MiMeDB: Showing metabocard for Hydrogenobyrinate a,c diamide (MMDBc0048057)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-04-29 21:47:06 UTC

Update Date

2025-10-07 16:08:10 UTC

Metabolite ID

MMDBc0048057

Metabolite Identification

Common Name

Hydrogenobyrinate a,c diamide

Description

Hydrogenobyrinate a,c diamide is a member of the class of metabolites known as amides. There is little literature available on this metabolite, indicating that it may not be extensively studied or characterized in biomedical research.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304292223472D          

 64 68  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
    3.5659   -0.5381    0.0000 N   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
    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 N   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
   -0.3584   -4.2998    0.0000 O   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
    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 N   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
    5.9118   -4.4023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4738   -3.7032    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7363   -4.3726    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
    7.9964   -1.8039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7617   -2.1121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3469   -2.3126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7961    0.7768    0.0000 C   0  0  2  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
    3.9879    2.9511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1946    3.1776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5807    3.5249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9793    0.6610    0.0000 C   0  0  1  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
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  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
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  2 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  6  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 20 26  1  0  0  0  0
 16 26  1  0  0  0  0
 26 27  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  2  0  0  0  0
 13 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  6  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 35 37  2  0  0  0  0
 32 38  1  0  0  0  0
 11 38  1  0  0  0  0
 38 39  1  1  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 41 43  2  0  0  0  0
  9 44  1  0  0  0  0
 44 45  1  0  0  0  0
 44 46  1  0  0  0  0
 44 47  1  0  0  0  0
  7 47  1  0  0  0  0
 47 48  1  1  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 50 51  1  0  0  0  0
 50 52  2  0  0  0  0
  4 53  1  0  0  0  0
 53 54  1  6  0  0  0
 53 55  1  1  0  0  0
 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
 57 59  2  0  0  0  0
 53 60  1  0  0  0  0
  2 60  1  0  0  0  0
 60 61  1  6  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 62 64  2  0  0  0  0
M  END


  Mrv1652304292223472D          

 64 68  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
    3.5659   -0.5381    0.0000 N   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
    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 N   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
   -0.3584   -4.2998    0.0000 O   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
    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
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    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
    5.9118   -4.4023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4738   -3.7032    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7363   -4.3726    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
    7.9964   -1.8039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7617   -2.1121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3469   -2.3126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7961    0.7768    0.0000 C   0  0  2  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
    3.9879    2.9511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1946    3.1776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5807    3.5249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9793    0.6610    0.0000 C   0  0  1  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
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  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
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  2 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  6  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 20 26  1  0  0  0  0
 16 26  1  0  0  0  0
 26 27  1  1  0  0  0
 27 28  1  0  0  0  0
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 29 30  1  0  0  0  0
 29 31  2  0  0  0  0
 13 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  6  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 35 37  2  0  0  0  0
 32 38  1  0  0  0  0
 11 38  1  0  0  0  0
 38 39  1  1  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 41 43  2  0  0  0  0
  9 44  1  0  0  0  0
 44 45  1  0  0  0  0
 44 46  1  0  0  0  0
 44 47  1  0  0  0  0
  7 47  1  0  0  0  0
 47 48  1  1  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 50 51  1  0  0  0  0
 50 52  2  0  0  0  0
  4 53  1  0  0  0  0
 53 54  1  6  0  0  0
 53 55  1  1  0  0  0
 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
 57 59  2  0  0  0  0
 53 60  1  0  0  0  0
  2 60  1  0  0  0  0
 60 61  1  6  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 62 64  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0048057

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12N=C(\C(C)=C3/N=C(/C=C4\N=C(\C(\C)=C5/N[C@]1(C)[C@@](C)(CC(N)=O)[C@@H]5CCC(O)=O)[C@@](C)(CC(N)=O)[C@@H]4CCC(O)=O)C(C)(C)[C@@H]3CCC(O)=O)[C@](C)(CCC(O)=O)[C@H]2CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C45H62N6O12/c1-21-36-24(10-13-32(56)57)41(3,4)28(49-36)18-27-23(9-12-31(54)55)43(6,19-29(46)52)39(48-27)22(2)37-25(11-14-33(58)59)44(7,20-30(47)53)45(8,51-37)40-26(17-35(62)63)42(5,38(21)50-40)16-15-34(60)61/h18,23-26,40,51H,9-17,19-20H2,1-8H3,(H2,46,52)(H2,47,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/b27-18-,36-21-,37-22-/t23-,24-,25-,26+,40-,42-,43+,44+,45+/m1/s1

