MiMeDB: Showing metabocard for Cobyrinate (MMDBc0048054)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 21:47:01 UTC

Update Date

2022-09-01 02:14:04 UTC

Metabolite ID

MMDBc0048054

Metabolite Identification

Common Name

Cobyrinate

Description

Cobyrinsaeure, also known as cobyrinic acid or cob(ii)yrinate, belongs to the class of organic compounds known as metallotetrapyrroles. These are polycyclic compounds containing a tetrapyrrole skeleton combined with a metal atom. Based on a literature review very few articles have been published on Cobyrinsaeure.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304292223472D          

 65 69  0  0  1  0            999 V2000
    2.0804    0.1773    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8370   -0.1516    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9793    0.6610    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4055    1.2538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6320    2.0471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0582    2.6399    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4322    2.2476    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7961    0.7768    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5710    1.0598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5956    1.5770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1884    2.1508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9817    1.9243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5745    2.4981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1822    1.1241    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1586    0.0357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5659   -0.5381    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6816   -1.3549    0.0000 Co  0  2  0  0  0  0  0  0  0  0  0  0
    5.1638   -0.3116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6429    0.3601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6725   -0.9611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2120   -1.6456    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7207   -2.2951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2702   -3.2585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5710   -3.6965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9384   -3.1670    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2393   -3.6050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3283   -3.0562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7201   -3.6136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9658   -2.3152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5586   -1.7414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1961   -1.0003    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7773   -0.2895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3792   -1.1161    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3495   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5562   -1.0595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1936   -0.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6294   -0.2618    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6542    0.3661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2369   -1.9287    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4958   -2.2912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4392   -3.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3019   -3.4768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9864   -3.0163    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3584   -4.2998    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4398   -4.4052    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6230   -4.5210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4696   -5.2297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7705   -5.6677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8002   -6.4921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0416   -5.2812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2629   -4.4618    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7009   -5.1609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5253   -5.1312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9633   -5.8303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7878   -5.8006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5769   -6.5592    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4956   -2.0121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3124   -1.8963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6961   -2.8123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4658   -1.1876    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.1153   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8806   -0.9871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5301   -0.4784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4144    0.3384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2954   -0.7866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
  8 15  1  0  0  0  0
 15 16  1  0  0  0  0
  2 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 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
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
  2 31  1  0  0  0  0
 31 32  1  1  0  0  0
 31 33  1  0  0  0  0
 33 34  1  1  0  0  0
 33 35  1  6  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  2  0  0  0  0
 33 39  1  0  0  0  0
 29 39  1  0  0  0  0
 39 40  1  1  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 42 44  2  0  0  0  0
 26 45  1  0  0  0  0
 45 46  1  1  0  0  0
 45 47  1  6  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 48 50  2  0  0  0  0
 45 51  1  0  0  0  0
 24 51  1  0  0  0  0
 51 52  1  1  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 54 56  2  0  0  0  0
 22 57  1  0  0  0  0
 57 58  1  0  0  0  0
 57 59  1  0  0  0  0
 57 60  1  0  0  0  0
 20 60  1  0  0  0  0
 60 61  1  1  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  1  0  0  0  0
 63 65  2  0  0  0  0
M  CHG  1  17   2
M  END


  Mrv1652304292223472D          

 65 69  0  0  1  0            999 V2000
    2.0804    0.1773    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8370   -0.1516    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9793    0.6610    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4055    1.2538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6320    2.0471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0582    2.6399    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4322    2.2476    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7961    0.7768    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5710    1.0598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5956    1.5770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1884    2.1508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9817    1.9243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5745    2.4981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1822    1.1241    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1586    0.0357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5659   -0.5381    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6816   -1.3549    0.0000 Co  0  2  0  0  0  0  0  0  0  0  0  0
    5.1638   -0.3116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6429    0.3601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6725   -0.9611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2120   -1.6456    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7207   -2.2951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2702   -3.2585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5710   -3.6965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9384   -3.1670    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2393   -3.6050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3283   -3.0562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7201   -3.6136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9658   -2.3152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5586   -1.7414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1961   -1.0003    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7773   -0.2895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3792   -1.1161    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3495   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5562   -1.0595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1936   -0.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6294   -0.2618    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6542    0.3661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2369   -1.9287    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4958   -2.2912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4392   -3.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3019   -3.4768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9864   -3.0163    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3584   -4.2998    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4398   -4.4052    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6230   -4.5210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4696   -5.2297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7705   -5.6677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8002   -6.4921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0416   -5.2812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2629   -4.4618    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7009   -5.1609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5253   -5.1312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9633   -5.8303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7878   -5.8006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5769   -6.5592    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4956   -2.0121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3124   -1.8963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6961   -2.8123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4658   -1.1876    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.1153   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8806   -0.9871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5301   -0.4784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4144    0.3384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2954   -0.7866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
  8 15  1  0  0  0  0
 15 16  1  0  0  0  0
  2 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 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
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
  2 31  1  0  0  0  0
 31 32  1  1  0  0  0
 31 33  1  0  0  0  0
 33 34  1  1  0  0  0
 33 35  1  6  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  2  0  0  0  0
 33 39  1  0  0  0  0
 29 39  1  0  0  0  0
 39 40  1  1  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 42 44  2  0  0  0  0
 26 45  1  0  0  0  0
 45 46  1  1  0  0  0
 45 47  1  6  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 48 50  2  0  0  0  0
 45 51  1  0  0  0  0
 24 51  1  0  0  0  0
 51 52  1  1  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 54 56  2  0  0  0  0
 22 57  1  0  0  0  0
 57 58  1  0  0  0  0
 57 59  1  0  0  0  0
 57 60  1  0  0  0  0
 20 60  1  0  0  0  0
 60 61  1  1  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  1  0  0  0  0
 63 65  2  0  0  0  0
M  CHG  1  17   2
M  END
> <DATABASE_ID>
MMDBc0048054

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12[C@H](CC(O)=O)[C@@](C)(CCC(O)=O)\C(N1[Co++])=C(C)\C1=N\C(=C/C3=N/C(=C(C)\C4=N[C@]2(C)[C@@](C)(CC(O)=O)[C@@H]4CCC(O)=O)/[C@@](C)(CC(O)=O)[C@@H]3CCC(O)=O)\C(C)(C)[C@@H]1CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C45H60N4O14.Co/c1-21-36-24(10-13-30(52)53)41(3,4)28(47-36)18-27-23(9-12-29(50)51)43(6,19-34(60)61)39(46-27)22(2)37-25(11-14-31(54)55)44(7,20-35(62)63)45(8,49-37)40-26(17-33(58)59)42(5,38(21)48-40)16-15-32(56)57;/h18,23-26,40H,9-17,19-20H2,1-8H3,(H8,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63);/q;+3/p-1/t23-,24-,25-,26+,40-,42-,43+,44+,45+;/m1./s1

> <INCHI_KEY>
SXATWJGWOIKDIW-OKJGWHJPSA-M

> <FORMULA>
C45H59CoN4O14

> <MOLECULAR_WEIGHT>
938.913

> <EXACT_MASS>
938.334874

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
123

> <JCHEM_AVERAGE_POLARIZABILITY>
91.71837828409025

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14,18-tetrakis(2-carboxyethyl)-3,8,19-tris(carboxymethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10(22),11,15(21),16-hexaen-20-yl]cobaltbis(ylium)

> <ALOGPS_LOGP>
1.90

> <JCHEM_LOGP>
-0.3741302418651627

> <ALOGPS_LOGS>
-5.14

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.600464257528869

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2223376957443013

> <JCHEM_PKA_STRONGEST_BASIC>
8.515455093737652

> <JCHEM_POLAR_SURFACE_AREA>
301.41999999999996

> <JCHEM_REFRACTIVITY>
224.53640000000019

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.37e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14,18-tetrakis(2-carboxyethyl)-3,8,19-tris(carboxymethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10(22),11,15(21),16-hexaen-20-yl]cobaltbis(ylium)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  H   UNK     0       3.883   0.331   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       5.296  -0.283   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.561   1.234   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.490   2.340   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.913   3.821   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.842   4.928   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       6.407   4.196   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       7.086   1.450   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.533   1.978   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.712   2.944   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.818   4.015   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.299   3.592   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      10.406   4.663   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       9.673   2.098   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       7.763   0.067   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       6.656  -1.004   0.000  0.00  0.00           N+0
HETATM   17 Co   UNK     0       6.872  -2.529   0.000  0.00  0.00          Co+2
HETATM   18  C   UNK     0       9.639  -0.582   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.533   0.672   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.589  -1.794   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       9.729  -3.072   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      10.679  -4.284   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.838  -6.083   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.533  -6.900   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0       7.352  -5.912   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       6.047  -6.729   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.346  -5.705   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.211  -6.745   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.669  -4.322   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       4.776  -3.251   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       4.099  -1.867   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.318  -0.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.575  -2.083   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.519  -0.544   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.038  -1.978   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.361  -0.594   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -1.175  -0.489   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       1.221   0.683   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       2.309  -3.600   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       0.926  -4.277   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       0.820  -5.813   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -0.563  -6.490   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      -1.841  -5.630   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      -0.669  -8.026   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       6.421  -8.223   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       4.896  -8.439   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       6.477  -9.762   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       5.172 -10.580   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0       5.227 -12.119   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0       3.811  -9.858   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0       7.957  -8.329   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       8.775  -9.634   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      10.314  -9.578   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      11.132 -10.883   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      12.671 -10.828   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      10.410 -12.244   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0      12.125  -3.756   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      13.650  -3.540   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      12.499  -5.250   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      12.070  -2.217   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      13.282  -1.267   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      14.710  -1.843   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      15.923  -0.893   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0      15.707   0.632   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      17.351  -1.468   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   16   31                                             
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    3    9   10   15                                             
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    8   16   18                                                  
CONECT   16   15    2   17                                                  
CONECT   17   16                                                            
CONECT   18   15   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   60                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   57                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   51                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   45                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   39                                                  
CONECT   30   29   31                                                       
CONECT   31   30    2   32   33                                             
CONECT   32   31                                                            
CONECT   33   31   34   35   39                                             
CONECT   34   33                                                            
CONECT   35   33   36                                                       
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36                                                            
CONECT   39   33   29   40                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43   44                                                  
CONECT   43   42                                                            
CONECT   44   42                                                            
CONECT   45   26   46   47   51                                             
CONECT   46   45                                                            
CONECT   47   45   48                                                       
CONECT   48   47   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48                                                            
CONECT   51   45   24   52                                                  
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55   56                                                  
CONECT   55   54                                                            
CONECT   56   54                                                            
CONECT   57   22   58   59   60                                             
CONECT   58   57                                                            
CONECT   59   57                                                            
CONECT   60   57   20   61                                                  
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64   65                                                  
CONECT   64   63                                                            
CONECT   65   63                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  138    0
END

Synonyms

Value	Source
Cob(II)yrinate	ChEBI
Cob(II)yrinic acid	ChEBI
Cobyrinate	ChEBI
Cobyrinic acid	ChEBI

Molecular Formula

C₄₅H₅₉CoN₄O₁₄

Average Mass

938.913

Monoisotopic Mass

938.334874

IUPAC Name

[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14,18-tetrakis(2-carboxyethyl)-3,8,19-tris(carboxymethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10(22),11,15(21),16-hexaen-20-yl]cobaltbis(ylium)

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@]12[C@H](CC(O)=O)[C@@](C)(CCC(O)=O)\C(N1[Co++])=C(C)\C1=N\C(=C/C3=N/C(=C(C)\C4=N[C@]2(C)[C@@](C)(CC(O)=O)[C@@H]4CCC(O)=O)/[C@@](C)(CC(O)=O)[C@@H]3CCC(O)=O)\C(C)(C)[C@@H]1CCC(O)=O

InChI Identifier

InChI=1S/C45H60N4O14.Co/c1-21-36-24(10-13-30(52)53)41(3,4)28(47-36)18-27-23(9-12-29(50)51)43(6,19-34(60)61)39(46-27)22(2)37-25(11-14-31(54)55)44(7,20-35(62)63)45(8,49-37)40-26(17-33(58)59)42(5,38(21)48-40)16-15-32(56)57;/h18,23-26,40H,9-17,19-20H2,1-8H3,(H8,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63);/q;+3/p-1/t23-,24-,25-,26+,40-,42-,43+,44+,45+;/m1./s1

InChI Key

SXATWJGWOIKDIW-OKJGWHJPSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as metallotetrapyrroles. These are polycyclic compounds containing a tetrapyrrole skeleton combined with a metal atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Metallotetrapyrroles

Direct Parent

Metallotetrapyrroles

Alternative Parents

Substituents

Metallotetrapyrrole skeleton
Pyrrolidine
Pyrroline
Ketimine
Carboxylic acid derivative
Carboxylic acid
Carbene-type 1,3-dipolar compound
Organic transition metal salt
Azacycle
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Organic salt
Organic cobalt salt
Carbonyl group
Imine
Hydrocarbon derivative
Organic cation
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

cobyrinic acid (CHEBI:33907 )
cobalt-corrinoid heptacarboxylic acid (CHEBI:33907 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0074 g/L	ALOGPS
logP	1.9	ALOGPS
logP	-0.37	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	3.22	ChemAxon
pKa (Strongest Basic)	8.52	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	301.42 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	224.54 m³·mol⁻¹	ChemAxon
Polarizability	91.72 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

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0006918	Cobalt-precorrin 8	Cobyrinate	Not Available		VMH	30371894
MMDBr0006920	Cobyrinate	Cob(II)yrinate a,c diamide	Not Available		VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	122	Human feces; Human ; Human pleural fluid plaque	Metabolic reconstruction
Bacteria	Actinobacteria	75	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Firmicutes	208	Human feces; Human ; Cattle ; Human stool; Human saliva	Metabolic reconstruction
Bacteria	Bacteroidetes	104	Human feces; Human appendix biopsy; Human ; Human stool; Human urine; Human gastric fluid; Human saliva; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

17625694

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16722116

PDB ID

Not Available

ChEBI ID

33907

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for Cobyrinate (MMDBc0048054)

MOL for #<Metabolite:0x00007fdb4000cbe8>

3D MOL for #<Metabolite:0x00007fdb4000cbe8>

3D SDF for #<Metabolite:0x00007fdb4000cbe8>

3D-SDF for #<Metabolite:0x00007fdb4000cbe8>

PDB for #<Metabolite:0x00007fdb4000cbe8>

3D PDB for #<Metabolite:0x00007fdb4000cbe8>

SMILES for #<Metabolite:0x00007fdb4000cbe8>

INCHI for #<Metabolite:0x00007fdb4000cbe8>

Structure for #<Metabolite:0x00007fdb4000cbe8>

3D Structure for #<Metabolite:0x00007fdb4000cbe8>