MiMeDB: Showing metabocard for Gramillin B (MMDBc0022796)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 12:51:26 UTC

Update Date

2022-08-31 06:47:52 UTC

Metabolite ID

MMDBc0022796

Metabolite Identification

Common Name

Gramillin B

Description

Gramillin B belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. Gramillin B is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152114512D          

 66 67  0  0  1  0            999 V2000
    8.2231   -1.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5547    6.7183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9636    6.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9375   -1.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6520   -1.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3665   -1.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0810   -1.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7954   -1.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5099   -1.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4360    5.8153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6369    6.0204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2244   -1.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1589    5.4178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0528    5.3789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4066   -0.2454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1163    2.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4075    0.3951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2556    2.1972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1903    6.1924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8119    6.0204    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.2244   -0.5361    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.6884    4.8531    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.9714    0.3560    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.9396    2.5485    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.6611    0.7463    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.5091    2.5485    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.6034   -0.0571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7603    4.8531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3650    0.7327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0128    5.8153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0429   -0.4327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2464    4.1565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6388   -0.1290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0942    1.7381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3816    1.5226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4573    3.3719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7085    6.8389    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.9297    1.3341    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.4059   -0.4327    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.2898    5.4178    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.4455    0.9916    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.9914    3.3719    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.8099   -0.1290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.7329    2.2690    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.6597    3.1839    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0387   -0.6585    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3960    5.3789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5618    0.9211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7091    6.5823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2480   -1.2317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4999    4.5078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2414   -0.8519    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3096    1.4832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5575    1.5614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2677    3.5265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2024    4.1565    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1838    0.6745    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   17.5350    1.4210    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   12.9153    5.2019    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2244    0.2889    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3241    4.3272    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5361    0.9574    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7630    2.6003    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.2713    1.3016    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.4702    1.7244    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1682    0.5443    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 19  2  1  0  0  0  0
 19  3  1  0  0  0  0
 19 14  1  0  0  0  0
 20 11  1  0  0  0  0
 21 12  1  1  0  0  0
 22 14  1  1  0  0  0
 23 15  1  1  0  0  0
 24 16  1  1  0  0  0
 25 17  1  0  0  0  0
 26 18  1  0  0  0  0
 27 15  1  0  0  0  0
 28 13  1  0  0  0  0
 29 27  1  0  0  0  0
 30 20  1  0  0  0  0
 31 21  1  0  0  0  0
 32 22  1  0  0  0  0
 33 23  1  0  0  0  0
 34 24  1  0  0  0  0
 35 25  1  0  0  0  0
 36 26  1  0  0  0  0
 20 37  1  6  0  0  0
 38 29  2  0  0  0  0
 39 21  1  0  0  0  0
 39 33  2  0  0  0  0
 40 22  1  0  0  0  0
 40 30  2  0  0  0  0
 41 23  1  0  0  0  0
 41 34  2  0  0  0  0
 42 24  1  0  0  0  0
 42 32  2  0  0  0  0
 43 25  1  0  0  0  0
 43 31  2  0  0  0  0
 44 26  1  0  0  0  0
 44 35  2  0  0  0  0
 45 16  1  0  0  0  0
 46 27  1  0  0  0  0
 47 28  2  0  0  0  0
 48 29  1  0  0  0  0
 30 49  1  4  0  0  0
 31 50  1  4  0  0  0
 32 51  1  4  0  0  0
 33 52  1  4  0  0  0
 34 53  1  4  0  0  0
 35 54  1  4  0  0  0
 55 36  2  0  0  0  0
 56 28  1  0  0  0  0
 56 36  1  0  0  0  0
 57 17  1  0  0  0  0
 58 18  1  0  0  0  0
 58 57  1  0  0  0  0
 20 59  1  6  0  0  0
 21 60  1  1  0  0  0
 22 61  1  1  0  0  0
 23 62  1  1  0  0  0
 24 63  1  1  0  0  0
 25 64  1  1  0  0  0
 26 65  1  1  0  0  0
 66 27  1  0  0  0  0
M  END


  Mrv1652305152114512D          

 66 67  0  0  1  0            999 V2000
    8.2231   -1.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5547    6.7183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9636    6.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9375   -1.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6520   -1.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3665   -1.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0810   -1.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7954   -1.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5099   -1.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4360    5.8153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6369    6.0204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2244   -1.3611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1589    5.4178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0528    5.3789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4066   -0.2454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1163    2.4967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4075    0.3951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2556    2.1972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1903    6.1924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8119    6.0204    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.2244   -0.5361    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.6884    4.8531    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.9714    0.3560    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.9396    2.5485    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.6611    0.7463    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.5091    2.5485    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.6034   -0.0571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7603    4.8531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3650    0.7327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0128    5.8153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0429   -0.4327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2464    4.1565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6388   -0.1290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0942    1.7381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3816    1.5226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4573    3.3719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7085    6.8389    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.9297    1.3341    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.4059   -0.4327    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.2898    5.4178    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.4455    0.9916    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.9914    3.3719    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.8099   -0.1290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.7329    2.2690    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.6597    3.1839    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0387   -0.6585    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3960    5.3789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5618    0.9211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7091    6.5823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2480   -1.2317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4999    4.5078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2414   -0.8519    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3096    1.4832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5575    1.5614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2677    3.5265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2024    4.1565    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1838    0.6745    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   17.5350    1.4210    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   12.9153    5.2019    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2244    0.2889    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3241    4.3272    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5361    0.9574    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7630    2.6003    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.2713    1.3016    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.4702    1.7244    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1682    0.5443    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 19  2  1  0  0  0  0
 19  3  1  0  0  0  0
 19 14  1  0  0  0  0
 20 11  1  0  0  0  0
 21 12  1  1  0  0  0
 22 14  1  1  0  0  0
 23 15  1  1  0  0  0
 24 16  1  1  0  0  0
 25 17  1  0  0  0  0
 26 18  1  0  0  0  0
 27 15  1  0  0  0  0
 28 13  1  0  0  0  0
 29 27  1  0  0  0  0
 30 20  1  0  0  0  0
 31 21  1  0  0  0  0
 32 22  1  0  0  0  0
 33 23  1  0  0  0  0
 34 24  1  0  0  0  0
 35 25  1  0  0  0  0
 36 26  1  0  0  0  0
 20 37  1  6  0  0  0
 38 29  2  0  0  0  0
 39 21  1  0  0  0  0
 39 33  2  0  0  0  0
 40 22  1  0  0  0  0
 40 30  2  0  0  0  0
 41 23  1  0  0  0  0
 41 34  2  0  0  0  0
 42 24  1  0  0  0  0
 42 32  2  0  0  0  0
 43 25  1  0  0  0  0
 43 31  2  0  0  0  0
 44 26  1  0  0  0  0
 44 35  2  0  0  0  0
 45 16  1  0  0  0  0
 46 27  1  0  0  0  0
 47 28  2  0  0  0  0
 48 29  1  0  0  0  0
 30 49  1  4  0  0  0
 31 50  1  4  0  0  0
 32 51  1  4  0  0  0
 33 52  1  4  0  0  0
 34 53  1  4  0  0  0
 35 54  1  4  0  0  0
 55 36  2  0  0  0  0
 56 28  1  0  0  0  0
 56 36  1  0  0  0  0
 57 17  1  0  0  0  0
 58 18  1  0  0  0  0
 58 57  1  0  0  0  0
 20 59  1  6  0  0  0
 21 60  1  1  0  0  0
 22 61  1  1  0  0  0
 23 62  1  1  0  0  0
 24 63  1  1  0  0  0
 25 64  1  1  0  0  0
 26 65  1  1  0  0  0
 66 27  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0022796

> <DATABASE_NAME>
MIME

> <SMILES>
[H]C(O)(C[C@]1([H])N=C(O)[C@]([H])(CO)N=C(O)[C@]([H])(CC(C)C)N=C(O)[C@@]([H])(N)CCCC(=O)OC(=O)[C@]2([H])CSSC[C@]([H])(N=C(O)[C@]([H])(CCCCCCCC)N=C1O)C(O)=N2)C(O)=N

> <INCHI_IDENTIFIER>
InChI=1S/C36H60N8O12S2/c1-4-5-6-7-8-9-12-21-31(50)43-25-17-57-58-18-26(44-35(25)54)36(55)56-28(47)13-10-11-20(37)30(49)40-22(14-19(2)3)32(51)42-24(16-45)34(53)41-23(33(52)39-21)15-27(46)29(38)48/h19-27,45-46H,4-18,37H2,1-3H3,(H2,38,48)(H,39,52)(H,40,49)(H,41,53)(H,42,51)(H,43,50)(H,44,54)/t20-,21-,22-,23-,24-,25-,26-,27?/m0/s1

> <INCHI_KEY>
ABYJOODEAJNHBQ-HRQFAISJSA-N

> <FORMULA>
C36H60N8O12S2

> <MOLECULAR_WEIGHT>
861.04

> <EXACT_MASS>
860.377211752

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
118

> <JCHEM_AVERAGE_POLARIZABILITY>
89.0705479010934

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(1R,4S,7S,10S,13S,16S,23R)-16-amino-3,6,9,12,15,28-hexahydroxy-10-(hydroxymethyl)-13-(2-methylpropyl)-4-octyl-20,22-dioxo-21-oxa-25,26-dithia-2,5,8,11,14,29-hexaazabicyclo[21.4.2]nonacosa-2,5,8,11,14,28-hexaen-7-yl]-2-hydroxypropanimidic acid

