MiMeDB: Showing metabocard for 3-oxo-5,6-didehydrosuberyl-CoA (MMDBc0055402)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:51:13 UTC

Update Date

2025-10-07 16:09:06 UTC

Metabolite ID

MMDBc0055402

Metabolite Identification

Common Name

3-oxo-5,6-didehydrosuberyl-CoA

Description

3-oxo-5,6-didehydrosuberyl-CoA is a thioester compound belonging to the class of CoA derivatives. There is limited literature available on this metabolite, indicating that further research may be necessary to fully understand its biological significance and functions.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221512D          

 65 67  0  0  1  0            999 V2000
    9.8906   12.8384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2406   12.8384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2064   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4920   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9209   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2225   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6367   16.1384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6367   15.3134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2077   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4933   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3499   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2090    8.3009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0656   12.0134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1829    5.7786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4622    8.4116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6354   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9235    7.8884    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.9222   16.5509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9370   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0643   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3554    7.4195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8167    6.8964    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.0097    7.0679    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.0656   13.6634    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.0228    6.9346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6017    7.0840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3512   14.0759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2292    7.6108    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.0656   12.8384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7765    7.2702    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9222   17.3759    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.3512   14.9009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.9366    6.1141    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.5155    6.2635    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.2692    8.2400    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.0497    7.6971    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6354   16.5509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2077   16.1384    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.6514   17.3759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9370   18.6134    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0643   16.5509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.1523    6.1427    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7801   14.0759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6367   13.6634    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   10.8670    7.5554    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   10.3571    5.9862    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    9.8274    7.0257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9071   10.2529    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0821    8.8239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6051   10.7759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9551   10.7759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2090    9.1259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7801   11.6009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6772    8.2239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3966    6.5159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7801    9.9509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6120    6.7708    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.4946    9.5384    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    9.7801   10.7759    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.7788   17.7884    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   11.2316    7.4391    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2975    6.2552    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6228    7.6199    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3512   13.2509    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6785    6.9189    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  4  6  1  4  0  0  0
  8  7  1  0  0  0  0
 10  9  1  0  0  0  0
 16  5  1  0  0  0  0
 16 11  1  0  0  0  0
 17 12  1  1  0  0  0
 18  7  1  0  0  0  0
 19  6  1  0  0  0  0
 20 11  1  0  0  0  0
 23 17  1  0  0  0  0
 23 22  1  0  0  0  0
 25 21  2  0  0  0  0
 26 21  1  0  0  0  0
 27 24  1  0  0  0  0
 28 22  1  0  0  0  0
 29  1  1  0  0  0  0
 29  2  1  0  0  0  0
 29 13  1  0  0  0  0
 29 24  1  0  0  0  0
 30 25  1  0  0  0  0
 31  9  1  4  0  0  0
 31 18  2  0  0  0  0
 32  8  1  4  0  0  0
 32 27  2  0  0  0  0
 33 14  2  0  0  0  0
 33 25  1  0  0  0  0
 34 14  1  0  0  0  0
 34 26  2  0  0  0  0
 35 15  2  0  0  0  0
 35 21  1  0  0  0  0
 36 15  1  0  0  0  0
 36 26  1  0  0  0  0
 28 36  1  1  0  0  0
 37 16  2  0  0  0  0
 38 18  1  0  0  0  0
 39 19  2  0  0  0  0
 40 19  1  0  0  0  0
 41 20  2  0  0  0  0
 22 42  1  6  0  0  0
 24 43  1  1  0  0  0
 44 27  1  0  0  0  0
 52 12  1  0  0  0  0
 53 13  1  0  0  0  0
 54 17  1  0  0  0  0
 54 28  1  0  0  0  0
 23 55  1  1  0  0  0
 57 45  1  0  0  0  0
 57 46  1  0  0  0  0
 57 47  2  0  0  0  0
 57 55  1  0  0  0  0
 58 48  1  0  0  0  0
 58 49  2  0  0  0  0
 58 52  1  0  0  0  0
 58 56  1  0  0  0  0
 59 50  1  0  0  0  0
 59 51  2  0  0  0  0
 59 53  1  0  0  0  0
 59 56  1  0  0  0  0
 60 10  1  0  0  0  0
 60 20  1  0  0  0  0
 17 61  1  6  0  0  0
 22 62  1  1  0  0  0
 23 63  1  1  0  0  0
 24 64  1  1  0  0  0
 28 65  1  6  0  0  0
M  CHG  5  38  -1  40  -1  44  -1  45  -1  46  -1
M  END


