data_A1IY5
# 
_chem_comp.id                                    A1IY5 
_chem_comp.name                                  "(3~{S},7~{S},8~{S})-7-oxidanyl-8-(phenylmethyl)-3-(pyridin-3-ylmethyl)-1,4,9-triazacyclotricosane-2,5,10-trione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C33 H48 N4 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-01-20 
_chem_comp.pdbx_modified_date                    2025-03-21 
_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                        564.759 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IY5 
_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        6R61 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
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.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
A1IY5 C4  C1  C 0 1 Y N N N N N -9.881  -14.120 4.088  0.542  -4.438 0.730  C4  A1IY5 1  
A1IY5 C14 C2  C 0 1 Y N N N N N -8.653  -14.930 14.203 5.980  -0.157 -0.308 C14 A1IY5 2  
A1IY5 C5  C3  C 0 1 Y N N N N N -8.972  -15.165 3.883  -0.480 -3.521 0.892  C5  A1IY5 3  
A1IY5 C6  C4  C 0 1 N N N N N N -8.615  -16.157 4.968  -0.198 -2.047 0.760  C6  A1IY5 4  
A1IY5 C11 C5  C 0 1 N N S N N N -7.891  -14.739 10.839 3.164  1.457  0.298  C11 A1IY5 5  
A1IY5 C7  C6  C 0 1 N N S N N N -7.371  -15.789 5.806  -0.247 -1.648 -0.716 C7  A1IY5 6  
A1IY5 C8  C7  C 0 1 N N S N N N -7.191  -16.819 6.924  0.862  -2.373 -1.480 C8  A1IY5 7  
A1IY5 C9  C8  C 0 1 N N N N N N -6.144  -16.399 7.972  2.211  -2.078 -0.822 C9  A1IY5 8  
A1IY5 C10 C9  C 0 1 N N N N N N -6.633  -15.310 8.782  2.455  -0.590 -0.819 C10 A1IY5 9  
A1IY5 C12 C10 C 0 1 N N N N N N -6.720  -14.164 11.645 1.961  2.184  -0.245 C12 A1IY5 10 
A1IY5 C13 C11 C 0 1 N N N N N N -8.906  -15.406 11.755 4.381  1.760  -0.579 C13 A1IY5 11 
A1IY5 N1  N1  N 0 1 N N N N N N -7.425  -15.669 9.829  2.910  0.015  0.296  N1  A1IY5 12 
A1IY5 N2  N2  N 0 1 N N N N N N -6.765  -12.862 11.962 1.680  3.433  0.232  N2  A1IY5 13 
A1IY5 C3  C12 C 0 1 Y N N N N N -10.190 -13.299 3.025  0.282  -5.790 0.845  C3  A1IY5 14 
A1IY5 O2  O1  O 0 1 N N N N N N -5.816  -14.863 12.020 1.257  1.671  -1.088 O2  A1IY5 15 
A1IY5 C15 C13 C 0 1 Y N N N N N -9.245  -14.590 12.987 5.609  1.134  0.032  C15 A1IY5 16 
A1IY5 C33 C14 C 0 1 Y N N N N N -8.940  -14.140 15.378 7.117  -0.693 0.279  C33 A1IY5 17 
A1IY5 C32 C15 C 0 1 Y N N N N N -9.838  -13.083 15.294 7.839  0.075  1.172  C32 A1IY5 18 
A1IY5 N15 N3  N 0 1 Y N N N N N -10.404 -12.794 14.071 7.458  1.303  1.468  N15 A1IY5 19 
A1IY5 C31 C16 C 0 1 Y N N N N N -10.144 -13.529 12.875 6.378  1.840  0.938  C31 A1IY5 20 
A1IY5 O1  O2  O 0 1 N N N N N N -6.303  -14.122 8.594  2.242  0.061  -1.820 O1  A1IY5 21 
A1IY5 O8  O3  O 0 1 N N N N N N -6.772  -18.076 6.346  0.883  -1.919 -2.835 O8  A1IY5 22 
A1IY5 C29 C17 C 0 1 N N N N N N -5.954  -12.184 12.920 0.489  4.084  -0.360 C29 A1IY5 23 
A1IY5 C28 C18 C 0 1 N N N N N N -5.329  -10.925 12.309 -0.507 4.393  0.761  C28 A1IY5 24 
A1IY5 C27 C19 C 0 1 N N N N N N -4.458  -11.124 11.042 -1.403 5.559  0.340  C27 A1IY5 25 
A1IY5 C26 C20 C 0 1 N N N N N N -2.941  -11.232 11.177 -2.818 5.335  0.878  C26 A1IY5 26 
A1IY5 C25 C21 C 0 1 N N N N N N -2.312  -12.640 10.915 -3.787 5.162  -0.293 C25 A1IY5 27 
A1IY5 C24 C22 C 0 1 N N N N N N -2.619  -13.293 9.579  -5.045 4.436  0.189  C24 A1IY5 28 
A1IY5 C23 C23 C 0 1 N N N N N N -1.391  -13.545 8.672  -4.789 2.928  0.204  C23 A1IY5 29 
A1IY5 C22 C24 C 0 1 N N N N N N -1.730  -14.677 7.747  -6.125 2.183  0.207  C22 A1IY5 30 
A1IY5 C21 C25 C 0 1 N N N N N N -0.902  -14.745 6.449  -5.952 0.828  0.896  C21 A1IY5 31 
A1IY5 C20 C26 C 0 1 N N N N N N -1.460  -13.893 5.323  -5.642 -0.242 -0.153 C20 A1IY5 32 
A1IY5 C19 C27 C 0 1 N N N N N N -2.818  -14.491 4.989  -5.933 -1.627 0.430  C19 A1IY5 33 
A1IY5 C18 C28 C 0 1 N N N N N N -3.318  -14.050 3.669  -4.851 -2.609 -0.022 C18 A1IY5 34 
A1IY5 C17 C29 C 0 1 N N N N N N -4.607  -14.767 3.347  -4.022 -1.977 -1.143 C17 A1IY5 35 
A1IY5 C16 C30 C 0 1 N N N N N N -5.641  -14.618 4.465  -2.658 -1.614 -0.615 C16 A1IY5 36 
A1IY5 O3  O4  O 0 1 N N N N N N -5.969  -13.524 4.910  -2.548 -0.957 0.399  O3  A1IY5 37 
A1IY5 N   N4  N 0 1 N N N N N N -6.255  -15.718 4.900  -1.553 -2.032 -1.289 N   A1IY5 38 
A1IY5 C   C31 C 0 1 Y N N N N N -8.406  -15.335 2.610  -1.762 -3.957 1.173  C   A1IY5 39 
A1IY5 C2  C32 C 0 1 Y N N N N N -9.601  -13.471 1.759  -1.000 -6.226 1.127  C2  A1IY5 40 
A1IY5 C1  C33 C 0 1 Y N N N N N -8.706  -14.489 1.557  -2.020 -5.309 1.295  C1  A1IY5 41 
A1IY5 H1  H1  H 0 1 N N N N N N -10.330 -13.961 5.057  1.543  -4.097 0.510  H1  A1IY5 42 
A1IY5 H2  H2  H 0 1 N N N N N N -7.986  -15.777 14.266 5.396  -0.734 -1.010 H2  A1IY5 43 
A1IY5 H3  H3  H 0 1 N N N N N N -9.474  -16.240 5.650  -0.948 -1.482 1.314  H3  A1IY5 44 
A1IY5 H4  H4  H 0 1 N N N N N N -8.430  -17.131 4.492  0.791  -1.829 1.163  H4  A1IY5 45 
A1IY5 H5  H5  H 0 1 N N N N N N -8.394  -13.899 10.338 3.360  1.789  1.318  H5  A1IY5 46 
A1IY5 H6  H6  H 0 1 N N N N N N -7.541  -14.803 6.264  -0.111 -0.570 -0.808 H6  A1IY5 47 
A1IY5 H7  H7  H 0 1 N N N N N N -8.157  -16.952 7.434  0.675  -3.447 -1.459 H7  A1IY5 48 
A1IY5 H8  H8  H 0 1 N N N N N N -5.920  -17.258 8.621  2.204  -2.447 0.203  H8  A1IY5 49 
A1IY5 H9  H9  H 0 1 N N N N N N -5.226  -16.080 7.456  3.005  -2.575 -1.381 H9  A1IY5 50 
A1IY5 H10 H10 H 0 1 N N N N N N -9.831  -15.574 11.184 4.222  1.350  -1.576 H10 A1IY5 51 