> <INCHI_KEY>
JJMDOVLPFPOLFZ-IPUCCYEASA-N

> <FORMULA>
C45H62N6O12

> <MOLECULAR_WEIGHT>
879.021

> <EXACT_MASS>
878.44257146

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
125

> <JCHEM_AVERAGE_POLARIZABILITY>
92.58424827310284

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(1R,2R,3R,4R,6Z,8S,11Z,13S,14S,16Z,18S,19S)-14,19-bis(carbamoylmethyl)-8,13,18-tris(2-carboxyethyl)-3-(carboxymethyl)-1,4,6,9,9,14,16,19-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-4-yl]propanoic acid

> <ALOGPS_LOGP>
0.87

> <JCHEM_LOGP>
-6.2523505892748945

> <ALOGPS_LOGS>
-4.88

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.9002053261031726

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4968408025990323

> <JCHEM_PKA_STRONGEST_BASIC>
8.972514269565089

> <JCHEM_POLAR_SURFACE_AREA>
321.78999999999996

> <JCHEM_REFRACTIVITY>
229.2895000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.15e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1R,2R,3R,4R,6Z,8S,11Z,13S,14S,16Z,18S,19S)-14,19-bis(carbamoylmethyl)-8,13,18-tris(2-carboxyethyl)-3-(carboxymethyl)-1,4,6,9,9,14,16,19-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-4-yl]propanoic acid

> <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  N   UNK     0       6.656  -1.004   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.763   0.067   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.639  -0.582   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.533   0.672   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.589  -1.794   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       9.729  -3.072   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      10.679  -4.284   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.838  -6.083   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.533  -6.900   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       7.352  -5.912   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       6.047  -6.729   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.346  -5.705   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.211  -6.745   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.669  -4.322   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       4.776  -3.251   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       4.099  -1.867   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.318  -0.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.575  -2.083   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.519  -0.544   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.038  -1.978   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.361  -0.594   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      -1.175  -0.489   0.000  0.00  0.00           N+0
HETATM   25  O   UNK     0       1.221   0.683   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       2.309  -3.600   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.926  -4.277   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.820  -5.813   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.563  -6.490   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -0.669  -8.026   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -1.841  -5.630   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       6.421  -8.223   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.896  -8.439   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.477  -9.762   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       5.172 -10.580   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0       5.227 -12.119   0.000  0.00  0.00           N+0
HETATM   37  O   UNK     0       3.811  -9.858   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       7.957  -8.329   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       8.775  -9.634   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      10.314  -9.578   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      11.035  -8.218   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      10.218  -6.913   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      12.574  -8.162   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      12.125  -3.756   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      13.650  -3.540   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      12.499  -5.250   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      12.070  -2.217   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      13.282  -1.267   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      14.710  -1.843   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      14.927  -3.367   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0      16.355  -3.943   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      13.714  -4.317   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0       7.086   1.450   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       8.533   1.978   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       6.712   2.944   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0       7.818   4.015   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       7.444   5.509   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0       5.963   5.931   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       8.551   6.580   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0       5.561   1.234   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       4.490   2.340   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       4.913   3.821   0.000  0.00  0.00           C+0
HETATM   63  O   UNK     0       3.842   4.928   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       6.407   4.196   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   18   60                                             
CONECT    3    2    4                                                       
CONECT    4    3    5   53                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   47                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   44                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   38                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   32                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   26                                                  
CONECT   17   16   18                                                       
CONECT   18   17    2   19   20                                             
CONECT   19   18                                                            
CONECT   20   18   21   22   26                                             
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   20   16   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   13   33   34   38                                             
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35                                                            
CONECT   38   32   11   39                                                  
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41                                                            
CONECT   44    9   45   46   47                                             
CONECT   45   44                                                            
CONECT   46   44                                                            
CONECT   47   44    7   48                                                  
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50                                                            
CONECT   53    4   54   55   60                                             
CONECT   54   53                                                            
CONECT   55   53   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58   59                                                  
CONECT   58   57                                                            
CONECT   59   57                                                            
CONECT   60   53    2   61                                                  
CONECT   61   60   62                                                       
CONECT   62   61   63   64                                                  
CONECT   63   62                                                            
CONECT   64   62                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  136    0
END