  Mrv1652306172221512D          

 65 67  0  0  1  0            999 V2000
    9.8906   12.8384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2406   12.8384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2064   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4920   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9209   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2225   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6367   16.1384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6367   15.3134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2077   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4933   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3499   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2090    8.3009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0656   12.0134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1829    5.7786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4622    8.4116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6354   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9235    7.8884    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.9222   16.5509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9370   17.7884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0643   17.3759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3554    7.4195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8167    6.8964    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.0097    7.0679    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.0656   13.6634    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.0228    6.9346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6017    7.0840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3512   14.0759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2292    7.6108    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.0656   12.8384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7765    7.2702    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9222   17.3759    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.3512   14.9009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.9366    6.1141    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.5155    6.2635    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.2692    8.2400    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.0497    7.6971    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6354   16.5509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2077   16.1384    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.6514   17.3759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9370   18.6134    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0643   16.5509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.1523    6.1427    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7801   14.0759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6367   13.6634    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   10.8670    7.5554    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   10.3571    5.9862    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    9.8274    7.0257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9071   10.2529    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0821    8.8239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6051   10.7759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9551   10.7759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2090    9.1259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7801   11.6009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6772    8.2239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3966    6.5159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7801    9.9509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6120    6.7708    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.4946    9.5384    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    9.7801   10.7759    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.7788   17.7884    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   11.2316    7.4391    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2975    6.2552    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6228    7.6199    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3512   13.2509    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6785    6.9189    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  4  6  1  4  0  0  0
  8  7  1  0  0  0  0
 10  9  1  0  0  0  0
 16  5  1  0  0  0  0
 16 11  1  0  0  0  0
 17 12  1  1  0  0  0
 18  7  1  0  0  0  0
 19  6  1  0  0  0  0
 20 11  1  0  0  0  0
 23 17  1  0  0  0  0
 23 22  1  0  0  0  0
 25 21  2  0  0  0  0
 26 21  1  0  0  0  0
 27 24  1  0  0  0  0
 28 22  1  0  0  0  0
 29  1  1  0  0  0  0
 29  2  1  0  0  0  0
 29 13  1  0  0  0  0
 29 24  1  0  0  0  0
 30 25  1  0  0  0  0
 31  9  1  4  0  0  0
 31 18  2  0  0  0  0
 32  8  1  4  0  0  0
 32 27  2  0  0  0  0
 33 14  2  0  0  0  0
 33 25  1  0  0  0  0
 34 14  1  0  0  0  0
 34 26  2  0  0  0  0
 35 15  2  0  0  0  0
 35 21  1  0  0  0  0
 36 15  1  0  0  0  0
 36 26  1  0  0  0  0
 28 36  1  1  0  0  0
 37 16  2  0  0  0  0
 38 18  1  0  0  0  0
 39 19  2  0  0  0  0
 40 19  1  0  0  0  0
 41 20  2  0  0  0  0
 22 42  1  6  0  0  0
 24 43  1  1  0  0  0
 44 27  1  0  0  0  0
 52 12  1  0  0  0  0
 53 13  1  0  0  0  0
 54 17  1  0  0  0  0
 54 28  1  0  0  0  0
 23 55  1  1  0  0  0
 57 45  1  0  0  0  0
 57 46  1  0  0  0  0
 57 47  2  0  0  0  0
 57 55  1  0  0  0  0
 58 48  1  0  0  0  0
 58 49  2  0  0  0  0
 58 52  1  0  0  0  0
 58 56  1  0  0  0  0
 59 50  1  0  0  0  0
 59 51  2  0  0  0  0
 59 53  1  0  0  0  0
 59 56  1  0  0  0  0
 60 10  1  0  0  0  0
 60 20  1  0  0  0  0
 17 61  1  6  0  0  0
 22 62  1  1  0  0  0
 23 63  1  1  0  0  0
 24 64  1  1  0  0  0
 28 65  1  6  0  0  0
M  CHG  5  38  -1  40  -1  44  -1  45  -1  46  -1
M  END
> <DATABASE_ID>
MMDBc0055402

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(C([O-])=NCCC([O-])=NCCSC(=O)CC(=O)CC=CCC([O-])=O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C29H44N7O20P3S/c1-29(2,24(43)27(44)32-8-7-18(38)31-9-10-60-20(41)11-16(37)5-3-4-6-19(39)40)13-53-59(50,51)56-58(48,49)52-12-17-23(55-57(45,46)47)22(42)28(54-17)36-15-35-21-25(30)33-14-34-26(21)36/h3-4,14-15,17,22-24,28,42-43H,5-13H2,1-2H3,(H,31,38)(H,32,44)(H,39,40)(H,48,49)(H,50,51)(H2,30,33,34)(H2,45,46,47)/p-5/t17-,22-,23-,24+,28-/m1/s1

> <INCHI_KEY>
IFFFDKYRRUVOFP-NOQDIWQESA-I

> <FORMULA>
C29H39N7O20P3S

> <MOLECULAR_WEIGHT>
930.64

> <EXACT_MASS>
930.121086751

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_ATOM_COUNT>
99

> <JCHEM_AVERAGE_POLARIZABILITY>
81.02104763202871

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
8-({2-[(3-{[(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-3,3-dimethyl-1-oxidobutylidene]amino}-1-oxidopropylidene)amino]ethyl}sulfanyl)-6,8-dioxooct-3-enoate

> <JCHEM_LOGP>
-3.673353764561108

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
1.8870489500438392

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8192159282875604

> <JCHEM_PKA_STRONGEST_BASIC>
4.315502071756337

> <JCHEM_POLAR_SURFACE_AREA>
439.13000000000005

> <JCHEM_REFRACTIVITY>
234.0528000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
26

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
8-({2-[(3-{[(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-2-hydroxy-3,3-dimethyl-1-oxidobutylidene]amino}-1-oxidopropylidene)amino]ethyl}sulfanyl)-6,8-dioxooct-3-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      18.462  23.965   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      15.382  23.965   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.252  32.435   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.918  33.205   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.586  33.205   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.415  32.435   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.255  30.125   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.255  28.585   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.588  33.205   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.254  32.435   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.253  33.205   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      20.924  15.495   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      16.922  22.425   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      28.341  10.787   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      26.996  15.702   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.919  32.435   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      22.257  14.725   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.921  30.895   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.749  33.205   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.587  32.435   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      28.663  13.850   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      23.925  12.873   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      22.418  13.193   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      16.922  25.505   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      29.909  12.945   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      27.257  13.223   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      15.589  26.275   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      24.695  14.207   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      16.922  23.965   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      31.316  13.571   0.000  0.00  0.00           N+0
HETATM   31  N   UNK     0      12.921  32.435   0.000  0.00  0.00           N+0
HETATM   32  N   UNK     0      15.589  27.815   0.000  0.00  0.00           N+0
HETATM   33  N   UNK     0      29.748  11.413   0.000  0.00  0.00           N+0
HETATM   34  N   UNK     0      27.096  11.692   0.000  0.00  0.00           N+0
HETATM   35  N   UNK     0      28.502  15.381   0.000  0.00  0.00           N+0
HETATM   36  N   UNK     0      26.226  14.368   0.000  0.00  0.00           N+0
HETATM   37  O   UNK     0       4.919  30.895   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      11.588  30.125   0.000  0.00  0.00           O-1
HETATM   39  O   UNK     0      -3.083  32.435   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      -1.749  34.745   0.000  0.00  0.00           O-1
HETATM   41  O   UNK     0       7.587  30.895   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      24.551  11.466   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      18.256  26.275   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      14.255  25.505   0.000  0.00  0.00           O-1
HETATM   45  O   UNK     0      20.285  14.103   0.000  0.00  0.00           O-1
HETATM   46  O   UNK     0      19.333  11.174   0.000  0.00  0.00           O-1
HETATM   47  O   UNK     0      18.344  13.115   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      20.360  19.139   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      18.820  16.471   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      19.796  20.115   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      16.716  20.115   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      20.924  17.035   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      18.256  21.655   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      23.664  15.351   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      21.274  12.163   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      18.256  18.575   0.000  0.00  0.00           O+0
HETATM   57  P   UNK     0      19.809  12.639   0.000  0.00  0.00           P+0
HETATM   58  P   UNK     0      19.590  17.805   0.000  0.00  0.00           P+0
HETATM   59  P   UNK     0      18.256  20.115   0.000  0.00  0.00           P+0
HETATM   60  S   UNK     0       8.920  33.205   0.000  0.00  0.00           S+0
HETATM   61  H   UNK     0      20.966  13.886   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0      22.955  11.676   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0      23.563  14.224   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0      15.589  24.735   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0      25.533  12.915   0.000  0.00  0.00           H+0
CONECT    1   29                                                            
CONECT    2   29                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    3   16                                                       
CONECT    6    4   19                                                       
CONECT    7    8   18                                                       
CONECT    8    7   32                                                       
CONECT    9   10   31                                                       
CONECT   10    9   60                                                       
CONECT   11   16   20                                                       
CONECT   12   17   52                                                       
CONECT   13   29   53                                                       
CONECT   14   33   34                                                       
CONECT   15   35   36                                                       
CONECT   16    5   11   37                                                  
CONECT   17   12   23   54   61                                             
CONECT   18    7   31   38                                                  
CONECT   19    6   39   40                                                  
CONECT   20   11   41   60                                                  
CONECT   21   25   26   35                                                  
CONECT   22   23   28   42   62                                             
CONECT   23   17   22   55   63                                             
CONECT   24   27   29   43   64                                             
CONECT   25   21   30   33                                                  
CONECT   26   21   34   36                                                  
CONECT   27   24   32   44                                                  
CONECT   28   22   36   54   65                                             
CONECT   29    1    2   13   24                                             
CONECT   30   25                                                            
CONECT   31    9   18                                                       
CONECT   32    8   27                                                       
CONECT   33   14   25                                                       
CONECT   34   14   26                                                       
CONECT   35   15   21                                                       
CONECT   36   15   26   28                                                  
CONECT   37   16                                                            
CONECT   38   18                                                            
CONECT   39   19                                                            
CONECT   40   19                                                            
CONECT   41   20                                                            
CONECT   42   22                                                            
CONECT   43   24                                                            
CONECT   44   27                                                            
CONECT   45   57                                                            
CONECT   46   57                                                            
CONECT   47   57                                                            
CONECT   48   58                                                            
CONECT   49   58                                                            
CONECT   50   59                                                            
CONECT   51   59                                                            
CONECT   52   12   58                                                       
CONECT   53   13   59                                                       
CONECT   54   17   28                                                       
CONECT   55   23   57                                                       
CONECT   56   58   59                                                       
CONECT   57   45   46   47   55                                             
CONECT   58   48   49   52   56                                             
CONECT   59   50   51   53   56                                             
CONECT   60   10   20                                                       
CONECT   61   17                                                            
CONECT   62   22                                                            
CONECT   63   23                                                            
CONECT   64   24                                                            
CONECT   65   28                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  134    0
END

Synonyms

Value	Source
3'-Phosphoadenosine 5'-{3-[(3R)-4-({3-[(2-{[3-oxo-5,6-dehydro-7-carboxylatoheptanoyl]sulfanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl] diphosphate}	ChEBI
3-oxo-5,6-Dehydrosuberyl-CoA pentaanion	ChEBI
3-oxo-5,6-Didehydrosuberyl-CoA	ChEBI
3'-Phosphoadenosine 5'-{3-[(3R)-4-({3-[(2-{[3-oxo-5,6-dehydro-7-carboxylatoheptanoyl]sulfanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl] diphosphoric acid}	Generator
3'-Phosphoadenosine 5'-{3-[(3R)-4-({3-[(2-{[3-oxo-5,6-dehydro-7-carboxylatoheptanoyl]sulphanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl] diphosphate}	Generator
3'-Phosphoadenosine 5'-{3-[(3R)-4-({3-[(2-{[3-oxo-5,6-dehydro-7-carboxylatoheptanoyl]sulphanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl] diphosphoric acid}	Generator

Molecular Formula

C₂₉H₃₉N₇O₂₀P₃S

Average Mass

930.64

Monoisotopic Mass

930.121086751

IUPAC Name

8-({2-[(3-{[(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-3,3-dimethyl-1-oxidobutylidene]amino}-1-oxidopropylidene)amino]ethyl}sulfanyl)-6,8-dioxooct-3-enoate

Traditional Name

8-({2-[(3-{[(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-2-hydroxy-3,3-dimethyl-1-oxidobutylidene]amino}-1-oxidopropylidene)amino]ethyl}sulfanyl)-6,8-dioxooct-3-enoate

CAS Registry Number

Not Available

SMILES

[H][C@](O)(C([O-])=NCCC([O-])=NCCSC(=O)CC(=O)CC=CCC([O-])=O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP([O-])([O-])=O

InChI Identifier

InChI=1S/C29H44N7O20P3S/c1-29(2,24(43)27(44)32-8-7-18(38)31-9-10-60-20(41)11-16(37)5-3-4-6-19(39)40)13-53-59(50,51)56-58(48,49)52-12-17-23(55-57(45,46)47)22(42)28(54-17)36-15-35-21-25(30)33-14-34-26(21)36/h3-4,14-15,17,22-24,28,42-43H,5-13H2,1-2H3,(H,31,38)(H,32,44)(H,39,40)(H,48,49)(H,50,51)(H2,30,33,34)(H2,45,46,47)/p-5/t17-,22-,23-,24+,28-/m1/s1

InChI Key

IFFFDKYRRUVOFP-NOQDIWQESA-I

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-oxo-acyl coas. These are organic compounds containing a 3-oxo acylated coenzyme A derivative.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl thioesters

Direct Parent

3-oxo-acyl CoAs

Alternative Parents

Substituents

Coenzyme a or derivatives
Purine ribonucleoside 3',5'-bisphosphate
Purine ribonucleoside bisphosphate
Purine ribonucleoside diphosphate
Ribonucleoside 3'-phosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-aminopurine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Medium-chain fatty acid
Aminopyrimidine
Hydroxy fatty acid
Monoalkyl phosphate
Alkyl phosphate
1,3-dicarbonyl compound
Unsaturated fatty acid
Organic phosphoric acid derivative
N-substituted imidazole
Pyrimidine
Monosaccharide
Imidolactam
Fatty acid
Phosphoric acid ester
Heteroaromatic compound
Tetrahydrofuran
Azole
Imidazole
Amino acid
Ketone
Carbothioic s-ester
Secondary alcohol
Amino acid or derivatives
Thiocarboxylic acid ester
Sulfenyl compound
Thiocarboxylic acid or derivatives
Organoheterocyclic compound
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid derivative
Carboxylic acid
Azacycle
Oxacycle
Monocarboxylic acid or derivatives
Organopnictogen compound
Organic oxygen compound
Organic oxide
Alcohol
Primary amine
Carbonyl group
Amine
Organic nitrogen compound
Hydrocarbon derivative
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

acyl-CoA oxoanion (CHEBI:63255 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.7	ChemAxon
pKa (Strongest Acidic)	0.82	ChemAxon
pKa (Strongest Basic)	4.32	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	22	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	439.13 Å²	ChemAxon
Rotatable Bond Count	26	ChemAxon
Refractivity	234.05 m³·mol⁻¹	ChemAxon
Polarizability	81.02 Å³	ChemAxon
Number of Rings	3	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	Deposition Date	View
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 (void)	2025-10-24	581.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	386.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	459.7
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	481.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	368.7
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	167.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1972.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	449.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	347.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	162.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	207.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	162.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	124.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	294.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	363.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	97.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	225.0
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	964.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	772.6

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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	Proteobacteria	1

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

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

26333057

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139031574

PDB ID

Not Available

ChEBI ID

63255

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 3-oxo-5,6-didehydrosuberyl-CoA (MMDBc0055402)

MOL for #<Metabolite:0x000055c207a62c40>

3D MOL for #<Metabolite:0x000055c207a62c40>

3D SDF for #<Metabolite:0x000055c207a62c40>

3D-SDF for #<Metabolite:0x000055c207a62c40>

PDB for #<Metabolite:0x000055c207a62c40>

3D PDB for #<Metabolite:0x000055c207a62c40>

SMILES for #<Metabolite:0x000055c207a62c40>

INCHI for #<Metabolite:0x000055c207a62c40>

Structure for #<Metabolite:0x000055c207a62c40>

3D Structure for #<Metabolite:0x000055c207a62c40>