A1IY5 H11 H11 H 0 1 N N N N N N -8.496  -16.373 12.081 4.519  2.839  -0.647 H11 A1IY5 52 
A1IY5 H12 H12 H 0 1 N N N N N N -7.701  -16.627 9.906  3.069  -0.506 1.098  H12 A1IY5 53 
A1IY5 H13 H13 H 0 1 N N N N N N -7.439  -12.307 11.475 2.222  3.863  0.911  H13 A1IY5 54 
A1IY5 H14 H14 H 0 1 N N N N N N -10.904 -12.501 3.168  1.079  -6.507 0.714  H14 A1IY5 55 
A1IY5 H15 H15 H 0 1 N N N N N N -8.459  -14.370 16.317 7.434  -1.697 0.041  H15 A1IY5 56 
A1IY5 H16 H16 H 0 1 N N N N N N -10.087 -12.500 16.168 8.725  -0.335 1.634  H16 A1IY5 57 
A1IY5 H17 H17 H 0 1 N N N N N N -10.616 -13.278 11.937 6.095  2.847  1.207  H17 A1IY5 58 
A1IY5 H18 H18 H 0 1 N N N N N N -6.659  -18.720 7.035  1.564  -2.338 -3.380 H18 A1IY5 59 
A1IY5 H19 H19 H 0 1 N N N N N N -6.576  -11.897 13.781 0.785  5.011  -0.851 H19 A1IY5 60 
A1IY5 H20 H20 H 0 1 N N N N N N -5.152  -12.858 13.256 0.029  3.415  -1.087 H20 A1IY5 61 
A1IY5 H21 H21 H 0 1 N N N N N N -4.696  -10.460 13.079 -1.122 3.513  0.952  H21 A1IY5 62 
A1IY5 H22 H22 H 0 1 N N N N N N -6.149  -10.240 12.046 0.037  4.661  1.666  H22 A1IY5 63 
A1IY5 H23 H23 H 0 1 N N N N N N -4.659  -10.270 10.379 -1.004 6.489  0.745  H23 A1IY5 64 
A1IY5 H24 H24 H 0 1 N N N N N N -4.802  -12.051 10.560 -1.434 5.620  -0.748 H24 A1IY5 65 
A1IY5 H25 H25 H 0 1 N N N N N N -2.675  -10.933 12.202 -2.833 4.438  1.497  H25 A1IY5 66 
A1IY5 H26 H26 H 0 1 N N N N N N -2.492  -10.528 10.462 -3.120 6.195  1.475  H26 A1IY5 67 
A1IY5 H27 H27 H 0 1 N N N N N N -2.670  -13.316 11.705 -4.061 6.141  -0.686 H27 A1IY5 68 
A1IY5 H28 H28 H 0 1 N N N N N N -1.220  -12.535 10.990 -3.308 4.577  -1.078 H28 A1IY5 69 
A1IY5 H29 H29 H 0 1 N N N N N N -3.317  -12.641 9.034  -5.296 4.772  1.195  H29 A1IY5 70 
A1IY5 H30 H30 H 0 1 N N N N N N -3.101  -14.262 9.776  -5.873 4.657  -0.485 H30 A1IY5 71 
A1IY5 H31 H31 H 0 1 N N N N N N -0.520  -13.813 9.288  -4.218 2.647  -0.681 H31 A1IY5 72 
A1IY5 H32 H32 H 0 1 N N N N N N -1.164  -12.640 8.089  -4.224 2.664  1.099  H32 A1IY5 73 
A1IY5 H33 H33 H 0 1 N N N N N N -2.790  -14.581 7.468  -6.868 2.772  0.744  H33 A1IY5 74 
A1IY5 H34 H34 H 0 1 N N N N N N -1.579  -15.619 8.295  -6.457 2.029  -0.820 H34 A1IY5 75 
A1IY5 H35 H35 H 0 1 N N N N N N -0.872  -15.791 6.111  -5.131 0.885  1.610  H35 A1IY5 76 
A1IY5 H36 H36 H 0 1 N N N N N N 0.119   -14.402 6.670  -6.872 0.567  1.420  H36 A1IY5 77 
A1IY5 H37 H37 H 0 1 N N N N N N -0.797  -13.934 4.446  -6.266 -0.080 -1.033 H37 A1IY5 78 
A1IY5 H38 H38 H 0 1 N N N N N N -1.571  -12.849 5.651  -4.592 -0.180 -0.436 H38 A1IY5 79 
A1IY5 H39 H39 H 0 1 N N N N N N -3.539  -14.184 5.761  -5.939 -1.568 1.518  H39 A1IY5 80 
A1IY5 H40 H40 H 0 1 N N N N N N -2.730  -15.587 4.985  -6.906 -1.971 0.079  H40 A1IY5 81 
