data_5BNJ # _model_server_result.job_id hRI2fIZ0Zx8vwZfKrWjtxw _model_server_result.datetime_utc '2025-01-08 21:28:25' _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 5bnj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5BNJ # _exptl.entry_id 5BNJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 421.923 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-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 90 _cell.angle_gamma 90 _cell.entry_id 5BNJ _cell.length_a 70.787 _cell.length_b 71.489 _cell.length_c 172.532 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BNJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C23 H24 Cl N5 O' _chem_comp.formula_weight 421.923 _chem_comp.id 4TV _chem_comp.mon_nstd_flag . _chem_comp.name 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-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 N2 4TV sing 1 n n N2 N6 4TV sing 2 n y N2 C3 4TV sing 3 n y N6 C5 4TV doub 4 n y C3 C4 4TV doub 5 n y C5 C4 4TV sing 6 n y C4 C7 4TV sing 7 n n C8 C7 4TV doub 8 n y C8 C9 4TV sing 9 n y C7 C12 4TV sing 10 n y C9 C10 4TV doub 11 n y C12 C11 4TV doub 12 n y C10 C11 4TV sing 13 n y C10 C13 4TV sing 14 n n C14 C13 4TV doub 15 n y C14 N15 4TV sing 16 n y C13 C19 4TV sing 17 n y N15 C16 4TV doub 18 n y C30 N20 4TV sing 19 n n C30 C29 4TV sing 20 n n C19 N20 4TV sing 21 n n C19 C17 4TV doub 22 n y N20 C21 4TV sing 23 n n C24 C23 4TV sing 24 n n C24 C25 4TV sing 25 n n C16 C17 4TV sing 26 n y C29 C23 4TV sing 27 n n C17 CL1 4TV sing 28 n n C21 C22 4TV sing 29 n n C23 C22 4TV sing 30 n n C23 C27 4TV sing 31 n n C25 N26 4TV sing 32 n n C27 N26 4TV sing 33 n n C27 O28 4TV doub 34 n n C1 H1 4TV sing 35 n n C1 H2 4TV sing 36 n n C1 H3 4TV sing 37 n n C3 H4 4TV sing 38 n n C5 H5 4TV sing 39 n n C8 H6 4TV sing 40 n n C11 H7 4TV sing 41 n n C12 H8 4TV sing 42 n n C16 H9 4TV sing 43 n n C21 H10 4TV sing 44 n n C21 H11 4TV sing 45 n n C24 H12 4TV sing 46 n n C24 H13 4TV sing 47 n n C30 H14 4TV sing 48 n n C30 H15 4TV sing 49 n n C9 H16 4TV sing 50 n n C14 H17 4TV sing 51 n n C22 H18 4TV sing 52 n n C22 H19 4TV sing 53 n n C25 H20 4TV sing 54 n n C25 H21 4TV sing 55 n n N26 H22 4TV sing 56 n n C29 H23 4TV sing 57 n n C29 H24 4TV sing 58 n n # _atom_sites.entry_id 5BNJ _atom_sites.fract_transf_matrix[1][1] 0.014127 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013988 _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] 0.005796 _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 3 4TV A 1 501 1 4TV INX . D 4 FMT B 1 301 1 FMT FMT . E 4 FMT B 1 302 2 FMT FMT . F 5 HOH A 1 601 35 HOH HOH . F 5 HOH A 2 602 8 HOH HOH . F 5 HOH A 3 603 56 HOH HOH . F 5 HOH A 4 604 41 HOH HOH . F 5 HOH A 5 605 7 HOH HOH . F 5 HOH A 6 606 55 HOH HOH . F 5 HOH A 7 607 33 HOH HOH . F 5 HOH A 8 608 3 HOH HOH . F 5 HOH A 9 609 20 HOH HOH . F 5 HOH A 10 610 32 HOH HOH . F 5 HOH A 11 611 6 HOH HOH . F 5 HOH A 12 612 11 HOH HOH . F 5 HOH A 13 613 51 HOH HOH . F 5 HOH A 14 614 2 HOH HOH . F 5 HOH A 15 615 34 HOH HOH . F 5 HOH A 16 616 21 HOH HOH . F 5 HOH A 17 617 54 HOH HOH . F 5 HOH A 18 618 5 HOH HOH . F 5 HOH A 19 619 30 HOH HOH . F 5 HOH A 20 620 53 HOH HOH . F 5 HOH A 21 621 1 HOH HOH . F 5 HOH A 22 622 18 HOH HOH . F 5 HOH A 23 623 29 HOH HOH . F 5 HOH A 24 624 4 HOH HOH . F 5 HOH A 25 625 28 HOH HOH . F 5 HOH A 26 626 19 HOH HOH . F 5 HOH A 27 627 31 HOH HOH . F 5 HOH A 28 628 9 HOH HOH . F 5 HOH A 29 629 17 HOH HOH . G 5 HOH B 1 401 38 HOH HOH . G 5 HOH B 2 402 14 HOH HOH . G 5 HOH B 3 403 47 HOH HOH . G 5 HOH B 4 404 39 HOH HOH . G 5 HOH B 5 405 57 HOH HOH . G 5 HOH B 6 406 37 HOH HOH . G 5 HOH B 7 407 44 HOH HOH . G 5 HOH B 8 408 22 HOH HOH . G 5 HOH B 9 409 26 HOH HOH . G 5 HOH B 10 410 27 HOH HOH . G 5 HOH B 11 411 45 HOH HOH . G 5 HOH B 12 412 52 HOH HOH . G 5 HOH B 13 413 36 HOH HOH . G 5 HOH B 14 414 42 HOH HOH . G 5 HOH B 15 415 43 HOH HOH . G 5 HOH B 16 416 23 HOH HOH . G 5 HOH B 17 417 16 HOH HOH . G 5 HOH B 18 418 13 HOH HOH . G 5 HOH B 19 419 24 HOH HOH . G 5 HOH B 20 420 48 HOH HOH . G 5 HOH B 21 421 49 HOH HOH . G 5 HOH B 22 422 40 HOH HOH . G 5 HOH B 23 423 46 HOH HOH . G 5 HOH B 24 424 12 HOH HOH . G 5 HOH B 25 425 50 HOH HOH . G 5 HOH B 26 426 25 HOH HOH . G 5 HOH B 27 427 15 HOH HOH . G 5 HOH B 28 428 10 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 4TV . . . C 3 37.545 55.882 45.943 1 48.52 ? C1 4TV 501 A 1 HETATM 2 C C3 4TV . . . C 3 38.803 56.958 47.832 1 47.86 ? C3 4TV 501 A 1 HETATM 3 C C4 4TV . . . C 3 39.742 56.568 48.742 1 47.17 ? C4 4TV 501 A 1 HETATM 4 C C5 4TV . . . C 3 40.014 55.209 48.487 1 47.62 ? C5 4TV 501 A 1 HETATM 5 C C7 4TV . . . C 3 40.365 57.417 49.801 1 47.27 ? C7 4TV 501 A 1 HETATM 6 C C8 4TV . . . C 3 40.45 58.813 49.65 1 45.99 ? C8 4TV 501 A 1 HETATM 7 C C11 4TV . . . C 3 41.469 57.606 51.935 1 45.52 ? C11 4TV 501 A 1 HETATM 8 C C12 4TV . . . C 3 40.887 56.825 50.958 1 44.63 ? C12 4TV 501 A 1 HETATM 9 C C16 4TV . . . C 3 43.531 61.268 54.736 1 45.5 ? C16 4TV 501 A 1 HETATM 10 C C17 4TV . . . C 3 42.371 60.631 55.128 1 46.03 ? C17 4TV 501 A 1 HETATM 11 C C19 4TV . . . C 3 41.659 59.861 54.194 1 47.19 ? C19 4TV 501 A 1 HETATM 12 C C21 4TV . . . C 3 40.566 58.003 55.417 1 50.36 ? C21 4TV 501 A 1 HETATM 13 C C23 4TV . . . C 3 38.021 58.131 55.609 1 53.43 ? C23 4TV 501 A 1 HETATM 14 C C24 4TV . . . C 3 37.633 56.959 54.678 1 55.22 ? C24 4TV 501 A 1 HETATM 15 C C27 4TV . . . C 3 36.907 58.159 56.625 1 55.94 ? C27 4TV 501 A 1 HETATM 16 O O28 4TV . . . C 3 36.629 59.102 57.335 1 55.99 ? O28 4TV 501 A 1 HETATM 17 C C30 4TV . . . C 3 39.242 59.432 53.852 1 49.28 ? C30 4TV 501 A 1 HETATM 18 N N2 4TV . . . C 3 38.506 55.901 47.05 1 49.6 ? N2 4TV 501 A 1 HETATM 19 N N6 4TV . . . C 3 39.278 54.821 47.48 1 47.87 ? N6 4TV 501 A 1 HETATM 20 C C9 4TV . . . C 3 41.035 59.597 50.633 1 45.39 ? C9 4TV 501 A 1 HETATM 21 C C10 4TV . . . C 3 41.547 58.996 51.786 1 46.03 ? C10 4TV 501 A 1 HETATM 22 C C13 4TV . . . C 3 42.182 59.788 52.867 1 47.31 ? C13 4TV 501 A 1 HETATM 23 C C14 4TV . . . C 3 43.371 60.468 52.571 1 47.19 ? C14 4TV 501 A 1 HETATM 24 N N15 4TV . . . C 3 43.996 61.176 53.496 1 46 ? N15 4TV 501 A 1 HETATM 25 CL CL1 4TV . . . C 3 41.837 60.811 56.776 1 47.66 ? CL1 4TV 501 A 1 HETATM 26 N N20 4TV . . . C 3 40.483 59.23 54.612 1 48.15 ? N20 4TV 501 A 1 HETATM 27 C C22 4TV . . . C 3 39.345 57.886 56.341 1 50.55 ? C22 4TV 501 A 1 HETATM 28 C C25 4TV . . . C 3 36.852 56.053 55.65 1 56.44 ? C25 4TV 501 A 1 HETATM 29 N N26 4TV . . . C 3 36.268 56.974 56.632 1 56.57 ? N26 4TV 501 A 1 HETATM 30 C C29 4TV . . . C 3 38.066 59.447 54.831 1 51.43 ? C29 4TV 501 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #