data_4JZR # _model_server_result.job_id IA3q83XekUm8ee4X223CNw _model_server_result.datetime_utc '2025-02-23 02:37:38' _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 4jzr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4JZR # _exptl.entry_id 4JZR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 400.516 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(biphenyl-4-yl)-8-[(1-methyl-1H-imidazol-2-yl)methyl]-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 120 _cell.entry_id 4JZR _cell.length_a 111.455 _cell.length_b 111.455 _cell.length_c 39.974 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JZR _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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,D,E _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 18 A CYS 201 1_555 A SG CYS 25 A CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc1 A NE2 HIS 130 A HIS 313 1_555 B NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 A OD2 ASP 132 A ASP 315 1_555 B NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc3 A NE2 HIS 191 A HIS 374 1_555 B NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc4 B NI NI . A NI 401 1_555 C N2 4JR . A 4JR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc5 B NI NI . A NI 401 1_555 C N3 4JR . A 4JR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc6 B NI NI . A NI 401 1_555 E O HOH . A HOH 537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? # _chem_comp.formula 'C25 H28 N4 O' _chem_comp.formula_weight 400.516 _chem_comp.id 4JR _chem_comp.mon_nstd_flag . _chem_comp.name 2-(biphenyl-4-yl)-8-[(1-methyl-1H-imidazol-2-yl)methyl]-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 C20 C21 4JR doub 1 n y C20 C19 4JR sing 2 n y C21 C22 4JR sing 3 n y C19 C18 4JR doub 4 n y C22 C23 4JR doub 5 n y C18 C23 4JR sing 6 n y C18 C15 4JR sing 7 n n C14 C15 4JR doub 8 n y C14 C13 4JR sing 9 n y C15 C16 4JR sing 10 n y C13 C12 4JR doub 11 n y C16 C17 4JR doub 12 n y C12 C17 4JR sing 13 n y C12 N4 4JR sing 14 n n C10 N4 4JR sing 15 n n C10 C9 4JR sing 16 n n N4 C11 4JR sing 17 n n C9 C8 4JR sing 18 n n C24 C8 4JR sing 19 n n C24 C25 4JR sing 20 n n C11 O 4JR doub 21 n n C11 C8 4JR sing 22 n n C8 C7 4JR sing 23 n n C25 N3 4JR sing 24 n n C1 N1 4JR sing 25 n n N1 C2 4JR sing 26 n y N1 C4 4JR sing 27 n y N3 C5 4JR sing 28 n n N3 C6 4JR sing 29 n n C7 C6 4JR sing 30 n n C2 C3 4JR doub 31 n y C5 C4 4JR sing 32 n n C4 N2 4JR doub 33 n y C3 N2 4JR sing 34 n y C5 H2 4JR sing 35 n n C5 H3 4JR sing 36 n n C6 H4 4JR sing 37 n n C6 H5 4JR sing 38 n n C7 H6 4JR sing 39 n n C7 H7 4JR sing 40 n n C10 H8 4JR sing 41 n n C10 H9 4JR sing 42 n n C13 H10 4JR sing 43 n n C17 H11 4JR sing 44 n n C20 H12 4JR sing 45 n n C21 H13 4JR sing 46 n n C22 H14 4JR sing 47 n n C24 H15 4JR sing 48 n n C24 H16 4JR sing 49 n n C1 H17 4JR sing 50 n n C1 H18 4JR sing 51 n n C1 H19 4JR sing 52 n n C2 H20 4JR sing 53 n n C3 H21 4JR sing 54 n n C25 H22 4JR sing 55 n n C25 H23 4JR sing 56 n n C9 H24 4JR sing 57 n n C9 H25 4JR sing 58 n n C14 H26 4JR sing 59 n n C16 H27 4JR sing 60 n n C23 H28 4JR sing 61 n n C19 H29 4JR sing 62 n n # _atom_sites.entry_id 4JZR _atom_sites.fract_transf_matrix[1][1] 0.008972 _atom_sites.fract_transf_matrix[1][2] 0.00518 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01036 _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] 0.025016 _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 NI A 1 401 1 NI NI . C 3 4JR A 1 402 1 4JR LIG . D 4 EDO A 1 403 1 EDO EDO . E 5 HOH A 1 501 1 HOH HOH . E 5 HOH A 2 502 2 HOH HOH . E 5 HOH A 3 503 3 HOH HOH . E 5 HOH A 4 504 4 HOH HOH . E 5 HOH A 5 505 5 HOH HOH . E 5 HOH A 6 506 6 HOH HOH . E 5 HOH A 7 507 7 HOH HOH . E 5 HOH A 8 508 8 HOH HOH . E 5 HOH A 9 509 9 HOH HOH . E 5 HOH A 10 510 10 HOH HOH . E 5 HOH A 11 511 11 HOH HOH . E 5 HOH A 12 512 12 HOH HOH . E 5 HOH A 13 513 13 HOH HOH . E 5 HOH A 14 514 14 HOH HOH . E 5 HOH A 15 515 15 HOH HOH . E 5 HOH A 16 516 16 HOH HOH . E 5 HOH A 17 517 17 HOH HOH . E 5 HOH A 18 518 18 HOH HOH . E 5 HOH A 19 519 19 HOH HOH . E 5 HOH A 20 520 20 HOH HOH . E 5 HOH A 21 521 21 HOH HOH . E 5 HOH A 22 522 22 HOH HOH . E 5 HOH A 23 523 23 HOH HOH . E 5 HOH A 24 524 24 HOH HOH . E 5 HOH A 25 525 25 HOH HOH . E 5 HOH A 26 526 26 HOH HOH . E 5 HOH A 27 527 27 HOH HOH . E 5 HOH A 28 528 28 HOH HOH . E 5 HOH A 29 529 29 HOH HOH . E 5 HOH A 30 530 30 HOH HOH . E 5 HOH A 31 531 31 HOH HOH . E 5 HOH A 32 532 32 HOH HOH . E 5 HOH A 33 533 33 HOH HOH . E 5 HOH A 34 534 34 HOH HOH . E 5 HOH A 35 535 35 HOH HOH . E 5 HOH A 36 536 36 HOH HOH . E 5 HOH A 37 537 37 HOH HOH . E 5 HOH A 38 538 38 HOH HOH . E 5 HOH A 39 539 39 HOH HOH . E 5 HOH A 40 540 40 HOH HOH . E 5 HOH A 41 541 41 HOH HOH . E 5 HOH A 42 542 42 HOH HOH . E 5 HOH A 43 543 43 HOH HOH . E 5 HOH A 44 544 44 HOH HOH . E 5 HOH A 45 545 45 HOH HOH . E 5 HOH A 46 546 46 HOH HOH . E 5 HOH A 47 547 47 HOH HOH . E 5 HOH A 48 548 48 HOH HOH . E 5 HOH A 49 549 49 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 4JR . . . C 3 40.709 18.884 -4.567 1 41.88 ? N1 4JR 402 A 1 HETATM 2 N N3 4JR . . . C 3 42.383 21.992 -4.508 1 41.86 ? N3 4JR 402 A 1 HETATM 3 C C4 4JR . . . C 3 41.116 20.052 -4.026 1 41.05 ? C4 4JR 402 A 1 HETATM 4 C C5 4JR . . . C 3 42.485 20.638 -4.051 1 41.9 ? C5 4JR 402 A 1 HETATM 5 C C6 4JR . . . C 3 43.53 22.777 -3.937 1 42.98 ? C6 4JR 402 A 1 HETATM 6 C C7 4JR . . . C 3 44.915 22.516 -4.506 1 43.47 ? C7 4JR 402 A 1 HETATM 7 C C8 4JR . . . C 3 44.953 22.597 -6.032 1 45.09 ? C8 4JR 402 A 1 HETATM 8 C C10 4JR . . . C 3 46.382 22.76 -7.915 1 46.21 ? C10 4JR 402 A 1 HETATM 9 C C13 4JR . . . C 3 45.424 25.703 -9.441 1 52.26 ? C13 4JR 402 A 1 HETATM 10 C C15 4JR . . . C 3 46.968 27.554 -9.825 1 55.73 ? C15 4JR 402 A 1 HETATM 11 C C17 4JR . . . C 3 47.326 25.937 -8.025 1 52.09 ? C17 4JR 402 A 1 HETATM 12 C C20 4JR . . . C 3 47.122 30.316 -12.354 1 60.34 ? C20 4JR 402 A 1 HETATM 13 C C21 4JR . . . C 3 48.318 30.942 -12.021 1 60.83 ? C21 4JR 402 A 1 HETATM 14 C C22 4JR . . . C 3 49.064 30.45 -10.962 1 60.51 ? C22 4JR 402 A 1 HETATM 15 C C24 4JR . . . C 3 43.77 21.773 -6.571 1 43.88 ? C24 4JR 402 A 1 HETATM 16 C C1 4JR . . . C 3 41.445 17.852 -5.313 1 42.56 ? C1 4JR 402 A 1 HETATM 17 C C2 4JR . . . C 3 39.406 18.796 -4.311 1 41.77 ? C2 4JR 402 A 1 HETATM 18 C C3 4JR . . . C 3 38.997 19.857 -3.632 1 40.81 ? C3 4JR 402 A 1 HETATM 19 N N2 4JR . . . C 3 40.083 20.666 -3.458 1 37.58 ? N2 4JR 402 A 1 HETATM 20 C C25 4JR . . . C 3 42.435 22.141 -5.922 1 42.85 ? C25 4JR 402 A 1 HETATM 21 C C11 4JR . . . C 3 44.994 24.023 -6.544 1 45.91 ? C11 4JR 402 A 1 HETATM 22 O O 4JR . . . C 3 44.411 24.984 -6.052 1 45.68 ? O 4JR 402 A 1 HETATM 23 C C9 4JR . . . C 3 46.261 22.021 -6.584 1 45.63 ? C9 4JR 402 A 1 HETATM 24 N N4 4JR . . . C 3 45.805 24.081 -7.611 1 47.19 ? N4 4JR 402 A 1 HETATM 25 C C12 4JR . . . C 3 46.17 25.248 -8.361 1 50.56 ? C12 4JR 402 A 1 HETATM 26 C C14 4JR . . . C 3 45.808 26.835 -10.164 1 54.31 ? C14 4JR 402 A 1 HETATM 27 C C16 4JR . . . C 3 47.718 27.07 -8.74 1 54.23 ? C16 4JR 402 A 1 HETATM 28 C C18 4JR . . . C 3 47.395 28.693 -10.556 1 58.22 ? C18 4JR 402 A 1 HETATM 29 C C23 4JR . . . C 3 48.602 29.345 -10.258 1 59.58 ? C23 4JR 402 A 1 HETATM 30 C C19 4JR . . . C 3 46.667 29.208 -11.637 1 58.87 ? C19 4JR 402 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #