data_A1BYO
# 
_chem_comp.id                                    A1BYO 
_chem_comp.name                                  "Limertinib. bound form" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H34 Cl 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                        548.079 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1BYO 
_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        9MSS 
_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 
A1BYO C01  C1  C  0 1 N N N N N N 16.220 3.829  47.927 9.420  -2.204 1.038  C01  A1BYO 1  
A1BYO C03  C2  C  0 1 N N N N N N 14.621 3.006  46.389 7.481  -2.131 2.487  C03  A1BYO 2  
A1BYO C04  C3  C  0 1 N N N N N N 14.344 2.575  48.695 7.349  -1.235 0.241  C04  A1BYO 3  
A1BYO C05  C4  C  0 1 N N N N N N 15.016 2.322  50.048 5.842  -1.480 0.136  C05  A1BYO 4  
A1BYO C07  C5  C  0 1 N N N N N N 15.095 -0.039 49.175 5.710  -0.585 -2.110 C07  A1BYO 5  
A1BYO C08  C6  C  0 1 Y N N N N N 16.625 0.568  51.017 3.839  -0.509 -0.664 C08  A1BYO 6  
A1BYO C09  C7  C  0 1 Y N N N N N 16.411 -0.659 51.606 3.173  -1.668 -1.036 C09  A1BYO 7  
A1BYO C10  C8  C  0 1 Y N N N N N 17.313 -1.175 52.503 1.789  -1.721 -0.976 C10  A1BYO 8  
A1BYO C11  C9  C  0 1 Y N N N N N 18.451 -0.470 52.810 1.067  -0.613 -0.542 C11  A1BYO 9  
A1BYO C12  C10 C  0 1 Y N N N N N 18.673 0.764  52.222 1.732  0.547  -0.170 C12  A1BYO 10 
A1BYO C13  C11 C  0 1 Y N N N N N 17.770 1.299  51.316 3.116  0.599  -0.225 C13  A1BYO 11 
A1BYO C15  C12 C  0 1 N N N N N N 18.917 3.635  51.071 3.180  2.668  0.955  C15  A1BYO 12 
A1BYO C17  C13 C  0 1 N N N N N N 18.864 4.862  50.377 3.858  3.976  1.272  C17  A1BYO 13 
A1BYO C18  C14 C  0 1 N N N N N N 18.869 6.120  51.083 2.959  4.806  2.191  C18  A1BYO 14 
A1BYO C20  C15 C  0 1 Y N N N N N 20.794 -0.972 53.733 -1.078 0.494  -0.596 C20  A1BYO 15 
A1BYO C22  C16 C  0 1 Y N N N N N 22.778 -1.503 54.696 -1.139 2.763  -1.003 C22  A1BYO 16 
A1BYO C23  C17 C  0 1 Y N N N N N 23.446 -0.805 53.705 -2.509 2.753  -0.821 C23  A1BYO 17 
A1BYO C24  C18 C  0 1 Y N N N N N 22.700 -0.188 52.724 -3.132 1.538  -0.522 C24  A1BYO 18 
A1BYO C27  C19 C  0 1 Y N N N N N 22.806 1.342  50.627 -5.131 0.247  -0.133 C27  A1BYO 19 
A1BYO C28  C20 C  0 1 Y N N N N N 21.628 0.983  49.988 -6.185 0.151  0.748  C28  A1BYO 20 
A1BYO C29  C21 C  0 1 Y N N N N N 21.109 1.811  48.953 -6.812 -1.090 0.944  C29  A1BYO 21 
A1BYO C30  C22 C  0 1 Y N N N N N 19.901 1.451  48.303 -7.892 -1.228 1.834  C30  A1BYO 22 
A1BYO C31  C23 C  0 1 Y N N N N N 19.399 2.262  47.296 -8.477 -2.446 2.000  C31  A1BYO 23 
A1BYO C32  C24 C  0 1 Y N N N N N 20.076 3.418  46.911 -8.021 -3.561 1.300  C32  A1BYO 24 
A1BYO C33  C25 C  0 1 Y N N N N N 21.259 3.766  47.542 -6.979 -3.466 0.430  C33  A1BYO 25 
A1BYO C34  C26 C  0 1 Y N N N N N 21.768 2.939  48.579 -6.349 -2.225 0.232  C34  A1BYO 26 
A1BYO C35  C27 C  0 1 Y N N N N N 22.977 3.300  49.225 -5.270 -2.092 -0.660 C35  A1BYO 27 
A1BYO C36  C28 C  0 1 Y N N N N N 23.476 2.493  50.233 -4.683 -0.879 -0.837 C36  A1BYO 28 
A1BYO C39  C29 C  0 1 N N N N N N 15.858 -2.966 52.709 1.940  -3.956 -1.777 C39  A1BYO 29 
A1BYO N02  N1  N  0 1 N N N N N N 15.320 2.734  47.628 7.953  -2.261 1.102  N02  A1BYO 30 
A1BYO N06  N2  N  0 1 N N N N N N 15.590 0.983  50.080 5.238  -0.455 -0.725 N06  A1BYO 31 
A1BYO N14  N3  N  0 1 N N N N N N 17.992 2.587  50.684 3.790  1.770  0.157  N14  A1BYO 32 
A1BYO N19  N4  N  0 1 N N N N N N 19.353 -1.076 53.774 -0.334 -0.668 -0.482 N19  A1BYO 33 
A1BYO N21  N5  N  0 1 Y N N N N N 21.467 -1.572 54.683 -0.461 1.630  -0.885 N21  A1BYO 34 
A1BYO N25  N6  N  0 1 Y N N N N N 21.396 -0.299 52.777 -2.390 0.441  -0.419 N25  A1BYO 35 
A1BYO N26  N7  N  0 1 N N N N N N 23.405 0.546  51.684 -4.505 1.480  -0.331 N26  A1BYO 36 
A1BYO O16  O1  O  0 1 N N N N N N 19.646 3.554  51.993 2.086  2.423  1.419  O16  A1BYO 37 
A1BYO O38  O2  O  0 1 N N N N N N 17.078 -2.412 53.092 1.137  -2.858 -1.342 O38  A1BYO 38 
A1BYO CL3  CL1 CL 0 0 N N N N N N 25.213 -0.683 53.682 -3.435 4.214  -0.967 CL3  A1BYO 39 
A1BYO H011 H1  H  0 0 N N N N N N 16.751 3.622  48.868 9.841  -2.974 1.684  H011 A1BYO 40 
A1BYO H013 H2  H  0 0 N N N N N N 16.950 3.937  47.111 9.746  -2.373 0.012  H013 A1BYO 41 
A1BYO H012 H3  H  0 0 N N N N N N 15.643 4.760  48.029 9.760  -1.223 1.371  H012 A1BYO 42 
A1BYO H031 H4  H  0 0 N N N N N N 13.938 2.174  46.163 6.397  -2.246 2.513  H031 A1BYO 43 
A1BYO H033 H5  H  0 0 N N N N N N 14.044 3.937  46.490 7.944  -2.902 3.102  H033 A1BYO 44 
A1BYO H032 H6  H  0 0 N N N N N N 15.350 3.114  45.573 7.751  -1.148 2.872  H032 A1BYO 45 
A1BYO H041 H7  H  0 0 N N N N N N 13.739 3.491  48.764 7.795  -1.286 -0.752 H041 A1BYO 46 
A1BYO H042 H8  H  0 0 N N N N N N 13.692 1.722  48.457 7.527  -0.249 0.670  H042 A1BYO 47 
A1BYO H052 H9  H  0 0 N N N N N N 15.814 3.063  50.202 5.663  -2.466 -0.293 H052 A1BYO 48 
A1BYO H051 H10 H  0 0 N N N N N N 14.268 2.416  50.849 5.396  -1.430 1.129  H051 A1BYO 49 
A1BYO H071 H11 H  0 0 N N N N N N 15.644 -0.977 49.344 5.303  0.228  -2.711 H071 A1BYO 50 
A1BYO H073 H12 H  0 0 N N N N N N 14.023 -0.204 49.359 6.799  -0.540 -2.128 H073 A1BYO 51 
A1BYO H072 H13 H  0 0 N N N N N N 15.242 0.289  48.136 5.379  -1.540 -2.518 H072 A1BYO 52 
A1BYO H091 H14 H  0 0 N N N N N N 15.523 -1.222 51.359 3.732  -2.528 -1.373 H091 A1BYO 53 
A1BYO H121 H15 H  0 0 N N N N N N 19.565 1.319  52.473 1.171  1.406  0.166  H121 A1BYO 54 
A1BYO H171 H16 H  0 0 N N N N N N 19.735 4.878  49.705 4.807  3.782  1.771  H171 A1BYO 55 
A1BYO H182 H17 H  0 0 N N N N N N 18.823 6.947  50.360 2.010  5.000  1.693  H182 A1BYO 56 
A1BYO H181 H18 H  0 0 N N N N N N 17.997 6.168  51.752 2.779  4.257  3.116  H181 A1BYO 57 
A1BYO H221 H19 H  0 0 N N N N N N 23.336 -1.992 55.481 -0.627 3.684  -1.239 H221 A1BYO 58 
A1BYO H281 H20 H  0 0 N N N N N N 21.108 0.081  50.274 -6.527 1.024  1.284  H281 A1BYO 59 
A1BYO H301 H21 H  0 0 N N N N N N 19.376 0.552  48.590 -8.255 -0.372 2.384  H301 A1BYO 60 
A1BYO H311 H22 H  0 0 N N N N N N 18.475 1.995  46.805 -9.305 -2.549 2.685  H311 A1BYO 61 
A1BYO H321 H23 H  0 0 N N N N N N 19.679 4.041  46.123 -8.503 -4.516 1.450  H321 A1BYO 62 
A1BYO H331 H24 H  0 0 N N N N N N 21.790 4.659  47.248 -6.637 -4.339 -0.105 H331 A1BYO 63 
A1BYO H351 H25 H  0 0 N N N N N N 23.504 4.196  48.933 -4.911 -2.951 -1.207 H351 A1BYO 64 
A1BYO H361 H26 H  0 0 N N N N N N 24.401 2.763  50.721 -3.858 -0.782 -1.526 H361 A1BYO 65 
A1BYO H393 H27 H  0 0 N N N N N N 15.726 -3.940 53.203 2.521  -3.658 -2.651 H393 A1BYO 66 
A1BYO H391 H28 H  0 0 N N N N N N 15.041 -2.291 53.003 2.616  -4.252 -0.975 H391 A1BYO 67 
A1BYO H392 H29 H  0 0 N N N N N N 15.845 -3.104 51.618 1.297  -4.796 -2.039 H392 A1BYO 68 
A1BYO H141 H31 H  0 0 N N N N N N 17.434 2.776  49.876 4.694  1.932  -0.155 H141 A1BYO 69 
A1BYO H191 H32 H  0 0 N N N N N N 18.947 -1.604 54.520 -0.781 -1.520 -0.361 H191 A1BYO 70 
A1BYO H261 H33 H  0 0 N N N N N N 24.404 0.497  51.698 -5.030 2.295  -0.335 H261 A1BYO 71 
A1BYO H2   H35 H  0 1 N N N N N N 17.940 4.843  49.780 4.038  4.525  0.348  H2   A1BYO 72 
A1BYO H3   H34 H  0 1 N N N N N N 19.791 6.204  51.677 3.449  5.753  2.421  H3   A1BYO 73 
# 
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 
A1BYO N02 C01  SING N N 1  
A1BYO C03 N02  SING N N 2  
A1BYO C04 N02  SING N N 3  
A1BYO C05 C04  SING N N 4  
A1BYO N06 C05  SING N N 5  
A1BYO C07 N06  SING N N 6  
A1BYO C08 N06  SING N N 7  
A1BYO C09 C08  DOUB Y N 8  
A1BYO C10 C09  SING Y N 9  
A1BYO C13 C12  DOUB Y N 10 
A1BYO N14 C13  SING N N 11 
A1BYO C15 N14  SING N N 12 
A1BYO O16 C15  DOUB N N 13 
A1BYO C17 C15  SING N N 14 
A1BYO C18 C17  SING N N 15 
A1BYO C12 C11  SING Y N 16 
A1BYO N19 C11  SING N N 17 
A1BYO C20 N19  SING N N 18 
A1BYO N21 C20  DOUB Y N 19 
A1BYO C22 N21  SING Y N 20 
A1BYO C23 C22  DOUB Y N 21 
A1BYO N25 C24  DOUB Y N 22 
A1BYO N26 C24  SING N N 23 
A1BYO C27 N26  SING N N 24 
A1BYO C28 C27  DOUB Y N 25 
A1BYO C29 C28  SING Y N 26 
A1BYO C30 C29  DOUB Y N 27 
A1BYO C31 C30  SING Y N 28 
A1BYO C32 C31  DOUB Y N 29 
A1BYO C33 C32  SING Y N 30 
A1BYO C34 C33  DOUB Y N 31 
A1BYO C35 C34  SING Y N 32 
A1BYO C36 C35  DOUB Y N 33 
A1BYO C24 C23  SING Y N 34 
A1BYO CL3 C23  SING N N 35 
A1BYO C11 C10  DOUB Y N 36 
A1BYO O38 C10  SING N N 37 
A1BYO C39 O38  SING N N 38 
A1BYO C08 C13  SING Y N 39 
A1BYO C20 N25  SING Y N 40 
A1BYO C27 C36  SING Y N 41 
A1BYO C29 C34  SING Y N 42 
A1BYO C01 H011 SING N N 43 
A1BYO C01 H013 SING N N 44 
A1BYO C01 H012 SING N N 45 
A1BYO C03 H031 SING N N 46 
A1BYO C03 H033 SING N N 47 
A1BYO C03 H032 SING N N 48 
A1BYO C04 H041 SING N N 49 
A1BYO C04 H042 SING N N 50 
A1BYO C05 H052 SING N N 51 
A1BYO C05 H051 SING N N 52 
A1BYO C07 H071 SING N N 53 
A1BYO C07 H073 SING N N 54 
A1BYO C07 H072 SING N N 55 
A1BYO C09 H091 SING N N 56 
A1BYO C12 H121 SING N N 57 
A1BYO C17 H171 SING N N 58 
A1BYO C18 H182 SING N N 59 
A1BYO C18 H181 SING N N 60 
A1BYO C22 H221 SING N N 61 
A1BYO C28 H281 SING N N 62 
A1BYO C30 H301 SING N N 63 
A1BYO C31 H311 SING N N 64 
A1BYO C32 H321 SING N N 65 
A1BYO C33 H331 SING N N 66 
A1BYO C35 H351 SING N N 67 
A1BYO C36 H361 SING N N 68 
A1BYO C39 H393 SING N N 69 
A1BYO C39 H391 SING N N 70 
A1BYO C39 H392 SING N N 71 
A1BYO N14 H141 SING N N 72 
A1BYO N19 H191 SING N N 73 
A1BYO N26 H261 SING N N 74 
A1BYO C17 H2   SING N N 75 
A1BYO C18 H3   SING N N 76 
# 
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 
A1BYO SMILES           ACDLabs              14.52   "CN(C)CCN(C)c1cc(OC)c(Nc2nc(Nc3cc4ccccc4cc3)c(Cl)cn2)cc1NC(=O)CC"                                                                                                                                       
A1BYO InChI            InChI                1.06    "InChI=1S/C29H34ClN7O2/c1-6-27(38)33-23-16-24(26(39-5)17-25(23)37(4)14-13-36(2)3)34-29-31-18-22(30)28(35-29)32-21-12-11-19-9-7-8-10-20(19)15-21/h7-12,15-18H,6,13-14H2,1-5H3,(H,33,38)(H2,31,32,34,35)" 
A1BYO InChIKey         InChI                1.06    ANMRFDWESUKWDW-UHFFFAOYSA-N                                                                                                                                                                             
A1BYO SMILES_CANONICAL CACTVS               3.385   "CCC(=O)Nc1cc(Nc2ncc(Cl)c(Nc3ccc4ccccc4c3)n2)c(OC)cc1N(C)CCN(C)C"                                                                                                                                       
A1BYO SMILES           CACTVS               3.385   "CCC(=O)Nc1cc(Nc2ncc(Cl)c(Nc3ccc4ccccc4c3)n2)c(OC)cc1N(C)CCN(C)C"                                                                                                                                       
A1BYO SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CCC(=O)Nc1cc(c(cc1N(C)CCN(C)C)OC)Nc2ncc(c(n2)Nc3ccc4ccccc4c3)Cl"                                                                                                                                       
A1BYO SMILES           "OpenEye OEToolkits" 3.1.0.0 "CCC(=O)Nc1cc(c(cc1N(C)CCN(C)C)OC)Nc2ncc(c(n2)Nc3ccc4ccccc4c3)Cl"                                                                                                                                       
# 
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 
A1BYO "SYSTEMATIC NAME" ACDLabs              14.52   "N-[5-({5-chloro-4-[(naphthalen-2-yl)amino]pyrimidin-2-yl}amino)-2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxyphenyl]propanamide"    
A1BYO "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "~{N}-[5-[[5-chloranyl-4-(naphthalen-2-ylamino)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 
A1BYO "Create component" 2025-02-27 RCSB 
A1BYO "Modify PCM"       2025-02-27 RCSB 
A1BYO "Modify atom id"   2025-10-01 RCSB 
A1BYO "Initial release"  2025-10-08 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1BYO 
_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      ? 
# 
