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 ? #