data_ODB
#

_chem_comp.id                                   ODB
_chem_comp.name                                 "(10S,14S,17R)-14-(3-carbamimidamidopropyl)-3-[[2-(hydroxymethyl)phenyl]methyl]-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(21),22,24-triene-17-carboxamide"
_chem_comp.type                                 peptide-like
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C33 H46 N8 O5 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "P2 macrocycle; (10S,14S,17R)-14-(3-guanidinopropyl)-3-[[2-(hydroxymethyl)phenyl]methyl]-5,12,15-trioxo-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.06,10]pentacosa-1(25),21,23-triene-17-carboxamide"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-02-27
_chem_comp.pdbx_modified_date                   2021-08-28
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       666.834
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    ODB
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       6GWE
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
ODB  O2   O1   O  0  1  N  N  N  34.397  58.428  18.157  -0.653  -1.221   0.920  O2   ODB   1  
ODB  C8   C1   C  0  1  N  N  S  31.828  56.338  16.367   0.897  -3.559   0.977  C8   ODB   2  
ODB  C7   C2   C  0  1  N  N  N  32.473  54.914  16.195   1.350  -2.717  -0.219  C7   ODB   3  
ODB  C6   C3   C  0  1  N  N  N  33.951  54.863  15.549   1.897  -1.401   0.271  C6   ODB   4  
ODB  N1   N1   N  0  1  N  N  N  36.114  48.167  16.837  10.019  -2.055   0.602  N1   ODB   5  
ODB  C5   C4   C  0  1  N  N  S  36.333  54.426  16.106   3.225   0.594  -0.004  C5   ODB   6  
ODB  C4   C5   C  0  1  N  N  N  36.441  53.577  14.923   4.671   0.810  -0.455  C4   ODB   7  
ODB  C3   C6   C  0  1  N  N  N  36.079  52.233  15.621   5.565  -0.265   0.166  C3   ODB   8  
ODB  C2   C7   C  0  1  N  N  N  36.487  51.076  14.716   7.011  -0.049  -0.285  C2   ODB   9  
ODB  O1   O2   O  0  1  N  N  N  34.204  55.018  14.453   1.605  -0.985   1.372  O1   ODB  10  
ODB  S1   S1   S  0  1  N  N  N  38.260  57.099  18.775  -1.674   4.034   0.388  S1   ODB  11  
ODB  C1   C8   C  0  1  N  N  N  35.764  49.136  16.167   9.216  -1.089   0.045  C1   ODB  12  
ODB  C10  C9   C  0  1  N  N  N  31.966  57.999  14.811  -0.120  -5.792   0.882  C10  ODB  13  
ODB  C11  C10  C  0  1  N  N  N  33.276  57.979  15.566  -1.131  -4.750   1.378  C11  ODB  14  
ODB  C12  C11  C  0  1  N  N  N  33.692  57.540  17.942  -1.237  -2.265   1.122  C12  ODB  15  
ODB  C13  C12  C  0  1  N  N  N  32.775  56.951  19.115  -2.728  -2.265   1.336  C13  ODB  16  
ODB  C14  C13  C  0  1  N  N  N  32.910  56.285  21.428  -4.621  -1.129   0.341  C14  ODB  17  
ODB  C15  C14  C  0  1  Y  N  N  31.887  57.366  21.777  -4.523  -1.942  -0.925  C15  ODB  18  
ODB  C16  C15  C  0  1  Y  N  N  30.555  57.004  21.829  -4.951  -3.256  -0.938  C16  ODB  19  
ODB  C17  C16  C  0  1  Y  N  N  29.606  57.940  22.146  -4.862  -4.001  -2.099  C17  ODB  20  
ODB  C18  C17  C  0  1  Y  N  N  29.977  59.245  22.419  -4.344  -3.431  -3.247  C18  ODB  21  
