Showing metabocard for Protoporphyrinogen IX (MMDBc0029556)

Plant
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:32:09 UTC
Update Date2022-08-31 13:43:34 UTC
Metabolite IDMMDBc0029556
Metabolite Identification
Common NameProtoporphyrinogen IX
DescriptionProtoporphyrinogen IX is an intermediate in heme biosynthesis. It is a porphyrinogen in which 2 pyrrole rings each have one methyl and one propionate side chain and the other two pyrrole rings each have one methyl and one vinyl side chain. 15 isomers are possible but only one, type IX, occurs naturally. Protoporphyrinogen is produced by oxidative decarboxylation of coproporphyrinogen.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560bdf8ff3e0>


  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
   -0.7095    1.6679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7305    1.6679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6695    0.7079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0870   -0.0015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6695   -0.7111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7305   -1.6712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.0885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7095   -1.6712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6485   -0.7111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0660   -0.0015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8556    0.8540    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8556   -0.8572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -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
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    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
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    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
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   -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
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 33  8  2  0  0  0  0
 14  8  1  0  0  0  0
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 18 27  1  0  0  0  0
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 20 21  1  0  0  0  0
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 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
Download

3D MOL for #<Metabolite:0x0000560bdf8ff3e0>

HMDB0001097
     RDKit          3D
Protoporphyrinogen IX
 82 86  0  0  0  0  0  0  0  0999 V2000
    4.5727   -4.6923    1.6814 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5636   -4.5750    0.8724 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3981   -3.7003    1.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3754   -2.3913    1.5808 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005   -2.0036    1.7076 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2933   -3.0119    1.3216 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0883   -4.0911    0.9409 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6462   -5.4515    0.4371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2090   -3.0251    1.1919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8346   -1.8534    0.4888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2731   -0.7505   -0.0276 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2793    0.0137   -0.5208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4849   -0.6280   -0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.4186   -0.1600   -2.6381 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.2298   -1.8118    0.3280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2417   -2.8315    0.7626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2306    1.3640   -1.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3966    3.7847   -0.3575 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8857    5.1031    0.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9532    3.4225   -0.4317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0443    4.2870    0.0807 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4222    4.2103    1.4924 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.3043    1.8829    1.9453 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9516    2.9553    2.9936 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6411    2.7385   -0.8118 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2415    1.4734   -0.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8888    0.7689    0.8380 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6536   -0.3439    0.8281 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4998   -0.3491   -0.2677 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5195   -1.3689   -0.7007 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2418    0.8097   -0.9610 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9949    1.1886   -2.1607 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3740    2.3928   -2.4748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6123   -1.5159    1.8094 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.5656   -5.1619   -0.0518 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.8878   -1.6096   -2.3285 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.3271    1.7238   -2.9853 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.0925    1.9246   -0.6793 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.5766    0.7914   -1.7852 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.7955    5.3710   -0.3816 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.9689    4.0710   -0.5293 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.2594    4.9924    1.6235 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.1464    1.0519    1.6108 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0023   -2.1502   -1.2978 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.4965   -2.1788    1.5555 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
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 13 19  1  0
 19 20  1  0
 12 21  1  0
 21 22  1  0
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 29 30  1  0
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 24 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  2  0
 37 38  1  0
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 39 40  1  0
 40 41  2  3
 36 42  1  0
  7  3  1  0
 19 10  2  0
 27 22  2  0
 39 34  2  0
 42  4  1  0
  1 43  1  0
  1 44  1  0
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  5 46  1  0
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 11 52  1  0
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 38 76  1  0
 38 77  1  0
 40 78  1  0
 41 79  1  0
 41 80  1  0
 42 81  1  0
 42 82  1  0
M  END
Download

3D SDF for #<Metabolite:0x0000560bdf8ff3e0>


  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
   -0.7095    1.6679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7305    1.6679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6695    0.7079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0870   -0.0015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6695   -0.7111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7305   -1.6712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.0885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.6485   -0.7111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0660   -0.0015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8556    0.8540    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8556   -0.8572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -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>
MMDBc0029556

> <DATABASE_NAME>
MIME

> <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

$$$$
Download

3D-SDF for #<Metabolite:0x0000560bdf8ff3e0>

HMDB0001097
     RDKit          3D
Protoporphyrinogen IX
 82 86  0  0  0  0  0  0  0  0999 V2000
    4.5727   -4.6923    1.6814 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5636   -4.5750    0.8724 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3981   -3.7003    1.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3754   -2.3913    1.5808 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1005   -2.0036    1.7076 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2933   -3.0119    1.3216 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0883   -4.0911    0.9409 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6462   -5.4515    0.4371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2090   -3.0251    1.1919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8346   -1.8534    0.4888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2731   -0.7505   -0.0276 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2793    0.0137   -0.5208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4849   -0.6280   -0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8774   -0.2103   -0.6967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0632   -0.5271   -2.1427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4186   -0.1600   -2.6381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3510   -0.9618   -2.4097 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7023    0.9989   -3.3256 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2298   -1.8118    0.3280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2417   -2.8315    0.7626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2306    1.3640   -1.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9698    2.1524   -0.9995 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2984    1.7386   -1.2751 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1145    2.7215   -0.8790 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3966    3.7847   -0.3575 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8857    5.1031    0.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9532    3.4225   -0.4317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0443    4.2870    0.0807 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4222    4.2103    1.4924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8475    2.9837    2.1159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3043    1.8829    1.9453 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9516    2.9553    2.9936 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6411    2.7385   -0.8118 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2415    1.4734   -0.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8888    0.7689    0.8380 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6536   -0.3439    0.8281 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4998   -0.3491   -0.2677 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5195   -1.3689   -0.7007 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2418    0.8097   -0.9610 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9949    1.1886   -2.1607 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3740    2.3928   -2.4748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6123   -1.5159    1.8094 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6631   -4.1637    2.6109 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4128   -5.3578    1.4584 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5656   -5.1619   -0.0518 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7555   -1.0077    2.1160 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4096   -6.1697    0.7542 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4680   -5.4185   -0.6586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3007   -5.6651    0.9369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6469   -3.1812    2.1813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5513   -3.9732    0.6617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1976   -0.5156   -0.0610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5775   -0.7721   -0.0558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0335    0.8653   -0.4640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8878   -1.6096   -2.3285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3506    0.0189   -2.7582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3271    1.7238   -2.9853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8513   -3.4717    1.5620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0791   -2.2564    1.2098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6347   -3.4029   -0.1008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0925    1.9246   -0.6793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5187    1.3676   -2.2075 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5766    0.7914   -1.7852 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1446    5.8881    0.0152 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7955    5.3710   -0.3816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1802    5.0034    1.2543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9689    4.0710   -0.5293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8374    5.3655   -0.1631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6017    4.7145    2.1126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2594    4.9924    1.6235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1247    3.7945    3.5289 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0445    3.6374   -0.3071 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9485    2.9170   -1.8491 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1464    1.0519    1.6108 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0023   -2.1502   -1.2978 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0370   -1.7605    0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2717   -0.8868   -1.3523 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2357    0.3495   -2.8242 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1827    3.2662   -1.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9279    2.5499   -3.3891 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8646   -1.2967    2.8362 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4965   -2.1788    1.5555 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 13 19  1  0
 19 20  1  0
 12 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 25 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  2  0
 30 32  1  0
 24 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  2  0
 37 38  1  0
 37 39  1  0
 39 40  1  0
 40 41  2  3
 36 42  1  0
  7  3  1  0
 19 10  2  0
 27 22  2  0
 39 34  2  0
 42  4  1  0
  1 43  1  0
  1 44  1  0
  2 45  1  0
  5 46  1  0
  8 47  1  0
  8 48  1  0
  8 49  1  0
  9 50  1  0
  9 51  1  0
 11 52  1  0
 14 53  1  0
 14 54  1  0
 15 55  1  0
 15 56  1  0
 18 57  1  0
 20 58  1  0
 20 59  1  0
 20 60  1  0
 21 61  1  0
 21 62  1  0
 23 63  1  0
 26 64  1  0
 26 65  1  0
 26 66  1  0
 28 67  1  0
 28 68  1  0
 29 69  1  0
 29 70  1  0
 32 71  1  0
 33 72  1  0
 33 73  1  0
 35 74  1  0
 38 75  1  0
 38 76  1  0
 38 77  1  0
 40 78  1  0
 41 79  1  0
 41 80  1  0
 42 81  1  0
 42 82  1  0
M  END
Download

PDB for #<Metabolite:0x0000560bdf8ff3e0>

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
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3D PDB for #<Metabolite:0x0000560bdf8ff3e0>

COMPND    HMDB0001097
HETATM    1  C1  UNL     1       4.573  -4.692   1.681  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.564  -4.575   0.872  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.398  -3.700   1.106  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.375  -2.391   1.581  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.100  -2.004   1.708  1.00  0.00           N  
HETATM    6  C5  UNL     1       0.293  -3.012   1.322  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.088  -4.091   0.941  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.646  -5.451   0.437  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.209  -3.025   1.192  1.00  0.00           C  
HETATM   10  C9  UNL     1      -1.835  -1.853   0.489  1.00  0.00           C  
HETATM   11  N2  UNL     1      -1.273  -0.750  -0.028  1.00  0.00           N  
HETATM   12  C10 UNL     1      -2.279   0.014  -0.521  1.00  0.00           C  
HETATM   13  C11 UNL     1      -3.485  -0.628  -0.310  1.00  0.00           C  
HETATM   14  C12 UNL     1      -4.877  -0.210  -0.697  1.00  0.00           C  
HETATM   15  C13 UNL     1      -5.063  -0.527  -2.143  1.00  0.00           C  
HETATM   16  C14 UNL     1      -6.419  -0.160  -2.638  1.00  0.00           C  
HETATM   17  O1  UNL     1      -7.351  -0.962  -2.410  1.00  0.00           O  
HETATM   18  O2  UNL     1      -6.702   0.999  -3.326  1.00  0.00           O  
HETATM   19  C15 UNL     1      -3.230  -1.812   0.328  1.00  0.00           C  
HETATM   20  C16 UNL     1      -4.242  -2.831   0.763  1.00  0.00           C  
HETATM   21  C17 UNL     1      -2.231   1.364  -1.163  1.00  0.00           C  
HETATM   22  C18 UNL     1      -0.970   2.152  -0.999  1.00  0.00           C  
HETATM   23  N3  UNL     1       0.298   1.739  -1.275  1.00  0.00           N  
HETATM   24  C19 UNL     1       1.115   2.722  -0.879  1.00  0.00           C  
HETATM   25  C20 UNL     1       0.397   3.785  -0.357  1.00  0.00           C  
HETATM   26  C21 UNL     1       0.886   5.103   0.198  1.00  0.00           C  
HETATM   27  C22 UNL     1      -0.953   3.423  -0.432  1.00  0.00           C  
HETATM   28  C23 UNL     1      -2.044   4.287   0.081  1.00  0.00           C  
HETATM   29  C24 UNL     1      -2.422   4.210   1.492  1.00  0.00           C  
HETATM   30  C25 UNL     1      -2.848   2.984   2.116  1.00  0.00           C  
HETATM   31  O3  UNL     1      -2.304   1.883   1.945  1.00  0.00           O  
HETATM   32  O4  UNL     1      -3.952   2.955   2.994  1.00  0.00           O  
HETATM   33  C26 UNL     1       2.641   2.739  -0.812  1.00  0.00           C  
HETATM   34  C27 UNL     1       3.241   1.473  -0.256  1.00  0.00           C  
HETATM   35  N4  UNL     1       2.889   0.769   0.838  1.00  0.00           N  
HETATM   36  C28 UNL     1       3.654  -0.344   0.828  1.00  0.00           C  
HETATM   37  C29 UNL     1       4.500  -0.349  -0.268  1.00  0.00           C  
HETATM   38  C30 UNL     1       5.520  -1.369  -0.701  1.00  0.00           C  
HETATM   39  C31 UNL     1       4.242   0.810  -0.961  1.00  0.00           C  
HETATM   40  C32 UNL     1       4.995   1.189  -2.161  1.00  0.00           C  
HETATM   41  C33 UNL     1       5.374   2.393  -2.475  1.00  0.00           C  
HETATM   42  C34 UNL     1       3.612  -1.516   1.809  1.00  0.00           C  
HETATM   43  H1  UNL     1       4.663  -4.164   2.611  1.00  0.00           H  
HETATM   44  H2  UNL     1       5.413  -5.358   1.458  1.00  0.00           H  
HETATM   45  H3  UNL     1       3.566  -5.162  -0.052  1.00  0.00           H  
HETATM   46  H4  UNL     1       0.756  -1.008   2.116  1.00  0.00           H  
HETATM   47  H5  UNL     1       1.410  -6.170   0.754  1.00  0.00           H  
HETATM   48  H6  UNL     1       0.468  -5.418  -0.659  1.00  0.00           H  
HETATM   49  H7  UNL     1      -0.301  -5.665   0.937  1.00  0.00           H  
HETATM   50  H8  UNL     1      -1.647  -3.181   2.181  1.00  0.00           H  
HETATM   51  H9  UNL     1      -1.551  -3.973   0.662  1.00  0.00           H  
HETATM   52  H10 UNL     1      -0.198  -0.516  -0.061  1.00  0.00           H  
HETATM   53  H11 UNL     1      -5.577  -0.772  -0.056  1.00  0.00           H  
HETATM   54  H12 UNL     1      -5.033   0.865  -0.464  1.00  0.00           H  
HETATM   55  H13 UNL     1      -4.888  -1.610  -2.329  1.00  0.00           H  
HETATM   56  H14 UNL     1      -4.351   0.019  -2.758  1.00  0.00           H  
HETATM   57  H15 UNL     1      -7.327   1.724  -2.985  1.00  0.00           H  
HETATM   58  H16 UNL     1      -3.851  -3.472   1.562  1.00  0.00           H  
HETATM   59  H17 UNL     1      -5.079  -2.256   1.210  1.00  0.00           H  
HETATM   60  H18 UNL     1      -4.635  -3.403  -0.101  1.00  0.00           H  
HETATM   61  H19 UNL     1      -3.093   1.925  -0.679  1.00  0.00           H  
HETATM   62  H20 UNL     1      -2.519   1.368  -2.207  1.00  0.00           H  
HETATM   63  H21 UNL     1       0.577   0.791  -1.785  1.00  0.00           H  
HETATM   64  H22 UNL     1       0.145   5.888   0.015  1.00  0.00           H  
HETATM   65  H23 UNL     1       1.795   5.371  -0.382  1.00  0.00           H  
HETATM   66  H24 UNL     1       1.180   5.003   1.254  1.00  0.00           H  
HETATM   67  H25 UNL     1      -2.969   4.071  -0.529  1.00  0.00           H  
HETATM   68  H26 UNL     1      -1.837   5.365  -0.163  1.00  0.00           H  
HETATM   69  H27 UNL     1      -1.602   4.714   2.113  1.00  0.00           H  
HETATM   70  H28 UNL     1      -3.259   4.992   1.624  1.00  0.00           H  
HETATM   71  H29 UNL     1      -4.125   3.795   3.529  1.00  0.00           H  
HETATM   72  H30 UNL     1       3.045   3.637  -0.307  1.00  0.00           H  
HETATM   73  H31 UNL     1       2.949   2.917  -1.849  1.00  0.00           H  
HETATM   74  H32 UNL     1       2.146   1.052   1.611  1.00  0.00           H  
HETATM   75  H33 UNL     1       5.002  -2.150  -1.298  1.00  0.00           H  
HETATM   76  H34 UNL     1       6.037  -1.760   0.181  1.00  0.00           H  
HETATM   77  H35 UNL     1       6.272  -0.887  -1.352  1.00  0.00           H  
HETATM   78  H36 UNL     1       5.236   0.350  -2.824  1.00  0.00           H  
HETATM   79  H37 UNL     1       5.183   3.266  -1.891  1.00  0.00           H  
HETATM   80  H38 UNL     1       5.928   2.550  -3.389  1.00  0.00           H  
HETATM   81  H39 UNL     1       3.865  -1.297   2.836  1.00  0.00           H  
HETATM   82  H40 UNL     1       4.497  -2.179   1.556  1.00  0.00           H  
CONECT    1    2    2   43   44
CONECT    2    3   45
CONECT    3    4    4    7
CONECT    4    5   42
CONECT    5    6   46
CONECT    6    7    7    9
CONECT    7    8
CONECT    8   47   48   49
CONECT    9   10   50   51
CONECT   10   11   19   19
CONECT   11   12   52
CONECT   12   13   13   21
CONECT   13   14   19
CONECT   14   15   53   54
CONECT   15   16   55   56
CONECT   16   17   17   18
CONECT   18   57
CONECT   19   20
CONECT   20   58   59   60
CONECT   21   22   61   62
CONECT   22   23   27   27
CONECT   23   24   63
CONECT   24   25   25   33
CONECT   25   26   27
CONECT   26   64   65   66
CONECT   27   28
CONECT   28   29   67   68
CONECT   29   30   69   70
CONECT   30   31   31   32
CONECT   32   71
CONECT   33   34   72   73
CONECT   34   35   39   39
CONECT   35   36   74
CONECT   36   37   37   42
CONECT   37   38   39
CONECT   38   75   76   77
CONECT   39   40
CONECT   40   41   41   78
CONECT   41   79   80
CONECT   42   81   82
END
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SMILES for #<Metabolite:0x0000560bdf8ff3e0>

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
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INCHI for #<Metabolite:0x0000560bdf8ff3e0>

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)
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Synonyms
ValueSource
7,12-Diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoic acidChEBI
7,12-Diethenyl-3,8,13,17-tetramethyl-5,10,15,20,22,24-hexahydroporphyrin-2,18-dipropanoateGenerator
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-dipropanoateHMDB
7,12-Diethenyl-5,10,15,20,22,24-hexahydro-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-dipropanoic acidHMDB
ProtoporphyrinogenHMDB
Protoporphyrinogen-IXHMDB
Molecular FormulaC34H40N4O4
Average Mass568.7058
Monoisotopic Mass568.304955788
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 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
CAS Registry Number7412-77-3
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 KeyUHSGPDMIQQYNAX-UHFFFAOYSA-N