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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 17:15:44 UTC

Update Date

2021-09-26 23:12:35 UTC

HMDB ID

HMDB0256709

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Porphyrinogen

Description

porphyrinogen, also known as calix[4]pyrrole, 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. Based on a literature review a significant number of articles have been published on porphyrinogen. This compound has been identified in human blood as reported by (PMID: 31557052 ). Porphyrinogen is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Porphyrinogen is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0256709
     RDKit          3D
Porphyrinogen
 44 48  0  0  0  0  0  0  0  0999 V2000
   -2.9756    2.4517   -1.1577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9286    3.3310   -1.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0123    2.9246   -0.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4924    1.8505    0.4076 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6752    1.5359   -0.1406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5764    0.3552    0.0960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8788   -0.9820    0.2328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1080   -1.8442    1.3186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2576   -2.8997    1.1740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5255   -2.6643    0.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9203   -1.5063   -0.5483 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3935   -3.5730   -0.4702 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9633   -2.9000   -0.2480 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8793   -3.3348    0.7079 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9381   -2.4557    0.6615 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5121   -0.3194 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4361   -1.8064   -0.8582 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5261   -0.3194   -0.6438 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8904    0.9945   -0.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3409    1.7360    0.9012 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4917    2.7869    1.0550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5200    2.6628    0.0348 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7925    1.5797   -0.6956 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3334    3.6098   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8781    2.4852   -1.8049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8336    4.1910   -1.9041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0154    1.3239    1.2825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4172    0.2800   -0.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1294    0.5822    1.0186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8371   -1.7092    2.1410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1855   -3.7578    1.8640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5375   -1.0767   -1.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4148   -4.5075    0.2035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5410   -4.0478   -1.4378 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8060   -4.2082    1.3882 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8434   -2.5207    1.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9352   -1.2396   -1.6906 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4412   -0.4629    0.0065 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9574   -0.3032   -1.6528 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2265    1.5311    1.5439 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5466    3.5822    1.8201 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2274    1.2254   -1.6043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5260    4.3503   -0.9147 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2744    4.2615    0.7971 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 24  1  0
  5  1  2  0
 11  7  1  0
 17 13  1  0
 23 19  1  0
 24  3  1  0
  1 25  1  0
  2 26  1  0
  4 27  1  0
  6 28  1  0
  6 29  1  0
  8 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 14 35  1  0
 15 36  1  0
 17 37  1  0
 18 38  1  0
 18 39  1  0
 20 40  1  0
 21 41  1  0
 23 42  1  0
 24 43  1  0
 24 44  1  0
M  END


  Mrv1652309112119162D          

 24 28  0  0  0  0            999 V2000
    0.0112   -2.0494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7243   -1.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4819   -2.0624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0430   -1.5110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6690   -0.7465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8480   -0.8857    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0558   -0.0472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6818    0.7174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0393    1.4169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4588    2.0076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7239    1.6627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8926    0.8706    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0047    2.0496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7107    1.6752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4686    2.0624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0297    1.5110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6265    0.7462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8643    0.8567    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0427    0.0179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6683   -0.6881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0558   -1.4752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5044   -2.0364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7106   -1.6627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8501   -0.8709    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
  8 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 14 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
  1 23  1  0  0  0  0
 23 24  1  0  0  0  0
 20 24  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256709

> <DATABASE_NAME>
hmdb

> <SMILES>
C1C2=CC=C(CC3=CC=C(CC4=CC=C(CC5=CC=C1N5)N4)N3)N2

> <INCHI_IDENTIFIER>
InChI=1S/C20H20N4/c1-2-14-10-16-5-6-18(23-16)12-20-8-7-19(24-20)11-17-4-3-15(22-17)9-13(1)21-14/h1-8,21-24H,9-12H2

> <INCHI_KEY>
VCRBUDCZLSQJPZ-UHFFFAOYSA-N

> <FORMULA>
C20H20N4

> <MOLECULAR_WEIGHT>
316.408

> <EXACT_MASS>
316.16879666

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
35.549347203544116

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
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-octaene

> <ALOGPS_LOGP>
3.30

> <JCHEM_LOGP>
2.5082858439999995

> <ALOGPS_LOGS>
-4.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.882754345256146

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.330118003226307

> <JCHEM_POLAR_SURFACE_AREA>
63.16

> <JCHEM_REFRACTIVITY>
98.06160000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.90e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
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-octaene

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0256709
     RDKit          3D
Porphyrinogen
 44 48  0  0  0  0  0  0  0  0999 V2000
   -2.9756    2.4517   -1.1577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9286    3.3310   -1.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0123    2.9246   -0.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4924    1.8505    0.4076 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6752    1.5359   -0.1406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5764    0.3552    0.0960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8788   -0.9820    0.2328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1080   -1.8442    1.3186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2576   -2.8997    1.1740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5255   -2.6643    0.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9203   -1.5063   -0.5483 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3935   -3.5730   -0.4702 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9633   -2.9000   -0.2480 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8793   -3.3348    0.7079 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9381   -2.4557    0.6615 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5121   -0.3194 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4361   -1.8064   -0.8582 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5261   -0.3194   -0.6438 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8904    0.9945   -0.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3409    1.7360    0.9012 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4917    2.7869    1.0550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5200    2.6628    0.0348 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7925    1.5797   -0.6956 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3334    3.6098   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8781    2.4852   -1.8049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8336    4.1910   -1.9041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0154    1.3239    1.2825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4172    0.2800   -0.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1294    0.5822    1.0186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8371   -1.7092    2.1410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1855   -3.7578    1.8640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5375   -1.0767   -1.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4148   -4.5075    0.2035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5410   -4.0478   -1.4378 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8060   -4.2082    1.3882 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8434   -2.5207    1.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9352   -1.2396   -1.6906 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4412   -0.4629    0.0065 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9574   -0.3032   -1.6528 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2265    1.5311    1.5439 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5466    3.5822    1.8201 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2274    1.2254   -1.6043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5260    4.3503   -0.9147 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2744    4.2615    0.7971 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 24  1  0
  5  1  2  0
 11  7  1  0
 17 13  1  0
 23 19  1  0
 24  3  1  0
  1 25  1  0
  2 26  1  0
  4 27  1  0
  6 28  1  0
  6 29  1  0
  8 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 14 35  1  0
 15 36  1  0
 17 37  1  0
 18 38  1  0
 18 39  1  0
 20 40  1  0
 21 41  1  0
 23 42  1  0
 24 43  1  0
 24 44  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       0.021  -3.826   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.352  -3.072   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.766  -3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.814  -2.821   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.115  -1.393   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -1.583  -1.653   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -3.837  -0.088   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.139   1.339   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.807   2.645   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.723   3.748   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.351   3.104   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -1.666   1.625   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       0.009   3.826   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.327   3.127   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.741   3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.789   2.821   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.036   1.393   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       1.613   1.599   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       3.813   0.033   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.114  -1.284   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.837  -2.754   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.808  -3.801   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.326  -3.104   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       1.587  -1.626   0.000  0.00  0.00           N+0
CONECT    1    2   23                                                       
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    2                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11    8                                                       
CONECT   13   11   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17   14                                                       
CONECT   19   17   20                                                       
CONECT   20   19   21   24                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22    1   24                                                  
CONECT   24   23   20                                                       
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