ODB  C19  C18  C  0  1  Y  N  N  31.310  59.607  22.364  -3.916  -2.117  -3.234  C19  ODB  22  
ODB  C20  C19  C  0  1  Y  N  N  32.270  58.681  22.036  -4.010  -1.370  -2.075  C20  ODB  23  
ODB  C21  C20  C  0  1  N  N  N  33.776  59.155  22.030  -3.549   0.064  -2.063  C21  ODB  24  
ODB  C22  C21  C  0  1  N  N  N  34.940  55.867  20.006  -3.309  -0.026   2.051  C22  ODB  25  
ODB  C23  C22  C  0  1  Y  N  N  35.962  56.186  21.203  -4.180   1.152   1.699  C23  ODB  26  
ODB  C24  C23  C  0  1  Y  N  N  35.850  55.486  22.394  -5.553   1.061   1.827  C24  ODB  27  
ODB  C25  C24  C  0  1  Y  N  N  36.707  55.743  23.450  -6.352   2.142   1.504  C25  ODB  28  
ODB  C26  C25  C  0  1  Y  N  N  37.681  56.720  23.309  -5.776   3.315   1.051  C26  ODB  29  
ODB  C27  C26  C  0  1  Y  N  N  37.788  57.429  22.135  -4.403   3.407   0.922  C27  ODB  30  
ODB  C28  C27  C  0  1  Y  N  N  36.925  57.170  21.080  -3.605   2.325   1.246  C28  ODB  31  
ODB  C29  C28  C  0  1  N  N  N  37.074  58.002  19.732  -2.108   2.425   1.106  C29  ODB  32  
ODB  C30  C29  C  0  1  N  N  N  38.640  57.891  17.125   0.065   4.237   0.861  C30  ODB  33  
ODB  C31  C30  C  0  1  N  N  R  37.266  58.137  16.435   0.962   3.645  -0.228  C31  ODB  34  
ODB  C32  C31  C  0  1  N  N  N  37.439  58.720  15.040   1.855   4.721  -0.790  C32  ODB  35  
ODB  C33  C32  C  0  1  N  N  N  37.173  55.734  15.972   2.359   1.712  -0.524  C33  ODB  36  
ODB  C9   C33  C  0  1  N  N  N  31.248  56.691  15.298   1.207  -5.037   0.719  C9   ODB  37  
ODB  N2   N2   N  0  1  N  N  N  34.409  49.430  15.881   9.733  -0.181  -0.735  N2   ODB  38  
ODB  N3   N3   N  0  1  N  N  N  36.821  49.939  15.580   7.867  -1.079   0.309  N3   ODB  39  
ODB  N4   N4   N  0  1  N  N  N  34.955  54.534  16.575   2.724  -0.687  -0.542  N4   ODB  40  
ODB  N5   N5   N  0  1  N  N  N  32.936  57.465  16.681  -0.551  -3.425   1.156  N5   ODB  41  
ODB  N6   N6   N  0  1  N  N  N  33.682  56.800  20.308  -3.283  -0.968   0.924  N6   ODB  42  
ODB  N7   N7   N  0  1  N  N  N  37.688  60.122  14.934   1.380   5.573  -1.720  N7   ODB  43  
ODB  N8   N8   N  0  1  N  N  N  36.488  56.936  16.494   1.792   2.574   0.375  N8   ODB  44  
ODB  O3   O3   O  0  1  N  N  N  34.259  59.390  20.792  -3.168   0.453  -3.384  O3   ODB  45  
ODB  O4   O4   O  0  1  N  N  N  37.356  58.049  14.087   3.000   4.821  -0.405  O4   ODB  46  
ODB  O5   O5   O  0  1  N  N  N  38.252  55.720  15.549   2.168   1.845  -1.714  O5   ODB  47  
ODB  H1   H1   H  0  1  N  N  N  31.142  56.299  17.226   1.412  -3.223   1.878  H1   ODB  48  
ODB  H2   H2   H  0  1  N  N  N  31.807  54.322  15.551   2.126  -3.253  -0.766  H2   ODB  49  
ODB  H3   H3   H  0  1  N  N  N  32.528  54.450  17.191   0.500  -2.535  -0.877  H3   ODB  50  
ODB  H4   H4   H  0  1  N  N  N  35.428  47.542  17.209  10.971  -2.061   0.416  H4   ODB  51  
ODB  H5   H5   H  0  1  N  N  N  37.085  48.004  17.010   9.634  -2.730   1.182  H5   ODB  52  