> <ALOGPS_LOGP>
1.30

> <JCHEM_LOGP>
0.5470609617190588

> <ALOGPS_LOGS>
-3.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
3.0301475388986936

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.6178087445351372

> <JCHEM_PKA_STRONGEST_BASIC>
9.612501898396971

> <JCHEM_POLAR_SURFACE_AREA>
349.47

> <JCHEM_REFRACTIVITY>
225.82020000000009

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.89e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1R,4S,7S,10S,13S,16S,23R)-16-amino-3,6,9,12,15,28-hexahydroxy-10-(hydroxymethyl)-13-(2-methylpropyl)-4-octyl-20,22-dioxo-21-oxa-25,26-dithia-2,5,8,11,14,29-hexaazabicyclo[21.4.2]nonacosa-2,5,8,11,14,28-hexaen-7-yl]-2-hydroxypropanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      15.350  -3.311   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.835  12.541   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      20.465  12.096   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.683  -2.541   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      18.017  -3.311   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      19.351  -2.541   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      20.684  -3.311   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      22.018  -2.541   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      23.352  -3.311   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.947  10.855   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      25.455  11.238   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.685  -2.541   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      28.297  10.113   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      18.765  10.041   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      19.426  -0.458   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      17.017   4.661   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      30.627   0.737   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      32.210   4.102   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      19.022  11.559   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      23.915  11.238   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      24.685  -1.001   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      19.952   9.059   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      20.480   0.664   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      18.554   4.757   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      29.234   1.393   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      30.817   4.757   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      17.926  -0.106   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      29.419   9.059   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      17.481   1.368   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      22.424  10.855   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      26.213  -0.808   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      19.127   7.759   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      21.726  -0.241   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      18.843   3.244   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      28.712   2.842   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      30.720   6.294   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0      23.722  12.766   0.000  0.00  0.00           N+0
HETATM   38  N   UNK     0      18.535   2.490   0.000  0.00  0.00           N+0
HETATM   39  N   UNK     0      23.158  -0.808   0.000  0.00  0.00           N+0
HETATM   40  N   UNK     0      21.074  10.113   0.000  0.00  0.00           N+0
HETATM   41  N   UNK     0      19.498   1.851   0.000  0.00  0.00           N+0
HETATM   42  N   UNK     0      18.651   6.294   0.000  0.00  0.00           N+0
HETATM   43  N   UNK     0      27.645  -0.241   0.000  0.00  0.00           N+0
HETATM   44  N   UNK     0      29.368   4.236   0.000  0.00  0.00           N+0
HETATM   45  O   UNK     0      16.165   5.943   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      16.872  -1.229   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      30.606  10.041   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      15.982   1.719   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      21.857  12.287   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      26.596  -2.299   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      17.733   8.414   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      20.984  -1.590   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      17.378   2.769   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      27.174   2.915   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      32.233   6.583   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      30.244   7.759   0.000  0.00  0.00           O+0
HETATM   57  S   UNK     0      32.076   1.259   0.000  0.00  0.00           S+0
HETATM   58  S   UNK     0      32.732   2.653   0.000  0.00  0.00           S+0
HETATM   59  H   UNK     0      24.109   9.710   0.000  0.00  0.00           H+0
HETATM   60  H   UNK     0      24.685   0.539   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0      21.138   8.077   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0      21.534   1.787   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0      20.091   4.854   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0      30.373   2.430   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0      30.744   3.219   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0      18.981   1.016   0.000  0.00  0.00           H+0
CONECT    1    4                                                            
CONECT    2   19                                                            
CONECT    3   19                                                            
CONECT    4    1    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   12                                                       
CONECT   10   11   13                                                       
CONECT   11   10   20                                                       
CONECT   12    9   21                                                       
CONECT   13   10   28                                                       
CONECT   14   19   22                                                       
CONECT   15   23   27                                                       
CONECT   16   24   45                                                       
CONECT   17   25   57                                                       
CONECT   18   26   58                                                       
CONECT   19    2    3   14                                                  
CONECT   20   11   30   37   59                                             
CONECT   21   12   31   39   60                                             
CONECT   22   14   32   40   61                                             
CONECT   23   15   33   41   62                                             
CONECT   24   16   34   42   63                                             
CONECT   25   17   35   43   64                                             
CONECT   26   18   36   44   65                                             
CONECT   27   15   29   46   66                                             
CONECT   28   13   47   56                                                  
CONECT   29   27   38   48                                                  
CONECT   30   20   40   49                                                  
CONECT   31   21   43   50                                                  
CONECT   32   22   42   51                                                  
CONECT   33   23   39   52                                                  
CONECT   34   24   41   53                                                  
CONECT   35   25   44   54                                                  
CONECT   36   26   55   56                                                  
CONECT   37   20                                                            
CONECT   38   29                                                            
CONECT   39   21   33                                                       
CONECT   40   22   30                                                       
CONECT   41   23   34                                                       
CONECT   42   24   32                                                       
CONECT   43   25   31                                                       
CONECT   44   26   35                                                       
CONECT   45   16                                                            
CONECT   46   27                                                            
CONECT   47   28                                                            
CONECT   48   29                                                            
CONECT   49   30                                                            
CONECT   50   31                                                            
CONECT   51   32                                                            
CONECT   52   33                                                            
CONECT   53   34                                                            
CONECT   54   35                                                            
CONECT   55   36                                                            
CONECT   56   28   36                                                       
CONECT   57   17   58                                                       
CONECT   58   18   57                                                       
CONECT   59   20                                                            
CONECT   60   21                                                            
CONECT   61   22                                                            
CONECT   62   23                                                            
CONECT   63   24                                                            
CONECT   64   25                                                            
CONECT   65   26                                                            
CONECT   66   27                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  134    0
END

Synonyms

Not Available

Molecular Formula

C₃₆H₆₀N₈O₁₂S₂

Average Mass

861.04

Monoisotopic Mass

860.377211752

IUPAC Name

3-[(1R,4S,7S,10S,13S,16S,23R)-16-amino-3,6,9,12,15,28-hexahydroxy-10-(hydroxymethyl)-13-(2-methylpropyl)-4-octyl-20,22-dioxo-21-oxa-25,26-dithia-2,5,8,11,14,29-hexaazabicyclo[21.4.2]nonacosa-2,5,8,11,14,28-hexaen-7-yl]-2-hydroxypropanimidic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

[H]C(O)(C[C@]1([H])N=C(O)[C@]([H])(CO)N=C(O)[C@]([H])(CC(C)C)N=C(O)[C@@]([H])(N)CCCC(=O)OC(=O)[C@]2([H])CSSC[C@]([H])(N=C(O)[C@]([H])(CCCCCCCC)N=C1O)C(O)=N2)C(O)=N

InChI Identifier

InChI=1S/C36H60N8O12S2/c1-4-5-6-7-8-9-12-21-31(50)43-25-17-57-58-18-26(44-35(25)54)36(55)56-28(47)13-10-11-20(37)30(49)40-22(14-19(2)3)32(51)42-24(16-45)34(53)41-23(33(52)39-21)15-27(46)29(38)48/h19-27,45-46H,4-18,37H2,1-3H3,(H2,38,48)(H,39,52)(H,40,49)(H,41,53)(H,42,51)(H,43,50)(H,44,54)/t20-,21-,22-,23-,24-,25-,26-,27?/m0/s1

InChI Key

ABYJOODEAJNHBQ-HRQFAISJSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Depsipeptides

Direct Parent

Cyclic depsipeptides

Alternative Parents

Substituents

Cyclic depsipeptide
Macrolactam
Delta amino acid or derivatives
Alpha-amino acid or derivatives
Dicarboxylic acid or derivatives
Cyclic carboximidic acid
Carboxylic acid anhydride
Secondary alcohol
Organic disulfide
Amino acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.089 g/L	ALOGPS
logP	1.3	ALOGPS
logP	0.55	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	2.62	ChemAxon
pKa (Strongest Basic)	9.61	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	349.47 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	225.82 m³·mol⁻¹	ChemAxon
Polarizability	89.07 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

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

Metabolic Reactions

Not Available

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
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

78440596

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139590175

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Gramillin B (MMDBc0022796)

MOL for #<Metabolite:0x00007fecaa88eed0>

3D MOL for #<Metabolite:0x00007fecaa88eed0>

3D SDF for #<Metabolite:0x00007fecaa88eed0>

3D-SDF for #<Metabolite:0x00007fecaa88eed0>

PDB for #<Metabolite:0x00007fecaa88eed0>

3D PDB for #<Metabolite:0x00007fecaa88eed0>

SMILES for #<Metabolite:0x00007fecaa88eed0>

INCHI for #<Metabolite:0x00007fecaa88eed0>

Structure for #<Metabolite:0x00007fecaa88eed0>

3D Structure for #<Metabolite:0x00007fecaa88eed0>