Synonyms

Value	Source
Hydrogenobyrinate a,c diamide	ChEBI
Hydrogenobyrinate diamide	ChEBI
Hydrogenobyrinic acid a,c diamide	ChEBI
Hydrogenobyrinic acid diamide	Generator
Hydrogenobyrinate a,c-diamide	Generator

Molecular Formula

C₄₅H₆₂N₆O₁₂

Average Mass

879.021

Monoisotopic Mass

878.44257146

IUPAC Name

3-[(1R,2R,3R,4R,6Z,8S,11Z,13S,14S,16Z,18S,19S)-14,19-bis(carbamoylmethyl)-8,13,18-tris(2-carboxyethyl)-3-(carboxymethyl)-1,4,6,9,9,14,16,19-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-4-yl]propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@]12N=C(\C(C)=C3/N=C(/C=C4\N=C(\C(\C)=C5/N[C@]1(C)[C@@](C)(CC(N)=O)[C@@H]5CCC(O)=O)[C@@](C)(CC(N)=O)[C@@H]4CCC(O)=O)C(C)(C)[C@@H]3CCC(O)=O)[C@](C)(CCC(O)=O)[C@H]2CC(O)=O

InChI Identifier

InChI=1S/C45H62N6O12/c1-21-36-24(10-13-32(56)57)41(3,4)28(49-36)18-27-23(9-12-31(54)55)43(6,19-29(46)52)39(48-27)22(2)37-25(11-14-33(58)59)44(7,20-30(47)53)45(8,51-37)40-26(17-35(62)63)42(5,38(21)50-40)16-15-34(60)61/h18,23-26,40,51H,9-17,19-20H2,1-8H3,(H2,46,52)(H2,47,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/b27-18-,36-21-,37-22-/t23-,24-,25-,26+,40-,42-,43+,44+,45+/m1/s1

InChI Key

JJMDOVLPFPOLFZ-IPUCCYEASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrapyrroles and derivatives. These are polycyclic aromatic compounds containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Not Available

Direct Parent

Tetrapyrroles and derivatives

Alternative Parents

Substituents

Tetrapyrrole skeleton
Pentacarboxylic acid or derivatives
Delta amino acid or derivatives
Pyrrolidine
Pyrroline
Amino acid or derivatives
Ketimine
Amino acid
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid derivative
Carboxylic acid
Secondary aliphatic amine
Enamine
Azacycle
Secondary amine
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Amine
Imine
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

precorrin (CHEBI:27914 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.012 g/L	ALOGPS
logP	0.87	ALOGPS
logP	-6.3	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	3.5	ChemAxon
pKa (Strongest Basic)	8.97	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	321.79 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	229.29 m³·mol⁻¹	ChemAxon
Polarizability	92.58 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	534.2
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	273.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	549.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	506.0
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	391.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	138.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	2591.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	417.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	425.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	300.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	345.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	152.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	189.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-24	264.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	259.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	127.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	322.5
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1546.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	955.3

Retention Indices

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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/Eubacteria	Proteobacteria	57	Human feces; Human pleural fluid plaque; Human	Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	143	Human feces; Human ; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	59	Human feces; Human ; Human urine	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	28	Human feces; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	18	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Bacteria	Firmicutes	1	Human feces; Human ; Human saliva	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

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

21864895

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

27914

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 Hydrogenobyrinate a,c diamide (MMDBc0048057)

MOL for #<Metabolite:0x00007f9ad11f8d58>

3D MOL for #<Metabolite:0x00007f9ad11f8d58>

3D SDF for #<Metabolite:0x00007f9ad11f8d58>

3D-SDF for #<Metabolite:0x00007f9ad11f8d58>

PDB for #<Metabolite:0x00007f9ad11f8d58>

3D PDB for #<Metabolite:0x00007f9ad11f8d58>

SMILES for #<Metabolite:0x00007f9ad11f8d58>

INCHI for #<Metabolite:0x00007f9ad11f8d58>

Structure for #<Metabolite:0x00007f9ad11f8d58>

3D Structure for #<Metabolite:0x00007f9ad11f8d58>