data_9LPD # _model_server_result.job_id aKOcRSMfpE90_YN1WAj7Yw _model_server_result.datetime_utc '2025-07-13 23:48:06' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 9lpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 9LPD # _exptl.entry_id 9LPD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 454.481 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Tirabrutinib _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.71 _cell.angle_gamma 90 _cell.entry_id 9LPD _cell.length_a 61.773 _cell.length_b 79.435 _cell.length_c 79.278 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9LPD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C25 H22 N6 O3' _chem_comp.formula_weight 454.481 _chem_comp.id A1EK0 _chem_comp.mon_nstd_flag . _chem_comp.name Tirabrutinib _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Btk Kinase inhibitor' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C7 C8 A1EK0 sing 1 n n C7 C6 A1EK0 sing 2 n n C8 N9 A1EK0 sing 3 n n C2 N3 A1EK0 doub 4 n y C2 N1 A1EK0 sing 5 n y N3 C4 A1EK0 sing 6 n y N1 C33 A1EK0 doub 7 n y C6 N5 A1EK0 sing 8 n n C6 C15 A1EK0 sing 9 n n C4 N5 A1EK0 sing 10 n n C4 C32 A1EK0 doub 11 n y C31 C30 A1EK0 doub 12 n y C31 C19 A1EK0 sing 13 n y C33 C32 A1EK0 sing 14 n y C33 N34 A1EK0 sing 15 n n N5 C16 A1EK0 sing 16 n n N9 C10 A1EK0 sing 17 n n N9 C15 A1EK0 sing 18 n n O11 C10 A1EK0 doub 19 n n C32 N18 A1EK0 sing 20 n n C30 C22 A1EK0 sing 21 n y C16 N18 A1EK0 sing 22 n n C16 O17 A1EK0 doub 23 n n N18 C19 A1EK0 sing 24 n n C10 C12 A1EK0 sing 25 n n C19 C20 A1EK0 doub 26 n y C22 O23 A1EK0 sing 27 n n C22 C21 A1EK0 doub 28 n y O23 C24 A1EK0 sing 29 n n C12 C13 A1EK0 trip 30 n n C20 C21 A1EK0 sing 31 n y C25 C24 A1EK0 doub 32 n y C25 C26 A1EK0 sing 33 n y C24 C29 A1EK0 sing 34 n y C13 C14 A1EK0 sing 35 n n C26 C27 A1EK0 doub 36 n y C29 C28 A1EK0 doub 37 n y C27 C28 A1EK0 sing 38 n y C2 H1 A1EK0 sing 39 n n C7 H2 A1EK0 sing 40 n n C7 H3 A1EK0 sing 41 n n C8 H4 A1EK0 sing 42 n n C8 H5 A1EK0 sing 43 n n C14 H6 A1EK0 sing 44 n n C14 H7 A1EK0 sing 45 n n C14 H8 A1EK0 sing 46 n n C15 H9 A1EK0 sing 47 n n C15 H10 A1EK0 sing 48 n n C20 H11 A1EK0 sing 49 n n C21 H12 A1EK0 sing 50 n n C25 H13 A1EK0 sing 51 n n C26 H14 A1EK0 sing 52 n n C27 H15 A1EK0 sing 53 n n C28 H16 A1EK0 sing 54 n n C29 H17 A1EK0 sing 55 n n C30 H18 A1EK0 sing 56 n n C31 H19 A1EK0 sing 57 n n C6 H20 A1EK0 sing 58 n n N34 H21 A1EK0 sing 59 n n N34 H22 A1EK0 sing 60 n n # _atom_sites.entry_id 9LPD _atom_sites.fract_transf_matrix[1][1] 0.016188 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004554 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012589 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013104 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 A1EK0 A 1 401 401 A1EK0 TRB . D 3 SO4 A 1 402 1 SO4 SO4 . E 3 SO4 A 1 403 2 SO4 SO4 . F 4 CLW B 1 401 402 CLW Chl . G 5 TYM B 1 402 403 TYM LIG . H 3 SO4 B 1 403 3 SO4 SO4 . I 6 HOH A 1 501 36 HOH HOH . I 6 HOH A 2 502 70 HOH HOH . I 6 HOH A 3 503 3 HOH HOH . I 6 HOH A 4 504 41 HOH HOH . I 6 HOH A 5 505 91 HOH HOH . I 6 HOH A 6 506 127 HOH HOH . I 6 HOH A 7 507 89 HOH HOH . I 6 HOH A 8 508 92 HOH HOH . I 6 HOH A 9 509 145 HOH HOH . I 6 HOH A 10 510 166 HOH HOH . I 6 HOH A 11 511 32 HOH HOH . I 6 HOH A 12 512 120 HOH HOH . I 6 HOH A 13 513 79 HOH HOH . I 6 HOH A 14 514 1 HOH HOH . I 6 HOH A 15 515 117 HOH HOH . I 6 HOH A 16 516 93 HOH HOH . I 6 HOH A 17 517 65 HOH HOH . I 6 HOH A 18 518 46 HOH HOH . I 6 HOH A 19 519 22 HOH HOH . I 6 HOH A 20 520 151 HOH HOH . I 6 HOH A 21 521 8 HOH HOH . I 6 HOH A 22 522 194 HOH HOH . I 6 HOH A 23 523 44 HOH HOH . I 6 HOH A 24 524 87 HOH HOH . I 6 HOH A 25 525 196 HOH HOH . I 6 HOH A 26 526 7 HOH HOH . I 6 HOH A 27 527 195 HOH HOH . I 6 HOH A 28 528 26 HOH HOH . I 6 HOH A 29 529 133 HOH HOH . I 6 HOH A 30 530 206 HOH HOH . I 6 HOH A 31 531 28 HOH HOH . I 6 HOH A 32 532 5 HOH HOH . I 6 HOH A 33 533 139 HOH HOH . I 6 HOH A 34 534 9 HOH HOH . I 6 HOH A 35 535 164 HOH HOH . I 6 HOH A 36 536 150 HOH HOH . I 6 HOH A 37 537 66 HOH HOH . I 6 HOH A 38 538 29 HOH HOH . I 6 HOH A 39 539 171 HOH HOH . I 6 HOH A 40 540 45 HOH HOH . I 6 HOH A 41 541 99 HOH HOH . I 6 HOH A 42 542 96 HOH HOH . I 6 HOH A 43 543 86 HOH HOH . I 6 HOH A 44 544 81 HOH HOH . I 6 HOH A 45 545 23 HOH HOH . I 6 HOH A 46 546 115 HOH HOH . I 6 HOH A 47 547 14 HOH HOH . I 6 HOH A 48 548 147 HOH HOH . I 6 HOH A 49 549 37 HOH HOH . I 6 HOH A 50 550 2 HOH HOH . I 6 HOH A 51 551 176 HOH HOH . I 6 HOH A 52 552 57 HOH HOH . I 6 HOH A 53 553 75 HOH HOH . I 6 HOH A 54 554 146 HOH HOH . I 6 HOH A 55 555 42 HOH HOH . I 6 HOH A 56 556 33 HOH HOH . I 6 HOH A 57 557 51 HOH HOH . I 6 HOH A 58 558 11 HOH HOH . I 6 HOH A 59 559 188 HOH HOH . I 6 HOH A 60 560 106 HOH HOH . I 6 HOH A 61 561 76 HOH HOH . I 6 HOH A 62 562 128 HOH HOH . I 6 HOH A 63 563 213 HOH HOH . I 6 HOH A 64 564 43 HOH HOH . I 6 HOH A 65 565 72 HOH HOH . I 6 HOH A 66 566 202 HOH HOH . I 6 HOH A 67 567 209 HOH HOH . I 6 HOH A 68 568 212 HOH HOH . I 6 HOH A 69 569 114 HOH HOH . I 6 HOH A 70 570 105 HOH HOH . I 6 HOH A 71 571 123 HOH HOH . I 6 HOH A 72 572 83 HOH HOH . I 6 HOH A 73 573 100 HOH HOH . I 6 HOH A 74 574 205 HOH HOH . I 6 HOH A 75 575 152 HOH HOH . I 6 HOH A 76 576 102 HOH HOH . I 6 HOH A 77 577 67 HOH HOH . I 6 HOH A 78 578 27 HOH HOH . I 6 HOH A 79 579 129 HOH HOH . I 6 HOH A 80 580 107 HOH HOH . I 6 HOH A 81 581 55 HOH HOH . I 6 HOH A 82 582 54 HOH HOH . I 6 HOH A 83 583 103 HOH HOH . I 6 HOH A 84 584 153 HOH HOH . I 6 HOH A 85 585 192 HOH HOH . I 6 HOH A 86 586 211 HOH HOH . I 6 HOH A 87 587 90 HOH HOH . I 6 HOH A 88 588 58 HOH HOH . I 6 HOH A 89 589 170 HOH HOH . I 6 HOH A 90 590 124 HOH HOH . I 6 HOH A 91 591 183 HOH HOH . J 6 HOH B 1 501 71 HOH HOH . J 6 HOH B 2 502 48 HOH HOH . J 6 HOH B 3 503 17 HOH HOH . J 6 HOH B 4 504 135 HOH HOH . J 6 HOH B 5 505 130 HOH HOH . J 6 HOH B 6 506 111 HOH HOH . J 6 HOH B 7 507 69 HOH HOH . J 6 HOH B 8 508 12 HOH HOH . J 6 HOH B 9 509 98 HOH HOH . J 6 HOH B 10 510 10 HOH HOH . J 6 HOH B 11 511 24 HOH HOH . J 6 HOH B 12 512 112 HOH HOH . J 6 HOH B 13 513 53 HOH HOH . J 6 HOH B 14 514 122 HOH HOH . J 6 HOH B 15 515 61 HOH HOH . J 6 HOH B 16 516 142 HOH HOH . J 6 HOH B 17 517 140 HOH HOH . J 6 HOH B 18 518 62 HOH HOH . J 6 HOH B 19 519 68 HOH HOH . J 6 HOH B 20 520 125 HOH HOH . J 6 HOH B 21 521 21 HOH HOH . J 6 HOH B 22 522 95 HOH HOH . J 6 HOH B 23 523 25 HOH HOH . J 6 HOH B 24 524 94 HOH HOH . J 6 HOH B 25 525 143 HOH HOH . J 6 HOH B 26 526 15 HOH HOH . J 6 HOH B 27 527 165 HOH HOH . J 6 HOH B 28 528 154 HOH HOH . J 6 HOH B 29 529 181 HOH HOH . J 6 HOH B 30 530 18 HOH HOH . J 6 HOH B 31 531 137 HOH HOH . J 6 HOH B 32 532 73 HOH HOH . J 6 HOH B 33 533 30 HOH HOH . J 6 HOH B 34 534 50 HOH HOH . J 6 HOH B 35 535 6 HOH HOH . J 6 HOH B 36 536 201 HOH HOH . J 6 HOH B 37 537 85 HOH HOH . J 6 HOH B 38 538 31 HOH HOH . J 6 HOH B 39 539 119 HOH HOH . J 6 HOH B 40 540 169 HOH HOH . J 6 HOH B 41 541 64 HOH HOH . J 6 HOH B 42 542 20 HOH HOH . J 6 HOH B 43 543 159 HOH HOH . J 6 HOH B 44 544 179 HOH HOH . J 6 HOH B 45 545 39 HOH HOH . J 6 HOH B 46 546 47 HOH HOH . J 6 HOH B 47 547 121 HOH HOH . J 6 HOH B 48 548 63 HOH HOH . J 6 HOH B 49 549 78 HOH HOH . J 6 HOH B 50 550 108 HOH HOH . J 6 HOH B 51 551 59 HOH HOH . J 6 HOH B 52 552 16 HOH HOH . J 6 HOH B 53 553 190 HOH HOH . J 6 HOH B 54 554 203 HOH HOH . J 6 HOH B 55 555 34 HOH HOH . J 6 HOH B 56 556 101 HOH HOH . J 6 HOH B 57 557 168 HOH HOH . J 6 HOH B 58 558 84 HOH HOH . J 6 HOH B 59 559 60 HOH HOH . J 6 HOH B 60 560 158 HOH HOH . J 6 HOH B 61 561 113 HOH HOH . J 6 HOH B 62 562 126 HOH HOH . J 6 HOH B 63 563 173 HOH HOH . J 6 HOH B 64 564 185 HOH HOH . J 6 HOH B 65 565 172 HOH HOH . J 6 HOH B 66 566 97 HOH HOH . J 6 HOH B 67 567 200 HOH HOH . J 6 HOH B 68 568 88 HOH HOH . J 6 HOH B 69 569 19 HOH HOH . J 6 HOH B 70 570 207 HOH HOH . J 6 HOH B 71 571 56 HOH HOH . J 6 HOH B 72 572 216 HOH HOH . J 6 HOH B 73 573 136 HOH HOH . J 6 HOH B 74 574 109 HOH HOH . J 6 HOH B 75 575 144 HOH HOH . J 6 HOH B 76 576 156 HOH HOH . J 6 HOH B 77 577 141 HOH HOH . J 6 HOH B 78 578 180 HOH HOH . J 6 HOH B 79 579 110 HOH HOH . J 6 HOH B 80 580 162 HOH HOH . J 6 HOH B 81 581 184 HOH HOH . J 6 HOH B 82 582 217 HOH HOH . J 6 HOH B 83 583 138 HOH HOH . J 6 HOH B 84 584 74 HOH HOH . J 6 HOH B 85 585 189 HOH HOH . J 6 HOH B 86 586 134 HOH HOH . J 6 HOH B 87 587 193 HOH HOH . J 6 HOH B 88 588 191 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 A1EK0 . . . C 2 17.513 6.04 -0.596 1 41.99 ? N1 A1EK0 401 A 1 HETATM 2 C C2 A1EK0 . . . C 2 17.939 7.258 -0.947 1 41.46 ? C2 A1EK0 401 A 1 HETATM 3 N N3 A1EK0 . . . C 2 19.159 7.785 -0.813 1 40.69 ? N3 A1EK0 401 A 1 HETATM 4 C C4 A1EK0 . . . C 2 20.029 6.922 -0.271 1 43.63 ? C4 A1EK0 401 A 1 HETATM 5 C C7 A1EK0 . . . C 2 23.223 8.106 -1.472 1 50.41 ? C7 A1EK0 401 A 1 HETATM 6 C C8 A1EK0 . . . C 2 24.021 9.404 -1.41 1 51.68 ? C8 A1EK0 401 A 1 HETATM 7 C C10 A1EK0 . . . C 2 24.667 10.821 0.608 1 58.07 ? C10 A1EK0 401 A 1 HETATM 8 C C12 A1EK0 . . . C 2 24.155 11.332 1.861 1 53.88 ? C12 A1EK0 401 A 1 HETATM 9 C C13 A1EK0 . . . C 2 23.627 11.721 2.852 1 57.16 ? C13 A1EK0 401 A 1 HETATM 10 C C14 A1EK0 . . . C 2 23.06 12.102 4.143 1 58.64 ? C14 A1EK0 401 A 1 HETATM 11 C C15 A1EK0 . . . C 2 22.934 8.972 0.709 1 50.91 ? C15 A1EK0 401 A 1 HETATM 12 C C16 A1EK0 . . . C 2 21.946 5.983 0.494 1 44.71 ? C16 A1EK0 401 A 1 HETATM 13 C C19 A1EK0 . . . C 2 21.157 3.65 0.899 1 40.56 ? C19 A1EK0 401 A 1 HETATM 14 C C20 A1EK0 . . . C 2 21.681 3.296 2.138 1 40.3 ? C20 A1EK0 401 A 1 HETATM 15 C C21 A1EK0 . . . C 2 21.988 1.971 2.411 1 40.08 ? C21 A1EK0 401 A 1 HETATM 16 C C22 A1EK0 . . . C 2 21.77 0.995 1.442 1 37.98 ? C22 A1EK0 401 A 1 HETATM 17 C C24 A1EK0 . . . C 2 23.009 -0.732 2.606 1 39.19 ? C24 A1EK0 401 A 1 HETATM 18 C C25 A1EK0 . . . C 2 24.356 -0.495 2.365 1 36.69 ? C25 A1EK0 401 A 1 HETATM 19 C C26 A1EK0 . . . C 2 25.293 -0.87 3.314 1 36.4 ? C26 A1EK0 401 A 1 HETATM 20 C C27 A1EK0 . . . C 2 24.894 -1.474 4.491 1 37.14 ? C27 A1EK0 401 A 1 HETATM 21 C C28 A1EK0 . . . C 2 23.548 -1.707 4.724 1 37.48 ? C28 A1EK0 401 A 1 HETATM 22 C C29 A1EK0 . . . C 2 22.597 -1.338 3.786 1 35.09 ? C29 A1EK0 401 A 1 HETATM 23 C C30 A1EK0 . . . C 2 21.244 1.344 0.206 1 38.82 ? C30 A1EK0 401 A 1 HETATM 24 C C31 A1EK0 . . . C 2 20.938 2.668 -0.064 1 41.58 ? C31 A1EK0 401 A 1 HETATM 25 C C32 A1EK0 . . . C 2 19.735 5.591 0.13 1 42.92 ? C32 A1EK0 401 A 1 HETATM 26 C C33 A1EK0 . . . C 2 18.395 5.177 -0.052 1 40.46 ? C33 A1EK0 401 A 1 HETATM 27 C C6 A1EK0 . . . C 2 22.138 8.339 -0.421 1 48.62 ? C6 A1EK0 401 A 1 HETATM 28 N N18 A1EK0 . . . C 2 20.927 5.03 0.577 1 43.13 ? N18 A1EK0 401 A 1 HETATM 29 N N34 A1EK0 . . . C 2 17.95 3.963 0.257 1 38.25 ? N34 A1EK0 401 A 1 HETATM 30 N N5 A1EK0 . . . C 2 21.379 7.128 -0.041 1 45.87 ? N5 A1EK0 401 A 1 HETATM 31 N N9 A1EK0 . . . C 2 23.923 9.792 0 1 53.91 ? N9 A1EK0 401 A 1 HETATM 32 O O11 A1EK0 . . . C 2 25.698 11.27 0.116 1 63.09 ? O11 A1EK0 401 A 1 HETATM 33 O O17 A1EK0 . . . C 2 23.099 5.819 0.855 1 43.08 ? O17 A1EK0 401 A 1 HETATM 34 O O23 A1EK0 . . . C 2 22.074 -0.355 1.638 1 40.87 ? O23 A1EK0 401 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 34 #