A1IY5 H41 H41 H 0 1 N N N N N N -2.568  -14.282 2.898  -4.201 -2.846 0.820  H41 A1IY5 82 
A1IY5 H42 H42 H 0 1 N N N N N N -3.499  -12.965 3.690  -5.319 -3.522 -0.388 H42 A1IY5 83 
A1IY5 H43 H43 H 0 1 N N N N N N -5.024  -14.348 2.419  -3.917 -2.688 -1.962 H43 A1IY5 84 
A1IY5 H44 H44 H 0 1 N N N N N N -4.392  -15.836 3.202  -4.523 -1.079 -1.503 H44 A1IY5 85 
A1IY5 H45 H45 H 0 1 N N N N N N -5.902  -16.589 4.560  -1.619 -2.555 -2.103 H45 A1IY5 86 
A1IY5 H46 H46 H 0 1 N N N N N N -7.716  -16.150 2.448  -2.560 -3.241 1.299  H46 A1IY5 87 
A1IY5 H47 H47 H 0 1 N N N N N N -9.853  -12.803 0.949  -1.203 -7.283 1.216  H47 A1IY5 88 
A1IY5 H48 H48 H 0 1 N N N N N N -8.242  -14.629 0.592  -3.022 -5.650 1.515  H48 A1IY5 89 
# 
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 
A1IY5 C1  C2  DOUB Y N 1  
A1IY5 C1  C   SING Y N 2  
A1IY5 C2  C3  SING Y N 3  
A1IY5 C   C5  DOUB Y N 4  
A1IY5 C3  C4  DOUB Y N 5  
A1IY5 C17 C18 SING N N 6  
A1IY5 C17 C16 SING N N 7  
A1IY5 C18 C19 SING N N 8  
A1IY5 C5  C4  SING Y N 9  
A1IY5 C5  C6  SING N N 10 
A1IY5 C16 N   SING N N 11 
A1IY5 C16 O3  DOUB N N 12 
A1IY5 N   C7  SING N N 13 
A1IY5 C6  C7  SING N N 14 
A1IY5 C19 C20 SING N N 15 
A1IY5 C20 C21 SING N N 16 
A1IY5 C7  C8  SING N N 17 
A1IY5 O8  C8  SING N N 18 
A1IY5 C21 C22 SING N N 19 
A1IY5 C8  C9  SING N N 20 
A1IY5 C22 C23 SING N N 21 
A1IY5 C9  C10 SING N N 22 
A1IY5 O1  C10 DOUB N N 23 
A1IY5 C23 C24 SING N N 24 
A1IY5 C10 N1  SING N N 25 
A1IY5 C24 C25 SING N N 26 
A1IY5 N1  C11 SING N N 27 
A1IY5 C11 C12 SING N N 28 
A1IY5 C11 C13 SING N N 29 
A1IY5 C25 C26 SING N N 30 
A1IY5 C27 C26 SING N N 31 
A1IY5 C27 C28 SING N N 32 
A1IY5 C12 N2  SING N N 33 
A1IY5 C12 O2  DOUB N N 34 
A1IY5 C13 C15 SING N N 35 
A1IY5 N2  C29 SING N N 36 
A1IY5 C28 C29 SING N N 37 
A1IY5 C31 C15 SING Y N 38 
A1IY5 C31 N15 DOUB Y N 39 
A1IY5 C15 C14 DOUB Y N 40 
A1IY5 N15 C32 SING Y N 41 
A1IY5 C14 C33 SING Y N 42 
A1IY5 C32 C33 DOUB Y N 43 
A1IY5 C4  H1  SING N N 44 
A1IY5 C14 H2  SING N N 45 
A1IY5 C6  H3  SING N N 46 
A1IY5 C6  H4  SING N N 47 
A1IY5 C11 H5  SING N N 48 
A1IY5 C7  H6  SING N N 49 
A1IY5 C8  H7  SING N N 50 
A1IY5 C9  H8  SING N N 51 
A1IY5 C9  H9  SING N N 52 
A1IY5 C13 H10 SING N N 53 
A1IY5 C13 H11 SING N N 54 
A1IY5 N1  H12 SING N N 55 
A1IY5 N2  H13 SING N N 56 
A1IY5 C3  H14 SING N N 57 
A1IY5 C33 H15 SING N N 58 
A1IY5 C32 H16 SING N N 59 
A1IY5 C31 H17 SING N N 60 
A1IY5 O8  H18 SING N N 61 
A1IY5 C29 H19 SING N N 62 
A1IY5 C29 H20 SING N N 63 
A1IY5 C28 H21 SING N N 64 
A1IY5 C28 H22 SING N N 65 
A1IY5 C27 H23 SING N N 66 
A1IY5 C27 H24 SING N N 67 
A1IY5 C26 H25 SING N N 68 
A1IY5 C26 H26 SING N N 69 
A1IY5 C25 H27 SING N N 70 
A1IY5 C25 H28 SING N N 71 
A1IY5 C24 H29 SING N N 72 
A1IY5 C24 H30 SING N N 73 
A1IY5 C23 H31 SING N N 74 
A1IY5 C23 H32 SING N N 75 
A1IY5 C22 H33 SING N N 76 
A1IY5 C22 H34 SING N N 77 
A1IY5 C21 H35 SING N N 78 
A1IY5 C21 H36 SING N N 79 
A1IY5 C20 H37 SING N N 80 
A1IY5 C20 H38 SING N N 81 
A1IY5 C19 H39 SING N N 82 
A1IY5 C19 H40 SING N N 83 
A1IY5 C18 H41 SING N N 84 
A1IY5 C18 H42 SING N N 85 
A1IY5 C17 H43 SING N N 86 
A1IY5 C17 H44 SING N N 87 
A1IY5 N   H45 SING N N 88 
A1IY5 C   H46 SING N N 89 
A1IY5 C2  H47 SING N N 90 
A1IY5 C1  H48 SING N N 91 
# 
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 
A1IY5 InChI            InChI                1.06  "InChI=1S/C33H48N4O4/c38-30-24-32(40)37-29(23-27-18-15-20-34-25-27)33(41)35-21-14-9-7-5-3-1-2-4-6-8-13-19-31(39)36-28(30)22-26-16-11-10-12-17-26/h10-12,15-18,20,25,28-30,38H,1-9,13-14,19,21-24H2,(H,35,41)(H,36,39)(H,37,40)/t28-,29-,30-/m0/s1" 
A1IY5 InChIKey         InChI                1.06  RYGGELGJKGMCRW-DTXPUJKBSA-N                                                                                                                                                                                                                        
A1IY5 SMILES_CANONICAL CACTVS               3.385 "O[C@H]1CC(=O)N[C@@H](Cc2cccnc2)C(=O)NCCCCCCCCCCCCCC(=O)N[C@H]1Cc3ccccc3"                                                                                                                                                                          
A1IY5 SMILES           CACTVS               3.385 "O[CH]1CC(=O)N[CH](Cc2cccnc2)C(=O)NCCCCCCCCCCCCCC(=O)N[CH]1Cc3ccccc3"                                                                                                                                                                              
A1IY5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C[C@H]2[C@H](CC(=O)N[C@H](C(=O)NCCCCCCCCCCCCCC(=O)N2)Cc3cccnc3)O"                                                                                                                                                                       
A1IY5 SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CC2C(CC(=O)NC(C(=O)NCCCCCCCCCCCCCC(=O)N2)Cc3cccnc3)O"                                                                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           A1IY5 
_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        "(3~{S},7~{S},8~{S})-7-oxidanyl-8-(phenylmethyl)-3-(pyridin-3-ylmethyl)-1,4,9-triazacyclotricosane-2,5,10-trione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1IY5 "Create component" 2025-01-20 PDBE 
A1IY5 "Initial release"  2025-03-26 RCSB 
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