data_A1BYL
# 
_chem_comp.id                                    A1BYL 
_chem_comp.name                                  "Almonertinib, bound form" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C30 H37 N7 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-02-27 
_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                        527.660 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1BYL 
_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        9NJ7 
_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 
A1BYL C01  C1  C 0 1 N N N N N N -3.738 14.587 46.684 9.802  -0.648 0.823  C01  A1BYL 1  
A1BYL C03  C2  C 0 1 N N N N N N -2.238 16.422 46.910 7.957  -0.649 2.392  C03  A1BYL 2  
A1BYL C04  C3  C 0 1 N N N N N N -1.629 14.246 47.765 7.548  -0.230 0.043  C04  A1BYL 3  
A1BYL C05  C4  C 0 1 N N N N N N -0.470 14.898 48.562 6.112  -0.754 0.108  C05  A1BYL 4  
A1BYL C07  C5  C 0 1 N N N N N N -1.724 13.950 50.592 5.703  -0.334 -2.241 C07  A1BYL 5  
A1BYL C08  C6  C 0 1 Y N N N N N -0.202 15.976 50.860 3.924  -0.321 -0.681 C08  A1BYL 6  
A1BYL C09  C7  C 0 1 Y N N N N N 0.989  15.726 51.532 3.472  -1.628 -0.787 C09  A1BYL 7  
A1BYL C10  C8  C 0 1 Y N N N N N 1.543  16.718 52.339 2.129  -1.914 -0.604 C10  A1BYL 8  
A1BYL C11  C9  C 0 1 Y N N N N N 0.918  17.946 52.479 1.232  -0.890 -0.314 C11  A1BYL 9  
A1BYL C12  C10 C 0 1 Y N N N N N -0.286 18.188 51.806 1.682  0.418  -0.207 C12  A1BYL 10 
A1BYL C13  C11 C 0 1 Y N N N N N -0.845 17.195 50.995 3.027  0.704  -0.385 C13  A1BYL 11 
A1BYL C15  C12 C 0 1 N N N N N N -3.226 18.205 50.608 2.839  2.895  0.531  C15  A1BYL 12 
A1BYL C17  C13 C 0 1 N N N N N N -4.690 18.213 49.889 3.263  4.341  0.570  C17  A1BYL 13 
A1BYL C18  C14 C 0 1 N N N N N N -5.918 17.874 50.279 2.376  5.106  1.554  C18  A1BYL 14 
A1BYL C20  C15 C 0 1 Y N N N N N 1.388  20.379 53.364 -1.091 -0.259 -0.506 C20  A1BYL 15 
A1BYL C22  C16 C 0 1 Y N N N N N 1.806  22.400 54.350 -1.608 1.740  -1.534 C22  A1BYL 16 
A1BYL C23  C17 C 0 1 Y N N N N N 1.059  23.054 53.373 -2.944 1.538  -1.246 C23  A1BYL 17 
A1BYL C24  C18 C 0 1 Y N N N N N 0.486  22.267 52.392 -3.310 0.371  -0.564 C24  A1BYL 18 
A1BYL C26  C19 C 0 1 Y N N N N N -0.365 22.892 51.274 -4.727 0.108  -0.233 C26  A1BYL 19 
A1BYL C27  C20 C 0 1 Y N N N N N -0.832 24.200 51.260 -5.790 0.899  -0.529 C27  A1BYL 20 
A1BYL C29  C21 C 0 1 Y N N N N N -1.536 23.196 49.411 -6.650 -0.873 0.553  C29  A1BYL 21 
A1BYL C30  C22 C 0 1 Y N N N N N -2.139 22.881 48.156 -7.439 -1.831 1.181  C30  A1BYL 22 
A1BYL C31  C23 C 0 1 Y N N N N N -1.997 21.600 47.620 -6.855 -2.957 1.719  C31  A1BYL 23 
A1BYL C32  C24 C 0 1 Y N N N N N -1.264 20.626 48.310 -5.483 -3.148 1.641  C32  A1BYL 24 
A1BYL C33  C25 C 0 1 Y N N N N N -0.674 20.940 49.537 -4.685 -2.212 1.022  C33  A1BYL 25 
A1BYL C34  C26 C 0 1 Y N N N N N -0.818 22.247 50.089 -5.261 -1.067 0.475  C34  A1BYL 26 
A1BYL C35  C27 C 0 1 N N N N N N -2.194 25.616 49.740 -8.274 0.902  -0.201 C35  A1BYL 27 
A1BYL C36  C28 C 0 1 N N N N N N -2.757 26.614 50.755 -8.425 2.138  -1.090 C36  A1BYL 28 
A1BYL C37  C29 C 0 1 N N N N N N -3.643 26.095 49.629 -8.521 2.274  0.431  C37  A1BYL 29 
A1BYL C39  C30 C 0 1 N N N N N N 3.501  15.443 52.462 2.662  -4.197 -1.009 C39  A1BYL 30 
A1BYL N02  N1  N 0 1 N N N N N N -2.744 15.203 47.561 8.377  -0.951 1.017  N02  A1BYL 31 
A1BYL N06  N2  N 0 1 N N N N N N -0.800 14.939 50.003 5.283  -0.032 -0.866 N06  A1BYL 32 
A1BYL N14  N3  N 0 1 N N N N N N -2.095 17.365 50.239 3.484  2.026  -0.271 N14  A1BYL 33 
A1BYL N19  N4  N 0 1 N N N N N N 1.580  18.925 53.369 -0.129 -1.181 -0.129 N19  A1BYL 34 
A1BYL N21  N5  N 0 1 Y N N N N N 1.956  21.083 54.316 -0.718 0.835  -1.155 N21  A1BYL 35 
A1BYL N25  N6  N 0 1 Y N N N N N 0.674  20.962 52.424 -2.360 -0.496 -0.214 N25  A1BYL 36 
A1BYL N28  N7  N 0 1 Y N N N N N -1.529 24.366 50.133 -6.934 0.327  -0.064 N28  A1BYL 37 
A1BYL O16  O1  O 0 1 N N N N N N -3.235 18.858 51.591 1.918  2.514  1.222  O16  A1BYL 38 
A1BYL O38  O2  O 0 1 N N N N N N 2.740  16.481 53.016 1.686  -3.197 -0.709 O38  A1BYL 39 
A1BYL H012 H1  H 0 0 N N N N N N -4.128 13.673 47.156 10.393 -1.195 1.557  H012 A1BYL 40 
A1BYL H013 H2  H 0 0 N N N N N N -4.565 15.293 46.514 10.103 -0.946 -0.181 H013 A1BYL 41 
A1BYL H011 H3  H 0 0 N N N N N N -3.270 14.332 45.722 9.966  0.422  0.949  H011 A1BYL 42 
A1BYL H032 H4  H 0 0 N N N N N N -1.488 16.899 47.557 6.918  -0.948 2.528  H032 A1BYL 43 
A1BYL H031 H5  H 0 0 N N N N N N -1.777 16.159 45.947 8.588  -1.196 3.093  H031 A1BYL 44 
A1BYL H033 H6  H 0 0 N N N N N N -3.071 17.119 46.739 8.055  0.421  2.575  H033 A1BYL 45 
A1BYL H041 H7  H 0 0 N N N N N N -2.002 13.374 48.322 7.946  -0.386 -0.960 H041 A1BYL 46 
A1BYL H042 H8  H 0 0 N N N N N N -1.252 13.920 46.784 7.557  0.835  0.276  H042 A1BYL 47 
A1BYL H052 H9  H 0 0 N N N N N N 0.448  14.309 48.416 6.103  -1.819 -0.125 H052 A1BYL 48 
A1BYL H051 H10 H 0 0 N N N N N N -0.310 15.923 48.197 5.714  -0.598 1.111  H051 A1BYL 49 
A1BYL H071 H11 H 0 0 N N N N N N -1.838 14.149 51.668 5.119  0.266  -2.939 H071 A1BYL 50 
A1BYL H073 H12 H 0 0 N N N N N N -2.705 14.026 50.099 6.761  -0.101 -2.357 H073 A1BYL 51 
A1BYL H072 H13 H 0 0 N N N N N N -1.318 12.938 50.448 5.539  -1.392 -2.447 H072 A1BYL 52 
A1BYL H091 H14 H 0 0 N N N N N N 1.481  14.770 51.429 4.168  -2.423 -1.013 H091 A1BYL 53 
A1BYL H121 H15 H 0 0 N N N N N N -0.783 19.141 51.913 0.986  1.212  0.018  H121 A1BYL 54 
A1BYL H171 H16 H 0 0 N N N N N N -4.809 19.263 49.582 4.302  4.407  0.892  H171 A1BYL 55 
A1BYL H182 H17 H 0 0 N N N N N N -6.625 18.044 49.454 2.476  4.671  2.548  H182 A1BYL 56 
A1BYL H181 H18 H 0 0 N N N N N N -5.933 16.811 50.561 2.682  6.152  1.582  H181 A1BYL 57 
A1BYL H221 H19 H 0 0 N N N N N N 2.267  22.971 55.142 -1.292 2.628  -2.062 H221 A1BYL 58 
A1BYL H231 H20 H 0 0 N N N N N N 0.933  24.127 53.382 -3.688 2.261  -1.543 H231 A1BYL 59 
A1BYL H271 H21 H 0 0 N N N N N N -0.662 24.947 52.022 -5.735 1.842  -1.053 H271 A1BYL 60 
A1BYL H301 H22 H 0 0 N N N N N N -2.703 23.632 47.623 -8.508 -1.692 1.247  H301 A1BYL 61 
A1BYL H311 H23 H 0 0 N N N N N N -2.453 21.359 46.671 -7.472 -3.699 2.205  H311 A1BYL 62 
A1BYL H321 H24 H 0 0 N N N N N N -1.155 19.635 47.895 -5.039 -4.036 2.067  H321 A1BYL 63 
A1BYL H331 H25 H 0 0 N N N N N N -0.107 20.190 50.069 -3.617 -2.364 0.963  H331 A1BYL 64 
A1BYL H351 H26 H 0 0 N N N N N N -1.578 26.156 49.006 -9.096 0.187  -0.189 H351 A1BYL 65 
A1BYL H361 H27 H 0 0 N N N N N N -2.944 26.297 51.792 -7.527 2.523  -1.573 H361 A1BYL 66 
A1BYL H362 H28 H 0 0 N N N N N N -2.414 27.659 50.747 -9.346 2.236  -1.664 H362 A1BYL 67 
A1BYL H371 H29 H 0 0 N N N N N N -4.469 25.404 49.854 -9.507 2.461  0.858  H371 A1BYL 68 
A1BYL H372 H30 H 0 0 N N N N N N -3.939 26.766 48.809 -7.687 2.747  0.948  H372 A1BYL 69 
A1BYL H393 H31 H 0 0 N N N N N N 4.425  15.314 53.045 3.132  -3.970 -1.966 H393 A1BYL 70 
A1BYL H391 H32 H 0 0 N N N N N N 2.920  14.509 52.485 3.420  -4.212 -0.226 H391 A1BYL 71 
A1BYL H392 H33 H 0 0 N N N N N N 3.756  15.690 51.421 2.177  -5.172 -1.064 H392 A1BYL 72 
A1BYL H141 H35 H 0 0 N N N N N N -2.177 16.852 49.385 4.264  2.313  -0.771 H141 A1BYL 73 
A1BYL H191 H36 H 0 0 N N N N N N 2.223  18.559 54.042 -0.395 -2.027 0.263  H191 A1BYL 74 
A1BYL H2   H38 H 0 1 N N N N N N -4.532 17.587 48.999 3.162  4.776  -0.424 H2   A1BYL 75 
A1BYL H3   H37 H 0 1 N N N N N N -6.210 18.487 51.144 1.336  5.041  1.232  H3   A1BYL 76 
# 
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 
A1BYL N02 C01  SING N N 1  
A1BYL C03 N02  SING N N 2  
A1BYL C04 N02  SING N N 3  
A1BYL C05 C04  SING N N 4  
A1BYL N06 C05  SING N N 5  
A1BYL C07 N06  SING N N 6  
A1BYL C08 N06  SING N N 7  
A1BYL C09 C08  DOUB Y N 8  
A1BYL C10 C09  SING Y N 9  
A1BYL C13 C12  DOUB Y N 10 
A1BYL N14 C13  SING N N 11 
A1BYL C15 N14  SING N N 12 
A1BYL O16 C15  DOUB N N 13 
A1BYL C17 C15  SING N N 14 
A1BYL C18 C17  SING N N 15 
A1BYL C12 C11  SING Y N 16 
A1BYL N19 C11  SING N N 17 
A1BYL C20 N19  SING N N 18 
A1BYL N21 C20  DOUB Y N 19 
A1BYL C22 N21  SING Y N 20 
A1BYL C23 C22  DOUB Y N 21 
A1BYL C24 C23  SING Y N 22 
A1BYL N25 C24  DOUB Y N 23 
A1BYL C26 C24  SING N N 24 
A1BYL C27 C26  DOUB Y N 25 
A1BYL N28 C27  SING Y N 26 
A1BYL C30 C29  DOUB Y N 27 
A1BYL C31 C30  SING Y N 28 
A1BYL C32 C31  DOUB Y N 29 
A1BYL C33 C32  SING Y N 30 
A1BYL C34 C33  DOUB Y N 31 
A1BYL C29 N28  SING Y N 32 
A1BYL C35 N28  SING N N 33 
A1BYL C36 C35  SING N N 34 
A1BYL C37 C36  SING N N 35 
A1BYL C11 C10  DOUB Y N 36 
A1BYL O38 C10  SING N N 37 
A1BYL C39 O38  SING N N 38 
A1BYL C08 C13  SING Y N 39 
A1BYL C20 N25  SING Y N 40 
A1BYL C26 C34  SING Y N 41 
A1BYL C29 C34  SING Y N 42 
A1BYL C35 C37  SING N N 43 
A1BYL C01 H012 SING N N 44 
A1BYL C01 H013 SING N N 45 
A1BYL C01 H011 SING N N 46 
A1BYL C03 H032 SING N N 47 
A1BYL C03 H031 SING N N 48 
A1BYL C03 H033 SING N N 49 
A1BYL C04 H041 SING N N 50 
A1BYL C04 H042 SING N N 51 
A1BYL C05 H052 SING N N 52 
A1BYL C05 H051 SING N N 53 
A1BYL C07 H071 SING N N 54 
A1BYL C07 H073 SING N N 55 
A1BYL C07 H072 SING N N 56 
A1BYL C09 H091 SING N N 57 
A1BYL C12 H121 SING N N 58 
A1BYL C17 H171 SING N N 59 
A1BYL C18 H182 SING N N 60 
A1BYL C18 H181 SING N N 61 
A1BYL C22 H221 SING N N 62 
A1BYL C23 H231 SING N N 63 
A1BYL C27 H271 SING N N 64 
A1BYL C30 H301 SING N N 65 
A1BYL C31 H311 SING N N 66 
A1BYL C32 H321 SING N N 67 
A1BYL C33 H331 SING N N 68 
A1BYL C35 H351 SING N N 69 
A1BYL C36 H361 SING N N 70 
A1BYL C36 H362 SING N N 71 
A1BYL C37 H371 SING N N 72 
A1BYL C37 H372 SING N N 73 
A1BYL C39 H393 SING N N 74 
A1BYL C39 H391 SING N N 75 
A1BYL C39 H392 SING N N 76 
A1BYL N14 H141 SING N N 77 
A1BYL N19 H191 SING N N 78 
A1BYL C17 H2   SING N N 79 
A1BYL C18 H3   SING N N 80 
# 
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 
A1BYL SMILES           ACDLabs              14.52   "CN(C)CCN(C)c1cc(OC)c(cc1NC(=O)CC)Nc1nccc(n1)c1cn(c2ccccc21)C1CC1"                                                                                                                                               
A1BYL InChI            InChI                1.06    "InChI=1S/C30H37N7O2/c1-6-29(38)32-24-17-25(28(39-5)18-27(24)36(4)16-15-35(2)3)34-30-31-14-13-23(33-30)22-19-37(20-11-12-20)26-10-8-7-9-21(22)26/h7-10,13-14,17-20H,6,11-12,15-16H2,1-5H3,(H,32,38)(H,31,33,34)" 
A1BYL InChIKey         InChI                1.06    FBRYXFGDUYYXEG-UHFFFAOYSA-N                                                                                                                                                                                      
A1BYL SMILES_CANONICAL CACTVS               3.385   "CCC(=O)Nc1cc(Nc2nccc(n2)c3cn(C4CC4)c5ccccc35)c(OC)cc1N(C)CCN(C)C"                                                                                                                                               
A1BYL SMILES           CACTVS               3.385   "CCC(=O)Nc1cc(Nc2nccc(n2)c3cn(C4CC4)c5ccccc35)c(OC)cc1N(C)CCN(C)C"                                                                                                                                               
A1BYL SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CCC(=O)Nc1cc(c(cc1N(C)CCN(C)C)OC)Nc2nccc(n2)c3cn(c4c3cccc4)C5CC5"                                                                                                                                               
A1BYL SMILES           "OpenEye OEToolkits" 3.1.0.0 "CCC(=O)Nc1cc(c(cc1N(C)CCN(C)C)OC)Nc2nccc(n2)c3cn(c4c3cccc4)C5CC5"                                                                                                                                               
# 
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 
A1BYL "SYSTEMATIC NAME" ACDLabs              14.52   "N-(5-{[(4P)-4-(1-cyclopropyl-1H-indol-3-yl)pyrimidin-2-yl]amino}-2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxyphenyl)propanamide" 
A1BYL "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "~{N}-[5-[[4-(1-cyclopropylindol-3-yl)pyrimidin-2-yl]amino]-2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-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 
A1BYL "Create component" 2025-02-27 RCSB 
A1BYL "Modify PCM"       2025-02-27 RCSB 
A1BYL "Modify atom id"   2025-10-01 RCSB 
A1BYL "Initial release"  2025-10-08 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1BYL 
_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               C18 
_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      ? 
# 