ODB  H6   H6   H  0  1  N  N  N  36.852  53.865  16.897   3.181   0.575   1.086  H6   ODB  53  
ODB  H7   H7   H  0  1  N  N  N  37.456  53.572  14.500   4.726   0.746  -1.541  H7   ODB  54  
ODB  H8   H8   H  0  1  N  N  N  35.719  53.852  14.140   5.009   1.795  -0.132  H8   ODB  55  
ODB  H9   H9   H  0  1  N  N  N  34.995  52.193  15.804   5.510  -0.201   1.253  H9   ODB  56  
ODB  H10  H10  H  0  1  N  N  N  36.616  52.159  16.578   5.227  -1.250  -0.157  H10  ODB  57  
ODB  H11  H11  H  0  1  N  N  N  37.363  51.360  14.114   7.066  -0.114  -1.372  H11  ODB  58  
ODB  H12  H12  H  0  1  N  N  N  35.654  50.809  14.049   7.349   0.935   0.038  H12  ODB  59  
ODB  H13  H13  H  0  1  N  N  N  32.137  57.973  13.725  -0.011  -6.590   1.617  H13  ODB  60  
ODB  H14  H14  H  0  1  N  N  N  31.376  58.891  15.069  -0.440  -6.202  -0.076  H14  ODB  61  
ODB  H15  H15  H  0  1  N  N  N  34.023  57.357  15.052  -2.062  -4.844   0.820  H15  ODB  62  
ODB  H16  H16  H  0  1  N  N  N  33.674  58.995  15.700  -1.321  -4.897   2.441  H16  ODB  63  
ODB  H17  H17  H  0  1  N  N  N  31.953  57.645  19.344  -3.180  -3.059   0.741  H17  ODB  64  
ODB  H18  H18  H  0  1  N  N  N  32.360  55.975  18.823  -2.944  -2.434   2.391  H18  ODB  65  
ODB  H19  H19  H  0  1  N  N  N  32.398  55.354  21.142  -5.038  -0.149   0.112  H19  ODB  66  
ODB  H20  H20  H  0  1  N  N  N  33.568  56.092  22.288  -5.268  -1.642   1.052  H20  ODB  67  
ODB  H21  H21  H  0  1  N  N  N  30.262  55.986  21.620  -5.356  -3.701  -0.040  H21  ODB  68  
ODB  H22  H22  H  0  1  N  N  N  28.564  57.658  22.183  -5.195  -5.028  -2.109  H22  ODB  69  
ODB  H23  H23  H  0  1  N  N  N  29.227  59.979  22.674  -4.273  -4.014  -4.154  H23  ODB  70  
ODB  H24  H24  H  0  1  N  N  N  31.599  60.625  22.580  -3.511  -1.672  -4.131  H24  ODB  71  
ODB  H25  H25  H  0  1  N  N  N  34.390  58.373  22.501  -4.361   0.704  -1.715  H25  ODB  72  
ODB  H26  H26  H  0  1  N  N  N  33.852  60.083  22.616  -2.695   0.166  -1.393  H26  ODB  73  
ODB  H27  H27  H  0  1  N  N  N  34.650  54.806  20.013  -2.297   0.320   2.259  H27  ODB  74  
ODB  H28  H28  H  0  1  N  N  N  35.388  56.118  19.033  -3.712  -0.525   2.932  H28  ODB  75  
ODB  H29  H29  H  0  1  N  N  N  35.085  54.731  22.499  -6.002   0.144   2.181  H29  ODB  76  
ODB  H30  H30  H  0  1  N  N  N  36.618  55.189  24.373  -7.424   2.070   1.605  H30  ODB  77  
ODB  H31  H31  H  0  1  N  N  N  38.359  56.925  24.125  -6.400   4.159   0.798  H31  ODB  78  
ODB  H32  H32  H  0  1  N  N  N  38.547  58.191  22.034  -3.954   4.323   0.568  H32  ODB  79  
ODB  H33  H33  H  0  1  N  N  N  37.438  59.019  19.942  -1.750   1.628   0.454  H33  ODB  80  
ODB  H34  H34  H  0  1  N  N  N  36.111  58.059  19.203  -1.644   2.329   2.087  H34  ODB  81  
ODB  H35  H35  H  0  1  N  N  N  39.259  57.219  16.513   0.288   5.298   0.978  H35  ODB  82  
ODB  H36  H36  H  0  1  N  N  N  39.169  58.844  17.272   0.248   3.721   1.803  H36  ODB  83  
