data_A1BYD
# 
_chem_comp.id                                    A1BYD 
_chem_comp.name                                  "Oritinib, bound form" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C31 H39 N7 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-02-26 
_chem_comp.pdbx_modified_date                    2025-10-03 
_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                        541.687 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1BYD 
_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        9NHW 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
A1BYD C10  C1  C 0 1 Y N N N N N 20.808 -1.239 53.962 -0.915 -0.361 0.079  C10  A1BYD 1  
A1BYD C02  C2  C 0 1 N N N N N N 18.733 3.067  51.233 2.890  3.104  0.180  C02  A1BYD 2  
A1BYD C03  C3  C 0 1 N N N N N N 18.640 4.427  50.746 3.342  4.432  -0.371 C03  A1BYD 3  
A1BYD C04  C4  C 0 1 N N N N N N 18.477 5.498  51.618 2.334  5.515  0.018  C04  A1BYD 4  
A1BYD C06  C5  C 0 1 Y N N N N N 17.558 0.751  51.616 3.157  0.746  0.387  C06  A1BYD 5  
A1BYD C07  C6  C 0 1 Y N N N N N 18.540 0.212  52.434 1.793  0.508  0.470  C07  A1BYD 6  
A1BYD C08  C7  C 0 1 Y N N N N N 18.362 -1.022 53.059 1.329  -0.729 0.890  C08  A1BYD 7  
A1BYD C12  C8  C 0 1 Y N N N N N 22.583 -0.071 53.065 -3.078 0.077  -0.595 C12  A1BYD 8  
A1BYD C13  C9  C 0 1 Y N N N N N 23.084 0.897  51.967 -4.536 -0.075 -0.403 C13  A1BYD 9  
A1BYD C14  C10 C 0 1 Y N N N N N 22.421 1.133  50.737 -5.223 0.070  0.761  C14  A1BYD 10 
A1BYD C15  C11 C 0 1 N N N N N N 21.108 0.561  50.112 -4.625 0.420  2.104  C15  A1BYD 11 
A1BYD C16  C12 C 0 1 N N N N N N 20.807 1.074  48.714 -5.758 0.866  3.035  C16  A1BYD 12 
A1BYD C17  C13 C 0 1 N N N N N N 21.331 2.463  48.466 -6.894 -0.158 2.967  C17  A1BYD 13 
A1BYD C18  C14 C 0 1 N N N N N N 22.818 2.554  48.715 -7.581 -0.071 1.602  C18  A1BYD 14 
A1BYD C20  C15 C 0 1 Y N N N N N 24.294 2.411  50.792 -6.775 -0.439 -0.771 C20  A1BYD 15 
A1BYD C21  C16 C 0 1 Y N N N N N 24.279 1.722  51.995 -5.522 -0.405 -1.429 C21  A1BYD 16 
A1BYD C22  C17 C 0 1 Y N N N N N 25.331 1.941  52.920 -5.409 -0.659 -2.796 C22  A1BYD 17 
A1BYD C23  C18 C 0 1 Y N N N N N 26.373 2.831  52.630 -6.571 -0.943 -3.472 C23  A1BYD 18 
A1BYD C24  C19 C 0 1 Y N N N N N 26.377 3.525  51.408 -7.801 -0.977 -2.836 C24  A1BYD 19 
A1BYD C25  C20 C 0 1 Y N N N N N 25.344 3.320  50.489 -7.939 -0.729 -1.481 C25  A1BYD 20 
A1BYD C26  C21 C 0 1 Y N N N N N 23.429 -0.578 54.043 -2.576 0.826  -1.665 C26  A1BYD 21 
A1BYD C27  C22 C 0 1 Y N N N N N 22.867 -1.440 54.983 -1.205 0.945  -1.800 C27  A1BYD 22 
A1BYD C29  C23 C 0 1 Y N N N N N 17.163 -1.709 52.860 2.232  -1.733 1.230  C29  A1BYD 23 
A1BYD C31  C24 C 0 1 N N N N N N 15.917 -3.702 52.893 2.758  -3.930 1.977  C31  A1BYD 24 
A1BYD C32  C25 C 0 1 Y N N N N N 16.166 -1.180 52.039 3.595  -1.497 1.149  C32  A1BYD 25 
A1BYD C33  C26 C 0 1 Y N N N N N 16.366 0.051  51.415 4.061  -0.262 0.722  C33  A1BYD 26 
A1BYD C35  C27 C 0 1 N N N N N N 14.297 1.530  51.096 6.072  -0.102 1.957  C35  A1BYD 27 
A1BYD C36  C28 C 0 1 N N N N N N 15.310 0.291  49.102 6.074  -0.955 -0.309 C36  A1BYD 28 
A1BYD C37  C29 C 0 1 N N N N N N 15.852 1.496  48.281 7.515  -0.513 -0.569 C37  A1BYD 29 
A1BYD C39  C30 C 0 1 N N N N N N 14.579 1.504  46.252 7.516  -1.367 -2.835 C39  A1BYD 30 
A1BYD C40  C31 C 0 1 N N N N N N 15.052 3.578  47.362 9.595  -1.196 -1.605 C40  A1BYD 31 
A1BYD N05  N1  N 0 1 N N N N N N 17.732 2.039  50.933 3.627  1.997  -0.038 N05  A1BYD 32 
A1BYD N09  N2  N 0 1 N N N N N N 19.384 -1.616 53.939 -0.051 -0.970 0.973  N09  A1BYD 33 
A1BYD N11  N3  N 0 1 Y N N N N N 21.313 -0.422 53.057 -2.220 -0.497 0.249  N11  A1BYD 34 
A1BYD N19  N4  N 0 1 Y N N N N N 23.167 2.036  50.060 -6.560 -0.149 0.547  N19  A1BYD 35 
A1BYD N28  N5  N 0 1 Y N N N N N 21.578 -1.742 54.906 -0.413 0.347  -0.923 N28  A1BYD 36 
A1BYD N34  N6  N 0 1 N N N N N N 15.320 0.627  50.540 5.439  -0.025 0.634  N34  A1BYD 37 
A1BYD N38  N7  N 0 1 N N N N N N 14.743 2.154  47.561 8.150  -1.444 -1.512 N38  A1BYD 38 
A1BYD O01  O1  O 0 1 N N N N N N 19.535 2.982  52.097 1.862  3.032  0.821  O01  A1BYD 39 
A1BYD O30  O2  O 0 1 N N N N N N 16.956 -2.950 53.488 1.776  -2.947 1.643  O30  A1BYD 40 
A1BYD H031 H1  H 0 0 N N N N N N 17.782 4.453  50.058 4.320  4.681  0.040  H031 A1BYD 41 
A1BYD H042 H2  H 0 0 N N N N N N 18.430 6.435  51.044 1.356  5.265  -0.393 H042 A1BYD 42 
A1BYD H041 H3  H 0 0 N N N N N N 17.544 5.369  52.186 2.267  5.576  1.104  H041 A1BYD 43 
A1BYD H071 H4  H 0 0 N N N N N N 19.459 0.758  52.590 1.093  1.287  0.206  H071 A1BYD 44 
A1BYD H152 H5  H 0 0 N N N N N N 21.197 -0.534 50.065 -4.128 -0.454 2.523  H152 A1BYD 45 
A1BYD H151 H6  H 0 0 N N N N N N 20.267 0.833  50.767 -3.905 1.230  1.985  H151 A1BYD 46 
A1BYD H161 H7  H 0 0 N N N N N N 21.267 0.391  47.985 -5.386 0.931  4.057  H161 A1BYD 47 
A1BYD H162 H8  H 0 0 N N N N N N 19.716 1.081  48.572 -6.127 1.842  2.719  H162 A1BYD 48 
A1BYD H172 H9  H 0 0 N N N N N N 21.127 2.739  47.421 -6.488 -1.160 3.106  H172 A1BYD 49 
A1BYD H171 H10 H 0 0 N N N N N N 20.814 3.164  49.138 -7.620 0.051  3.753  H171 A1BYD 50 
A1BYD H182 H11 H 0 0 N N N N N N 23.347 1.962  47.954 -8.283 -0.898 1.493  H182 A1BYD 51 
A1BYD H181 H12 H 0 0 N N N N N N 23.131 3.606  48.643 -8.118 0.875  1.524  H181 A1BYD 52 
A1BYD H221 H13 H 0 0 N N N N N N 25.329 1.414  53.862 -4.454 -0.633 -3.299 H221 A1BYD 53 
A1BYD H231 H14 H 0 0 N N N N N N 27.170 2.983  53.343 -6.524 -1.145 -4.532 H231 A1BYD 54 
A1BYD H241 H15 H 0 0 N N N N N N 27.176 4.215  51.180 -8.682 -1.205 -3.417 H241 A1BYD 55 
A1BYD H251 H16 H 0 0 N N N N N N 25.344 3.852  49.549 -8.904 -0.755 -0.998 H251 A1BYD 56 
A1BYD H261 H17 H 0 0 N N N N N N 24.476 -0.316 54.074 -3.243 1.304  -2.367 H261 A1BYD 57 
A1BYD H271 H18 H 0 0 N N N N N N 23.477 -1.859 55.769 -0.785 1.516  -2.615 H271 A1BYD 58 
A1BYD H313 H19 H 0 0 N N N N N N 15.804 -4.658 53.426 3.382  -3.559 2.790  H313 A1BYD 59 
A1BYD H311 H20 H 0 0 N N N N N N 14.975 -3.136 52.951 2.262  -4.848 2.289  H311 A1BYD 60 
A1BYD H312 H21 H 0 0 N N N N N N 16.163 -3.897 51.839 3.380  -4.132 1.104  H312 A1BYD 61 
A1BYD H321 H22 H 0 0 N N N N N N 15.244 -1.721 51.888 4.295  -2.276 1.413  H321 A1BYD 62 
A1BYD H353 H23 H 0 0 N N N N N N 13.615 1.850  50.294 7.128  0.154  1.870  H353 A1BYD 63 
A1BYD H351 H24 H 0 0 N N N N N N 13.726 1.002  51.874 5.583  0.597  2.635  H351 A1BYD 64 
A1BYD H352 H25 H 0 0 N N N N N N 14.786 2.412  51.535 5.976  -1.115 2.347  H352 A1BYD 65 
A1BYD H361 H26 H 0 0 N N N N N N 15.948 -0.588 48.927 5.519  -0.956 -1.247 H361 A1BYD 66 
A1BYD H362 H27 H 0 0 N N N N N N 14.281 0.066  48.786 6.072  -1.959 0.115  H362 A1BYD 67 
A1BYD H371 H28 H 0 0 N N N N N N 16.324 2.219  48.963 7.516  0.491  -0.993 H371 A1BYD 68 
A1BYD H372 H29 H 0 0 N N N N N N 16.596 1.137  47.555 8.070  -0.512 0.369  H372 A1BYD 69 
A1BYD H393 H30 H 0 0 N N N N N N 13.755 1.985  45.704 7.958  -2.115 -3.494 H393 A1BYD 70 
A1BYD H392 H31 H 0 0 N N N N N N 15.510 1.603  45.675 6.447  -1.554 -2.738 H392 A1BYD 71 
A1BYD H391 H32 H 0 0 N N N N N N 14.349 0.438  46.398 7.674  -0.374 -3.256 H391 A1BYD 72 
A1BYD H403 H33 H 0 0 N N N N N N 14.223 4.062  46.826 9.767  -0.176 -1.951 H403 A1BYD 73 
A1BYD H401 H34 H 0 0 N N N N N N 15.189 4.063  48.340 10.050 -1.328 -0.624 H401 A1BYD 74 
A1BYD H402 H35 H 0 0 N N N N N N 15.976 3.674  46.772 10.040 -1.898 -2.310 H402 A1BYD 75 
A1BYD H051 H36 H 0 0 N N N N N N 17.100 2.236  50.183 4.483  2.066  -0.490 H051 A1BYD 76 
A1BYD H091 H37 H 0 0 N N N N N N 19.087 -2.332 54.571 -0.400 -1.563 1.657  H091 A1BYD 77 
A1BYD H1   H38 H 0 1 N N N N N N 19.566 4.621  50.185 3.409  4.370  -1.457 H1   A1BYD 78 
A1BYD H2   H39 H 0 1 N N N N N N 19.328 5.537  52.314 2.661  6.476  -0.381 H2   A1BYD 79 
# 
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 
A1BYD C02 O01  DOUB N N 1  
A1BYD C04 C03  SING N N 2  
A1BYD C03 C02  SING N N 3  
A1BYD N05 C02  SING N N 4  
A1BYD C06 N05  SING N N 5  
A1BYD C07 C06  DOUB Y N 6  
A1BYD C08 C07  SING Y N 7  
A1BYD C10 N09  SING N N 8  
A1BYD N11 C10  DOUB Y N 9  
A1BYD C12 N11  SING Y N 10 
A1BYD C14 C13  DOUB Y N 11 
A1BYD C15 C14  SING N N 12 
A1BYD C16 C15  SING N N 13 
A1BYD C17 C16  SING N N 14 
A1BYD C18 C17  SING N N 15 
A1BYD N19 C18  SING N N 16 
A1BYD C20 N19  SING Y N 17 
A1BYD C21 C20  DOUB Y N 18 
A1BYD C22 C21  SING Y N 19 
A1BYD C23 C22  DOUB Y N 20 
A1BYD C24 C23  SING Y N 21 
A1BYD C25 C24  DOUB Y N 22 
A1BYD C13 C12  SING N N 23 
A1BYD C26 C12  DOUB Y N 24 
A1BYD C27 C26  SING Y N 25 
A1BYD N28 C27  DOUB Y N 26 
A1BYD N09 C08  SING N N 27 
A1BYD C29 C08  DOUB Y N 28 
A1BYD C31 O30  SING N N 29 
A1BYD O30 C29  SING N N 30 
A1BYD C32 C29  SING Y N 31 
A1BYD C33 C32  DOUB Y N 32 
A1BYD N34 C33  SING N N 33 
A1BYD C35 N34  SING N N 34 
A1BYD C36 N34  SING N N 35 
A1BYD C37 C36  SING N N 36 
A1BYD N38 C37  SING N N 37 
A1BYD C39 N38  SING N N 38 
A1BYD C40 N38  SING N N 39 
A1BYD C06 C33  SING Y N 40 
A1BYD C10 N28  SING Y N 41 
A1BYD C13 C21  SING Y N 42 
A1BYD C14 N19  SING Y N 43 
A1BYD C20 C25  SING Y N 44 
A1BYD C03 H031 SING N N 45 
A1BYD C04 H042 SING N N 46 
A1BYD C04 H041 SING N N 47 
A1BYD C07 H071 SING N N 48 
A1BYD C15 H152 SING N N 49 
A1BYD C15 H151 SING N N 50 
A1BYD C16 H161 SING N N 51 
A1BYD C16 H162 SING N N 52 
A1BYD C17 H172 SING N N 53 
A1BYD C17 H171 SING N N 54 
A1BYD C18 H182 SING N N 55 
A1BYD C18 H181 SING N N 56 
A1BYD C22 H221 SING N N 57 
A1BYD C23 H231 SING N N 58 
A1BYD C24 H241 SING N N 59 
A1BYD C25 H251 SING N N 60 
A1BYD C26 H261 SING N N 61 
A1BYD C27 H271 SING N N 62 
A1BYD C31 H313 SING N N 63 
A1BYD C31 H311 SING N N 64 
A1BYD C31 H312 SING N N 65 
A1BYD C32 H321 SING N N 66 
A1BYD C35 H353 SING N N 67 
A1BYD C35 H351 SING N N 68 
A1BYD C35 H352 SING N N 69 
A1BYD C36 H361 SING N N 70 
A1BYD C36 H362 SING N N 71 
A1BYD C37 H371 SING N N 72 
A1BYD C37 H372 SING N N 73 
A1BYD C39 H393 SING N N 74 
A1BYD C39 H392 SING N N 75 
A1BYD C39 H391 SING N N 76 
A1BYD C40 H403 SING N N 77 
A1BYD C40 H401 SING N N 78 
A1BYD C40 H402 SING N N 79 
A1BYD N05 H051 SING N N 80 
A1BYD N09 H091 SING N N 81 
A1BYD C03 H1   SING N N 82 
A1BYD C04 H2   SING N N 83 
# 
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 
A1BYD SMILES           ACDLabs              14.52   "CN(C)CCN(C)c1cc(OC)c(cc1NC(=O)CC)Nc1nccc(n1)c1c2ccccc2n2CCCCc12"                                                                                                                                                          
A1BYD InChI            InChI                1.06    "InChI=1S/C31H39N7O2/c1-6-29(39)33-23-19-24(28(40-5)20-27(23)37(4)18-17-36(2)3)35-31-32-15-14-22(34-31)30-21-11-7-8-12-25(21)38-16-10-9-13-26(30)38/h7-8,11-12,14-15,19-20H,6,9-10,13,16-18H2,1-5H3,(H,33,39)(H,32,34,35)" 
A1BYD InChIKey         InChI                1.06    MEDBOUCOFFVBAU-UHFFFAOYSA-N                                                                                                                                                                                                
A1BYD SMILES_CANONICAL CACTVS               3.385   "CCC(=O)Nc1cc(Nc2nccc(n2)c3c4CCCCn4c5ccccc35)c(OC)cc1N(C)CCN(C)C"                                                                                                                                                          
A1BYD SMILES           CACTVS               3.385   "CCC(=O)Nc1cc(Nc2nccc(n2)c3c4CCCCn4c5ccccc35)c(OC)cc1N(C)CCN(C)C"                                                                                                                                                          
A1BYD SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CCC(=O)Nc1cc(c(cc1N(C)CCN(C)C)OC)Nc2nccc(n2)c3c4ccccc4n5c3CCCC5"                                                                                                                                                          
A1BYD SMILES           "OpenEye OEToolkits" 3.1.0.0 "CCC(=O)Nc1cc(c(cc1N(C)CCN(C)C)OC)Nc2nccc(n2)c3c4ccccc4n5c3CCCC5"                                                                                                                                                          
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
A1BYD "SYSTEMATIC NAME" ACDLabs              14.52   "N-[2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-({(4M)-4-[(5R)-6,7,8,9-tetrahydropyrido[1,2-a]indol-10-yl]pyrimidin-2-yl}amino)phenyl]propanamide" 
A1BYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(6,7,8,9-tetrahydropyrido[1,2-a]indol-10-yl)pyrimidin-2-yl]amino]phenyl]propanamide"          
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1BYD "Create component"    2025-02-26 RCSB 
A1BYD "Modify linking type" 2025-02-27 RCSB 
A1BYD "Modify PCM"          2025-02-27 RCSB 
A1BYD "Initial release"     2025-10-08 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1BYD 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C04 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
