data_3R1N # _model_server_result.job_id IdobL-jHUZGBaE-fBjMIJA _model_server_result.datetime_utc '2024-12-27 00:24:40' _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 3r1n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3R1N # _exptl.entry_id 3R1N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.434 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-[2-(1,3-benzodioxol-5-yl)pyrimidin-4-yl]-5',6'-dihydrospiro[piperidine-4,7'-pyrrolo[3,2-c]pyridin]-4'(1'H)-one" _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 108.01 _cell.angle_gamma 90 _cell.entry_id 3R1N _cell.length_a 84.13 _cell.length_b 75.79 _cell.length_c 61.34 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3R1N _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C22 H21 N5 O3' _chem_comp.formula_weight 403.434 _chem_comp.id 05B _chem_comp.mon_nstd_flag . _chem_comp.name "2'-[2-(1,3-benzodioxol-5-yl)pyrimidin-4-yl]-5',6'-dihydrospiro[piperidine-4,7'-pyrrolo[3,2-c]pyridin]-4'(1'H)-one" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 C2 05B sing 1 n n C1 C6 05B sing 2 n n C1 C7 05B sing 3 n n C1 C11 05B sing 4 n n C2 N3 05B sing 5 n n N3 C4 05B sing 6 n n C4 O10 05B doub 7 n n C4 C12 05B sing 8 n n N5 C8 05B sing 9 n n N5 C9 05B sing 10 n n C6 C9 05B sing 11 n n C7 C8 05B sing 12 n n C11 C12 05B doub 13 n y C11 N15 05B sing 14 n y C12 C13 05B sing 15 n y C13 C14 05B doub 16 n y C14 N15 05B sing 17 n y C14 C16 05B sing 18 n y C16 C17 05B doub 19 n y C16 N21 05B sing 20 n y C17 C18 05B sing 21 n y C18 N19 05B doub 22 n y N19 C20 05B sing 23 n y C20 N21 05B doub 24 n y C20 C22 05B sing 25 n y C22 C23 05B doub 26 n y C22 C25 05B sing 27 n y C23 C24 05B sing 28 n y C24 C27 05B doub 29 n y C25 C26 05B doub 30 n y C26 C27 05B sing 31 n y C26 O30 05B sing 32 n n C27 O28 05B sing 33 n n O28 C29 05B sing 34 n n C29 O30 05B sing 35 n n C2 H2 05B sing 36 n n C2 H2A 05B sing 37 n n N3 HN3 05B sing 38 n n N5 HN5 05B sing 39 n n C6 H6 05B sing 40 n n C6 H6A 05B sing 41 n n C7 H7 05B sing 42 n n C7 H7A 05B sing 43 n n C8 H8 05B sing 44 n n C8 H8A 05B sing 45 n n C9 H9 05B sing 46 n n C9 H9A 05B sing 47 n n C13 H13 05B sing 48 n n N15 HN15 05B sing 49 n n C17 H17 05B sing 50 n n C18 H18 05B sing 51 n n C23 H23 05B sing 52 n n C24 H24 05B sing 53 n n C25 H25 05B sing 54 n n C29 H29 05B sing 55 n n C29 H29A 05B sing 56 n n # _atom_sites.entry_id 3R1N _atom_sites.fract_transf_matrix[1][1] 0.011886 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003864 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013194 _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] 0.017143 _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 B 2 05B A 1 1 1 05B 05B . C 3 HOH A 1 2 2 HOH HOH . C 3 HOH A 2 3 3 HOH HOH . C 3 HOH A 3 4 4 HOH HOH . C 3 HOH A 4 5 5 HOH HOH . C 3 HOH A 5 7 7 HOH HOH . C 3 HOH A 6 8 8 HOH HOH . C 3 HOH A 7 9 9 HOH HOH . C 3 HOH A 8 10 10 HOH HOH . C 3 HOH A 9 11 11 HOH HOH . C 3 HOH A 10 12 12 HOH HOH . C 3 HOH A 11 13 13 HOH HOH . C 3 HOH A 12 14 14 HOH HOH . C 3 HOH A 13 15 15 HOH HOH . C 3 HOH A 14 16 16 HOH HOH . C 3 HOH A 15 19 19 HOH HOH . C 3 HOH A 16 20 20 HOH HOH . C 3 HOH A 17 21 21 HOH HOH . C 3 HOH A 18 22 22 HOH HOH . C 3 HOH A 19 24 24 HOH HOH . C 3 HOH A 20 25 25 HOH HOH . C 3 HOH A 21 28 28 HOH HOH . C 3 HOH A 22 29 29 HOH HOH . C 3 HOH A 23 30 30 HOH HOH . C 3 HOH A 24 31 31 HOH HOH . C 3 HOH A 25 350 1 HOH HOH . C 3 HOH A 26 351 34 HOH HOH . C 3 HOH A 27 352 36 HOH HOH . C 3 HOH A 28 353 38 HOH HOH . C 3 HOH A 29 354 39 HOH HOH . C 3 HOH A 30 355 41 HOH HOH . C 3 HOH A 31 356 43 HOH HOH . C 3 HOH A 32 357 45 HOH HOH . C 3 HOH A 33 358 48 HOH HOH . C 3 HOH A 34 359 50 HOH HOH . C 3 HOH A 35 360 52 HOH HOH . C 3 HOH A 36 361 53 HOH HOH . C 3 HOH A 37 362 54 HOH HOH . C 3 HOH A 38 363 55 HOH HOH . C 3 HOH A 39 364 56 HOH HOH . C 3 HOH A 40 365 57 HOH HOH . C 3 HOH A 41 366 58 HOH HOH . C 3 HOH A 42 367 59 HOH HOH . C 3 HOH A 43 368 60 HOH HOH . C 3 HOH A 44 369 61 HOH HOH . C 3 HOH A 45 370 65 HOH HOH . C 3 HOH A 46 371 67 HOH HOH . C 3 HOH A 47 372 69 HOH HOH . C 3 HOH A 48 373 71 HOH HOH . C 3 HOH A 49 374 82 HOH HOH . C 3 HOH A 50 375 83 HOH HOH . C 3 HOH A 51 376 89 HOH HOH . C 3 HOH A 52 377 105 HOH HOH . C 3 HOH A 53 378 106 HOH HOH . C 3 HOH A 54 379 108 HOH HOH . C 3 HOH A 55 380 111 HOH HOH . C 3 HOH A 56 381 113 HOH HOH . C 3 HOH A 57 382 126 HOH HOH . C 3 HOH A 58 383 130 HOH HOH . C 3 HOH A 59 384 134 HOH HOH . C 3 HOH A 60 385 136 HOH HOH . C 3 HOH A 61 386 137 HOH HOH . C 3 HOH A 62 387 138 HOH HOH . C 3 HOH A 63 388 139 HOH HOH . C 3 HOH A 64 389 140 HOH HOH . C 3 HOH A 65 390 141 HOH HOH . C 3 HOH A 66 391 142 HOH HOH . C 3 HOH A 67 392 143 HOH HOH . C 3 HOH A 68 393 144 HOH HOH . C 3 HOH A 69 394 145 HOH HOH . C 3 HOH A 70 395 146 HOH HOH . C 3 HOH A 71 396 147 HOH HOH . C 3 HOH A 72 397 148 HOH HOH . C 3 HOH A 73 398 149 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 C C1 05B . . . B 2 16.85 8.271 12.722 1 52.12 ? C1 05B 1 A 1 HETATM 2 C C2 05B . . . B 2 17.45 7.894 11.379 1 52.32 ? C2 05B 1 A 1 HETATM 3 N N3 05B . . . B 2 16.573 7.024 10.563 1 55.26 ? N3 05B 1 A 1 HETATM 4 C C4 05B . . . B 2 15.242 7.266 10.323 1 54.07 ? C4 05B 1 A 1 HETATM 5 N N5 05B . . . B 2 18.941 8.002 14.79 1 48.53 ? N5 05B 1 A 1 HETATM 6 C C6 05B . . . B 2 16.883 7.1 13.685 1 52.56 ? C6 05B 1 A 1 HETATM 7 C C7 05B . . . B 2 17.636 9.46 13.319 1 52.31 ? C7 05B 1 A 1 HETATM 8 C C8 05B . . . B 2 19.029 9.175 13.949 1 50.4 ? C8 05B 1 A 1 HETATM 9 C C9 05B . . . B 2 18.335 6.814 14.18 1 53.17 ? C9 05B 1 A 1 HETATM 10 O O10 05B . . . B 2 14.607 6.717 9.379 1 51.09 ? O10 05B 1 A 1 HETATM 11 C C11 05B . . . B 2 15.393 8.677 12.389 1 50.46 ? C11 05B 1 A 1 HETATM 12 C C12 05B . . . B 2 14.675 8.268 11.268 1 48.5 ? C12 05B 1 A 1 HETATM 13 C C13 05B . . . B 2 13.426 8.878 11.313 1 48.23 ? C13 05B 1 A 1 HETATM 14 C C14 05B . . . B 2 13.414 9.647 12.413 1 49.52 ? C14 05B 1 A 1 HETATM 15 N N15 05B . . . B 2 14.634 9.522 13.041 1 49.44 ? N15 05B 1 A 1 HETATM 16 C C16 05B . . . B 2 12.389 10.558 12.924 1 44.78 ? C16 05B 1 A 1 HETATM 17 C C17 05B . . . B 2 11.129 10.672 12.349 1 43.54 ? C17 05B 1 A 1 HETATM 18 C C18 05B . . . B 2 10.227 11.553 12.904 1 43.27 ? C18 05B 1 A 1 HETATM 19 N N19 05B . . . B 2 10.509 12.282 13.955 1 43.98 ? N19 05B 1 A 1 HETATM 20 C C20 05B . . . B 2 11.747 12.167 14.473 1 51.41 ? C20 05B 1 A 1 HETATM 21 N N21 05B . . . B 2 12.677 11.327 13.984 1 46.67 ? N21 05B 1 A 1 HETATM 22 C C22 05B . . . B 2 12.022 12.98 15.633 1 51.94 ? C22 05B 1 A 1 HETATM 23 C C23 05B . . . B 2 11.475 14.249 15.648 1 54.59 ? C23 05B 1 A 1 HETATM 24 C C24 05B . . . B 2 11.658 15.092 16.724 1 57.31 ? C24 05B 1 A 1 HETATM 25 C C25 05B . . . B 2 12.803 12.527 16.695 1 55.32 ? C25 05B 1 A 1 HETATM 26 C C26 05B . . . B 2 13.005 13.392 17.761 1 57.16 ? C26 05B 1 A 1 HETATM 27 C C27 05B . . . B 2 12.437 14.683 17.778 1 59.99 ? C27 05B 1 A 1 HETATM 28 O O28 05B . . . B 2 12.736 15.34 18.942 1 64.13 ? O28 05B 1 A 1 HETATM 29 C C29 05B . . . B 2 13.223 14.311 19.822 1 59.88 ? C29 05B 1 A 1 HETATM 30 O O30 05B . . . B 2 13.688 13.247 18.917 1 61.81 ? O30 05B 1 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #