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 ? #