COMPND    HMDB0256709
HETATM    1  C1  UNL     1      -2.976   2.452  -1.158  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.929   3.331  -1.213  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.012   2.925  -0.222  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.492   1.851   0.408  1.00  0.00           N  
HETATM    5  C4  UNL     1      -2.675   1.536  -0.141  1.00  0.00           C  
HETATM    6  C5  UNL     1      -3.576   0.355   0.096  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.879  -0.982   0.233  1.00  0.00           C  
HETATM    8  C7  UNL     1      -3.108  -1.844   1.319  1.00  0.00           C  
HETATM    9  C8  UNL     1      -2.258  -2.900   1.174  1.00  0.00           C  
HETATM   10  C9  UNL     1      -1.525  -2.664   0.004  1.00  0.00           C  
HETATM   11  N2  UNL     1      -1.920  -1.506  -0.548  1.00  0.00           N  
HETATM   12  C10 UNL     1      -0.393  -3.573  -0.470  1.00  0.00           C  
HETATM   13  C11 UNL     1       0.963  -2.900  -0.248  1.00  0.00           C  
HETATM   14  C12 UNL     1       1.879  -3.335   0.708  1.00  0.00           C  
HETATM   15  C13 UNL     1       2.938  -2.456   0.662  1.00  0.00           C  
HETATM   16  C14 UNL     1       2.638  -1.512  -0.319  1.00  0.00           C  
HETATM   17  N3  UNL     1       1.436  -1.806  -0.858  1.00  0.00           N  
HETATM   18  C15 UNL     1       3.526  -0.319  -0.644  1.00  0.00           C  
HETATM   19  C16 UNL     1       2.890   0.994  -0.189  1.00  0.00           C  
HETATM   20  C17 UNL     1       3.341   1.736   0.901  1.00  0.00           C  
HETATM   21  C18 UNL     1       2.492   2.787   1.055  1.00  0.00           C  
HETATM   22  C19 UNL     1       1.520   2.663   0.035  1.00  0.00           C  
HETATM   23  N4  UNL     1       1.793   1.580  -0.696  1.00  0.00           N  
HETATM   24  C20 UNL     1       0.333   3.610  -0.078  1.00  0.00           C  
HETATM   25  H1  UNL     1      -3.878   2.485  -1.805  1.00  0.00           H  
HETATM   26  H2  UNL     1      -1.834   4.191  -1.904  1.00  0.00           H  
HETATM   27  H3  UNL     1      -1.015   1.324   1.283  1.00  0.00           H  
HETATM   28  H4  UNL     1      -4.417   0.280  -0.657  1.00  0.00           H  
HETATM   29  H5  UNL     1      -4.129   0.582   1.019  1.00  0.00           H  
HETATM   30  H6  UNL     1      -3.837  -1.709   2.141  1.00  0.00           H  
HETATM   31  H7  UNL     1      -2.185  -3.758   1.864  1.00  0.00           H  
HETATM   32  H8  UNL     1      -1.538  -1.077  -1.511  1.00  0.00           H  
HETATM   33  H9  UNL     1      -0.415  -4.507   0.204  1.00  0.00           H  
HETATM   34  H10 UNL     1      -0.541  -4.048  -1.438  1.00  0.00           H  
HETATM   35  H11 UNL     1       1.806  -4.208   1.388  1.00  0.00           H  
HETATM   36  H12 UNL     1       3.843  -2.521   1.302  1.00  0.00           H  
HETATM   37  H13 UNL     1       0.935  -1.240  -1.691  1.00  0.00           H  
HETATM   38  H14 UNL     1       4.441  -0.463   0.007  1.00  0.00           H  
HETATM   39  H15 UNL     1       3.957  -0.303  -1.653  1.00  0.00           H  
HETATM   40  H16 UNL     1       4.227   1.531   1.544  1.00  0.00           H  
HETATM   41  H17 UNL     1       2.547   3.582   1.820  1.00  0.00           H  
HETATM   42  H18 UNL     1       1.227   1.225  -1.604  1.00  0.00           H  
HETATM   43  H19 UNL     1       0.526   4.350  -0.915  1.00  0.00           H  
HETATM   44  H20 UNL     1       0.274   4.261   0.797  1.00  0.00           H  
CONECT    1    2    5    5   25
CONECT    2    3    3   26
CONECT    3    4   24
CONECT    4    5   27
CONECT    5    6
CONECT    6    7   28   29
CONECT    7    8    8   11
CONECT    8    9   30
CONECT    9   10   10   31
CONECT   10   11   12
CONECT   11   32
CONECT   12   13   33   34
CONECT   13   14   14   17
CONECT   14   15   35
CONECT   15   16   16   36
CONECT   16   17   18
CONECT   17   37
CONECT   18   19   38   39
CONECT   19   20   20   23
CONECT   20   21   40
CONECT   21   22   22   41
CONECT   22   23   24
CONECT   23   42
CONECT   24   43   44
END

HMDB0256709
     RDKit          3D
Porphyrinogen
 44 48  0  0  0  0  0  0  0  0999 V2000
   -2.9756    2.4517   -1.1577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9286    3.3310   -1.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0123    2.9246   -0.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4924    1.8505    0.4076 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6752    1.5359   -0.1406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5764    0.3552    0.0960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8788   -0.9820    0.2328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1080   -1.8442    1.3186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2576   -2.8997    1.1740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5255   -2.6643    0.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9203   -1.5063   -0.5483 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3935   -3.5730   -0.4702 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9633   -2.9000   -0.2480 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8793   -3.3348    0.7079 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9381   -2.4557    0.6615 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5121   -0.3194 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4361   -1.8064   -0.8582 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5261   -0.3194   -0.6438 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8904    0.9945   -0.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3409    1.7360    0.9012 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4917    2.7869    1.0550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5200    2.6628    0.0348 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7925    1.5797   -0.6956 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3334    3.6098   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8781    2.4852   -1.8049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8336    4.1910   -1.9041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0154    1.3239    1.2825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4172    0.2800   -0.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1294    0.5822    1.0186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8371   -1.7092    2.1410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1855   -3.7578    1.8640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5375   -1.0767   -1.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4148   -4.5075    0.2035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5410   -4.0478   -1.4378 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8060   -4.2082    1.3882 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8434   -2.5207    1.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9352   -1.2396   -1.6906 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4412   -0.4629    0.0065 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9574   -0.3032   -1.6528 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2265    1.5311    1.5439 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5466    3.5822    1.8201 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2274    1.2254   -1.6043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5260    4.3503   -0.9147 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2744    4.2615    0.7971 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 24  1  0
  5  1  2  0
 11  7  1  0
 17 13  1  0
 23 19  1  0
 24  3  1  0
  1 25  1  0
  2 26  1  0
  4 27  1  0
  6 28  1  0
  6 29  1  0
  8 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 14 35  1  0
 15 36  1  0
 17 37  1  0
 18 38  1  0
 18 39  1  0
 20 40  1  0
 21 41  1  0
 23 42  1  0
 24 43  1  0
 24 44  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Calix[4]pyrrole	ChEBI
Calix(4)pyrrole	MeSH

Chemical Formula

C₂₀H₂₀N₄

Average Molecular Weight

316.408

Monoisotopic Molecular Weight

316.16879666

IUPAC Name

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-octaene

Traditional Name

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-octaene

CAS Registry Number

Not Available

SMILES

C1C2=CC=C(CC3=CC=C(CC4=CC=C(CC5=CC=C1N5)N4)N3)N2

InChI Identifier

InChI=1S/C20H20N4/c1-2-14-10-16-5-6-18(23-16)12-20-8-7-19(24-20)11-17-4-3-15(22-17)9-13(1)21-14/h1-8,21-24H,9-12H2

InChI Key

VCRBUDCZLSQJPZ-UHFFFAOYSA-N

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
Heteroaromatic compound
Pyrrole
Azacycle
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

tetrapyrrole fundamental parent (CHEBI:26213 )
porphyrinogens (CHEBI:26213 )
calixpyrrole (CHEBI:26213 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.3	ALOGPS
logP	2.51	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	16.33	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	63.16 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	98.06 m³·mol⁻¹	ChemAxon
Polarizability	35.55 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	181.734	30932474
DeepCCS	[M-H]-	179.376	30932474
DeepCCS	[M-2H]-	213.189	30932474
DeepCCS	[M+Na]+	188.416	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Porphyrinogen	C1C2=CC=C(CC3=CC=C(CC4=CC=C(CC5=CC=C1N5)N4)N3)N2	4772.8	Standard polar	33892256
Porphyrinogen	C1C2=CC=C(CC3=CC=C(CC4=CC=C(CC5=CC=C1N5)N4)N3)N2	3250.7	Standard non polar	33892256
Porphyrinogen	C1C2=CC=C(CC3=CC=C(CC4=CC=C(CC5=CC=C1N5)N4)N3)N2	3555.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Porphyrinogen,1TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)[NH]1	3419.3	Semi standard non polar	33892256
Porphyrinogen,1TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)[NH]1	2966.0	Standard non polar	33892256
Porphyrinogen,1TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)[NH]1	3860.3	Standard polar	33892256
Porphyrinogen,2TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)N1[Si](C)(C)C	3507.3	Semi standard non polar	33892256
Porphyrinogen,2TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)N1[Si](C)(C)C	3185.9	Standard non polar	33892256
Porphyrinogen,2TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)N1[Si](C)(C)C	3714.8	Standard polar	33892256
Porphyrinogen,2TMS,isomer #2	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C)[NH]1	3496.1	Semi standard non polar	33892256
Porphyrinogen,2TMS,isomer #2	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C)[NH]1	3182.4	Standard non polar	33892256
Porphyrinogen,2TMS,isomer #2	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C)[NH]1	3715.3	Standard polar	33892256
Porphyrinogen,3TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C)N1[Si](C)(C)C	3592.2	Semi standard non polar	33892256
Porphyrinogen,3TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C)N1[Si](C)(C)C	3372.9	Standard non polar	33892256
Porphyrinogen,3TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C)N1[Si](C)(C)C	3542.3	Standard polar	33892256
Porphyrinogen,4TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)N4[Si](C)(C)C)N3[Si](C)(C)C)N1[Si](C)(C)C	3610.6	Semi standard non polar	33892256
Porphyrinogen,4TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)N4[Si](C)(C)C)N3[Si](C)(C)C)N1[Si](C)(C)C	3484.0	Standard non polar	33892256
Porphyrinogen,4TMS,isomer #1	C[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)N4[Si](C)(C)C)N3[Si](C)(C)C)N1[Si](C)(C)C	3399.0	Standard polar	33892256
Porphyrinogen,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)[NH]1	3621.0	Semi standard non polar	33892256
Porphyrinogen,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)[NH]1	3229.7	Standard non polar	33892256
Porphyrinogen,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)[NH]1	3928.8	Standard polar	33892256
Porphyrinogen,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)N1[Si](C)(C)C(C)(C)C	3884.2	Semi standard non polar	33892256
Porphyrinogen,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)N1[Si](C)(C)C(C)(C)C	3693.3	Standard non polar	33892256
Porphyrinogen,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)[NH]3)N1[Si](C)(C)C(C)(C)C	3769.2	Standard polar	33892256
Porphyrinogen,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C(C)(C)C)[NH]1	3868.3	Semi standard non polar	33892256
Porphyrinogen,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C(C)(C)C)[NH]1	3690.1	Standard non polar	33892256
Porphyrinogen,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C(C)(C)C)[NH]1	3765.4	Standard polar	33892256
Porphyrinogen,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	4090.6	Semi standard non polar	33892256
Porphyrinogen,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	4053.1	Standard non polar	33892256
Porphyrinogen,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)[NH]4)N3[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	3625.3	Standard polar	33892256
Porphyrinogen,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)N4[Si](C)(C)C(C)(C)C)N3[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	4289.2	Semi standard non polar	33892256
Porphyrinogen,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)N4[Si](C)(C)C(C)(C)C)N3[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	4291.5	Standard non polar	33892256
Porphyrinogen,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C2=CC=C1CC1=CC=C(CC3=CC=C(CC4=CC=C(C2)N4[Si](C)(C)C(C)(C)C)N3[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	3575.3	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Porphyrinogen GC-MS (Non-derivatized) - 70eV, Positive	splash10-014i-0009000000-97d128d7ea9738ef683e	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Porphyrinogen GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00007284

Chemspider ID

7827582

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Porphyrinogen

METLIN ID

Not Available

PubChem Compound

9548659

PDB ID

Not Available

ChEBI ID

26213

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Porphyrinogen (HMDB0256709)

MOL for HMDB0256709 (Porphyrinogen)

3D MOL for HMDB0256709 (Porphyrinogen)

3D SDF for HMDB0256709 (Porphyrinogen)

3D-SDF for HMDB0256709 (Porphyrinogen)

PDB for HMDB0256709 (Porphyrinogen)

3D PDB for HMDB0256709 (Porphyrinogen)

SMILES for HMDB0256709 (Porphyrinogen)

INCHI for HMDB0256709 (Porphyrinogen)

Structure for HMDB0256709 (Porphyrinogen)

3D Structure for HMDB0256709 (Porphyrinogen)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra