.0467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6744   -2.8436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4713   -3.0571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4605   -4.0675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6637   -3.8539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0804   -4.4373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1014   -4.4373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6847   -3.8539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4815   -4.0675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8347    0.8540    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1 42  1  0  0  0  0
 16  1  2  0  0  0  0
 12  1  1  0  0  0  0
  2  3  1  0  0  0  0
 42  2  1  0  0  0  0
 24  2  2  0  0  0  0
  3  4  1  0  0  0  0
  4 13  1  0  0  0  0
 18  4  2  0  0  0  0
  5  6  1  0  0  0  0
 13  5  1  0  0  0  0
 27  5  2  0  0  0  0
  6  7  1  0  0  0  0
  7 14  1  0  0  0  0
  7 20  2  0  0  0  0
  8  9  1  0  0  0  0
 33  8  2  0  0  0  0
 14  8  1  0  0  0  0
 10  9  1  0  0  0  0
 15 10  1  0  0  0  0
 30 10  2  0  0  0  0
 11 12  1  0  0  0  0
 15 11  1  0  0  0  0
 22 11  2  0  0  0  0
 24 16  1  0  0  0  0
 16 17  1  0  0  0  0
 18 27  1  0  0  0  0
 18 19  1  0  0  0  0
 20 33  1  0  0  0  0
 20 21  1  0  0  0  0
 22 30  1  0  0  0  0
 22 23  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 37  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 40  1  0  0  0  0
 37 36  1  0  0  0  0
 37 38  2  0  0  0  0
 40 39  1  0  0  0  0
 40 41  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0054936

> <DATABASE_NAME>
NP-MRD

> <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

> <INCHI_IDENTIFIER>
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)

> <INCHI_KEY>
UHSGPDMIQQYNAX-UHFFFAOYSA-N

> <FORMULA>
C34H40N4O4

> <MOLECULAR_WEIGHT>
568.7058

> <EXACT_MASS>
568.304955788

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
82

> <JCHEM_AVERAGE_POLARIZABILITY>
64.5199264797442

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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

> <ALOGPS_LOGP>
3.44

> <JCHEM_LOGP>
6.200009445999999

> <ALOGPS_LOGS>
-5.01

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.67011788729448

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.0668900795671075

> <JCHEM_POLAR_SURFACE_AREA>
137.76

> <JCHEM_REFRACTIVITY>
169.41620000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.51e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-MAR-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-MAR-18         0                                  
HETATM    1  C   UNK     0      -3.077   1.321   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.324   3.113   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   3.892   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.364   3.113   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.116   1.321   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.896  -0.003   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.116  -1.327   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.364  -3.120   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000  -3.899   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.324  -3.120   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.077  -1.327   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.856  -0.003   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       1.597   1.594   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       1.597  -1.600   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0      -1.558  -1.600   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      -3.779   2.724   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -5.266   3.122   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.727   3.815   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.126   5.302   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.857  -2.730   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.344  -3.128   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.779  -2.730   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.266  -3.128   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.688   3.815   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.086   5.302   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.574   5.701   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.857   2.724   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.344   3.122   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.743   4.610   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.688  -3.821   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.086  -5.308   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -4.574  -5.707   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.727  -3.821   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       3.126  -5.308   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.613  -5.707   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -6.460  -7.593   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -4.972  -7.194   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -3.883  -8.283   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       3.923  -8.283   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       5.011  -7.194   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       6.499  -7.593   0.000  0.00  0.00           O+0
HETATM   42  N   UNK     0      -1.558   1.594   0.000  0.00  0.00           N+0
CONECT    1   42   16   12                                                  
CONECT    2    3   42   24                                                  
CONECT    3    2    4                                                       
CONECT    4    3   13   18                                                  
CONECT    5    6   13   27                                                  
CONECT    6    5    7                                                       
CONECT    7    6   14   20                                                  
CONECT    8    9   33   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   15   30                                                  
CONECT   11   12   15   22                                                  
CONECT   12    1   11                                                       
CONECT   13    4    5                                                       
CONECT   14    7    8                                                       
CONECT   15   10   11                                                       
CONECT   16    1   24   17                                                  
CONECT   17   16                                                            
CONECT   18    4   27   19                                                  
CONECT   19   18                                                            
CONECT   20    7   33   21                                                  
CONECT   21   20                                                            
CONECT   22   11   30   23                                                  
CONECT   23   22                                                            
CONECT   24    2   16   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27    5   18   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   10   22   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31   37                                                       
CONECT   33    8   20   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   40                                                       
CONECT   36   37                                                            
CONECT   37   32   36   38                                                  
CONECT   38   37                                                            
CONECT   39   40                                                            
CONECT   40   35   39   41                                                  
CONECT   41   40                                                            
CONECT   42    1    2                                                       
MASTER        0    0    0    0    0    0    0    0   42    0   92    0
END

View in JSmol

Synonyms

Value	Source
7,12-Diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoic acid	ChEBI
7,12-Diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoate	Generator
5,10,15,20,22,24-Hexahydro protoporphyrin IX deriv.	HMDB
7,12-Diethenyl-5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-dipropanoate	HMDB
7,12-Diethenyl-5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-dipropanoic acid	HMDB
Protoporphyrinogen	HMDB
Protoporphyrinogen-IX	HMDB

Chemical Formula

C₃₄H₄₀N₄O₄

Average Mass

568.7058 Da

Monoisotopic Mass

568.30496 Da

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 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

CAS Registry Number

Not Available

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

InChI Identifier

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)

InChI Key

UHSGPDMIQQYNAX-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Arabidopsis thaliana	Plant	KNApSAcK
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0001097

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Protoporphyrinogen IX

METLIN ID

6003

PubChem Compound

121893

PDB ID

Not Available

ChEBI ID

15435

Good Scents ID

Not Available

References

General References

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. doi: 10.1021/ci049793p. [PubMed:15554680 ]
Herrick AL, Moore MR, Thompson GG, Ford GP, McColl KE: Cholelithiasis in patients with variegate porphyria. J Hepatol. 1991 Jan;12(1):50-3. doi: 10.1016/0168-8278(91)90908-t. [PubMed:2007776 ]
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 ]
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. doi: 10.1111/1523-1747.ep12479280. [PubMed:7252240 ]
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. doi: 10.1111/j.0906-6705.2005.00228.x. [PubMed:15660919 ]

Showing NP-Card for Protoporphyrinogen IX (NP0054936)

MOL for NP0054936 (Protoporphyrinogen IX)

3D MOL for NP0054936 (Protoporphyrinogen IX)

3D SDF for NP0054936 (Protoporphyrinogen IX)

3D-SDF for NP0054936 (Protoporphyrinogen IX)

PDB for NP0054936 (Protoporphyrinogen IX)

3D PDB for NP0054936 (Protoporphyrinogen IX)

SMILES for NP0054936 (Protoporphyrinogen IX)

INCHI for NP0054936 (Protoporphyrinogen IX)

Structure for NP0054936 (Protoporphyrinogen IX)

3D Structure for NP0054936 (Protoporphyrinogen IX)