ODB  H37  H37  H  0  1  N  N  N  36.751  58.901  17.036   0.345   3.226  -1.023  H37  ODB  84  
ODB  H38  H38  H  0  1  N  N  N  30.184  56.891  15.492   1.591  -5.168  -0.292  H38  ODB  85  
ODB  H39  H39  H  0  1  N  N  N  31.340  55.902  14.537   1.936  -5.398   1.445  H39  ODB  86  
ODB  H40  H40  H  0  1  N  N  N  33.787  48.761  16.287  10.685  -0.187  -0.921  H40  ODB  87  
ODB  H42  H42  H  0  1  N  N  N  37.778  49.717  15.765   7.482  -1.755   0.889  H42  ODB  88  
ODB  H43  H43  H  0  1  N  N  N  34.708  54.393  17.534   2.971  -1.002  -1.426  H43  ODB  89  
ODB  H45  H45  H  0  1  N  N  N  37.794  60.544  14.034   0.463   5.494  -2.028  H45  ODB  90  
ODB  H46  H46  H  0  1  N  N  N  37.756  60.682  15.760   1.954   6.266  -2.081  H46  ODB  91  
ODB  H47  H47  H  0  1  N  N  N  35.557  56.912  16.859   1.923   2.492   1.333  H47  ODB  92  
ODB  H48  H48  H  0  1  N  N  N  33.992  58.689  20.209  -2.860   1.367  -3.451  H48  ODB  93  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
ODB  O4   C32  DOUB  N  N   1  
ODB  O1   C6   DOUB  N  N   2  
ODB  C2   N3   SING  N  N   3  
ODB  C2   C3   SING  N  N   4  
ODB  C10  C9   SING  N  N   5  
ODB  C10  C11  SING  N  N   6  
ODB  C4   C3   SING  N  N   7  
ODB  C4   C5   SING  N  N   8  
ODB  N7   C32  SING  N  N   9  
ODB  C32  C31  SING  N  N  10  
ODB  C9   C8   SING  N  N  11  
ODB  C6   C7   SING  N  N  12  
ODB  C6   N4   SING  N  N  13  
ODB  O5   C33  DOUB  N  N  14  
ODB  C11  N5   SING  N  N  15  
ODB  N3   C1   SING  N  N  16  
ODB  N2   C1   DOUB  N  N  17  
ODB  C33  C5   SING  N  N  18  
ODB  C33  N8   SING  N  N  19  
ODB  C5   N4   SING  N  N  20  
ODB  C1   N1   SING  N  N  21  
ODB  C7   C8   SING  N  N  22  
ODB  C8   N5   SING  N  N  23  
ODB  C31  N8   SING  N  N  24  
ODB  C31  C30  SING  N  N  25  
ODB  N5   C12  SING  N  N  26  
ODB  C30  S1   SING  N  N  27  
ODB  C12  O2   DOUB  N  N  28  
ODB  C12  C13  SING  N  N  29  
ODB  S1   C29  SING  N  N  30  
ODB  C13  N6   SING  N  N  31  
ODB  C29  C28  SING  N  N  32  
ODB  C22  N6   SING  N  N  33  
ODB  C22  C23  SING  N  N  34  
ODB  N6   C14  SING  N  N  35  
ODB  O3   C21  SING  N  N  36  
ODB  C28  C23  DOUB  Y  N  37  
ODB  C28  C27  SING  Y  N  38  
ODB  C23  C24  SING  Y  N  39  
ODB  C14  C15  SING  N  N  40  
ODB  C15  C16  DOUB  Y  N  41  
ODB  C15  C20  SING  Y  N  42  
ODB  C16  C17  SING  Y  N  43  
ODB  C21  C20  SING  N  N  44  
ODB  C20  C19  DOUB  Y  N  45  
ODB  C27  C26  DOUB  Y  N  46  
ODB  C17  C18  DOUB  Y  N  47  
ODB  C19  C18  SING  Y  N  48  
ODB  C24  C25  DOUB  Y  N  49  
ODB  C26  C25  SING  Y  N  50  
ODB  C8   H1   SING  N  N  51  
ODB  C7   H2   SING  N  N  52  
ODB  C7   H3   SING  N  N  53  
ODB  N1   H4   SING  N  N  54  
ODB  N1   H5   SING  N  N  55  
ODB  C5   H6   SING  N  N  56  
ODB  C4   H7   SING  N  N  57  
ODB  C4   H8   SING  N  N  58  
ODB  C3   H9   SING  N  N  59  
ODB  C3   H10  SING  N  N  60  
ODB  C2   H11  SING  N  N  61  
ODB  C2   H12  SING  N  N  62  
ODB  C10  H13  SING  N  N  63  
ODB  C10  H14  SING  N  N  64  
ODB  C11  H15  SING  N  N  65  
ODB  C11  H16  SING  N  N  66  
ODB  C13  H17  SING  N  N  67  
ODB  C13  H18  SING  N  N  68  
ODB  C14  H19  SING  N  N  69  
ODB  C14  H20  SING  N  N  70  
ODB  C16  H21  SING  N  N  71  
ODB  C17  H22  SING  N  N  72  
ODB  C18  H23  SING  N  N  73  
ODB  C19  H24  SING  N  N  74  
ODB  C21  H25  SING  N  N  75  
ODB  C21  H26  SING  N  N  76  
ODB  C22  H27  SING  N  N  77  
ODB  C22  H28  SING  N  N  78  
ODB  C24  H29  SING  N  N  79  
ODB  C25  H30  SING  N  N  80  
ODB  C26  H31  SING  N  N  81  
ODB  C27  H32  SING  N  N  82  
ODB  C29  H33  SING  N  N  83  
ODB  C29  H34  SING  N  N  84  
ODB  C30  H35  SING  N  N  85  
ODB  C30  H36  SING  N  N  86  
ODB  C31  H37  SING  N  N  87  
ODB  C9   H38  SING  N  N  88  
ODB  C9   H39  SING  N  N  89  
ODB  N2   H40  SING  N  N  90  
ODB  N3   H42  SING  N  N  91  
ODB  N4   H43  SING  N  N  92  
ODB  N7   H45  SING  N  N  93  
ODB  N7   H46  SING  N  N  94  
ODB  N8   H47  SING  N  N  95  
ODB  O3   H48  SING  N  N  96  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
ODB  InChI             InChI                 1.03   "InChI=1S/C33H46N8O5S/c34-31(45)28-21-47-20-25-10-4-2-8-23(25)17-40(16-22-7-1-3-9-24(22)19-42)18-30(44)41-14-6-11-26(41)15-29(43)38-27(32(46)39-28)12-5-13-37-33(35)36/h1-4,7-10,26-28,42H,5-6,11-21H2,(H2,34,45)(H,38,43)(H,39,46)(H4,35,36,37)/t26-,27-,28-/m0/s1"  
ODB  InChIKey          InChI                 1.03   IXLKCOMKHVAIOV-KCHLEUMXSA-N  
ODB  SMILES_CANONICAL  CACTVS                3.385  "NC(=N)NCCC[C@@H]1NC(=O)C[C@@H]2CCCN2C(=O)CN(Cc3ccccc3CO)Cc4ccccc4CSC[C@H](NC1=O)C(N)=O"  
ODB  SMILES            CACTVS                3.385  "NC(=N)NCCC[CH]1NC(=O)C[CH]2CCCN2C(=O)CN(Cc3ccccc3CO)Cc4ccccc4CSC[CH](NC1=O)C(N)=O"  
ODB  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "[H]/N=C(/N)\NCCC[C@H]1C(=O)N[C@@H](CSCc2ccccc2CN(CC(=O)N3CCC[C@H]3CC(=O)N1)Cc4ccccc4CO)C(=O)N"  
ODB  SMILES            "OpenEye OEToolkits"  2.0.7  "c1ccc2c(c1)CN(CC(=O)N3CCCC3CC(=O)NC(C(=O)NC(CSC2)C(=O)N)CCCNC(=N)N)Cc4ccccc4CO"  
#
_pdbx_chem_comp_identifier.comp_id          ODB
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "(10~{S},14~{S},17~{R})-14-(3-carbamimidamidopropyl)-3-[[2-(hydroxymethyl)phenyl]methyl]-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(21),22,24-triene-17-carboxamide"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ODB  "Create component"  2020-02-27  PDBE  
ODB  "Initial release"   2020-03-18  RCSB  
ODB  "Modify synonyms"   2021-08-28  PDBE  
#   #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1  ODB  "P2 macrocycle"                                                                                                                                                                       AUTHOR  ?  
2  ODB  "(10S,14S,17R)-14-(3-guanidinopropyl)-3-[[2-(hydroxymethyl)phenyl]methyl]-5,12,15-trioxo-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.06,10]pentacosa-1(25),21,23-triene-17-carboxamide"  PDB     ?  
##
