data_4Y2R # _model_server_result.job_id 8gKviCrbYBdVSwVXxvRaeQ _model_server_result.datetime_utc '2024-10-18 14:36:05' _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 4y2r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":602}' # _entry.id 4Y2R # _exptl.entry_id 4Y2R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 188.229 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(piperazin-1-yl)pyridine-3-carbonitrile _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 4Y2R _cell.length_a 92.289 _cell.length_b 92.289 _cell.length_c 244.068 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y2R _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_455 -x+y-1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 -92.289 0 122.034 # _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 metalc ? metalc1 A OD2 ASP 9 A ASP 9 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc2 A O ASP 11 A ASP 11 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.91 ? metalc ? metalc3 A OD1 ASP 185 A ASP 185 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? # _chem_comp.formula 'C10 H12 N4' _chem_comp.formula_weight 188.229 _chem_comp.id 49O _chem_comp.mon_nstd_flag . _chem_comp.name 2-(piperazin-1-yl)pyridine-3-carbonitrile _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 N14 C11 49O sing 1 n n N14 C10 49O sing 2 n n C11 C6 49O sing 3 n n C10 C5 49O sing 4 n n C6 N2 49O sing 5 n n C5 N2 49O sing 6 n n N13 C8 49O trip 7 n n N2 C1 49O sing 8 n n C8 C3 49O sing 9 n n C1 C3 49O doub 10 n y C1 N4 49O sing 11 n y C3 C7 49O sing 12 n y N4 C9 49O doub 13 n y C7 C12 49O doub 14 n y C9 C12 49O sing 15 n y C12 H1 49O sing 16 n n C7 H2 49O sing 17 n n C9 H3 49O sing 18 n n C10 H4 49O sing 19 n n C10 H5 49O sing 20 n n C11 H6 49O sing 21 n n C11 H7 49O sing 22 n n C5 H8 49O sing 23 n n C5 H9 49O sing 24 n n C6 H10 49O sing 25 n n C6 H11 49O sing 26 n n N14 H12 49O sing 27 n n # _atom_sites.entry_id 4Y2R _atom_sites.fract_transf_matrix[1][1] 0.010836 _atom_sites.fract_transf_matrix[1][2] 0.006256 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012512 _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] 0.004097 _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 MG A 1 601 782 MG MG . C 3 49O A 1 602 1 49O UNL . D 4 HOH A 1 701 28 HOH HOH . D 4 HOH A 2 702 8 HOH HOH . D 4 HOH A 3 703 25 HOH HOH . D 4 HOH A 4 704 10 HOH HOH . D 4 HOH A 5 705 2 HOH HOH . D 4 HOH A 6 706 27 HOH HOH . D 4 HOH A 7 707 24 HOH HOH . D 4 HOH A 8 708 30 HOH HOH . D 4 HOH A 9 709 1 HOH HOH . D 4 HOH A 10 710 3 HOH HOH . D 4 HOH A 11 711 4 HOH HOH . D 4 HOH A 12 712 5 HOH HOH . D 4 HOH A 13 713 6 HOH HOH . D 4 HOH A 14 714 7 HOH HOH . D 4 HOH A 15 715 9 HOH HOH . D 4 HOH A 16 716 11 HOH HOH . D 4 HOH A 17 717 12 HOH HOH . D 4 HOH A 18 718 13 HOH HOH . D 4 HOH A 19 719 14 HOH HOH . D 4 HOH A 20 720 15 HOH HOH . D 4 HOH A 21 721 16 HOH HOH . D 4 HOH A 22 722 17 HOH HOH . D 4 HOH A 23 723 18 HOH HOH . D 4 HOH A 24 724 19 HOH HOH . D 4 HOH A 25 725 20 HOH HOH . D 4 HOH A 26 726 21 HOH HOH . D 4 HOH A 27 727 22 HOH HOH . D 4 HOH A 28 728 23 HOH HOH . D 4 HOH A 29 729 26 HOH HOH . D 4 HOH A 30 730 29 HOH HOH . D 4 HOH A 31 731 31 HOH HOH . D 4 HOH A 32 732 32 HOH HOH . D 4 HOH A 33 733 33 HOH HOH . D 4 HOH A 34 734 34 HOH HOH . D 4 HOH A 35 735 35 HOH HOH . D 4 HOH A 36 736 36 HOH HOH . D 4 HOH A 37 737 37 HOH HOH . D 4 HOH A 38 738 38 HOH HOH . D 4 HOH A 39 739 39 HOH HOH . D 4 HOH A 40 740 40 HOH HOH . D 4 HOH A 41 741 41 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 C8 49O . . . C 3 -17.765 -12.668 69.452 1 38.27 ? C8 49O 602 A 1 HETATM 2 C C12 49O . . . C 3 -16.772 -11.066 72.66 1 46.49 ? C12 49O 602 A 1 HETATM 3 C C7 49O . . . C 3 -17.138 -12.042 71.753 1 46.53 ? C7 49O 602 A 1 HETATM 4 C C9 49O . . . C 3 -16.657 -9.785 72.172 1 46.38 ? C9 49O 602 A 1 HETATM 5 C C3 49O . . . C 3 -17.368 -11.694 70.432 1 46.11 ? C3 49O 602 A 1 HETATM 6 C C1 49O . . . C 3 -17.245 -10.375 70.018 1 48.37 ? C1 49O 602 A 1 HETATM 7 C C10 49O . . . C 3 -18.823 -10.43 66.707 1 48.35 ? C10 49O 602 A 1 HETATM 8 C C11 49O . . . C 3 -17.013 -8.801 66.581 1 46.63 ? C11 49O 602 A 1 HETATM 9 C C5 49O . . . C 3 -18.88 -10.327 68.211 1 45.92 ? C5 49O 602 A 1 HETATM 10 C C6 49O . . . C 3 -16.95 -8.853 68.114 1 49.91 ? C6 49O 602 A 1 HETATM 11 N N13 49O . . . C 3 -18.018 -13.423 68.599 1 31.89 ? N13 49O 602 A 1 HETATM 12 N N4 49O . . . C 3 -16.88 -9.423 70.897 1 50.22 ? N4 49O 602 A 1 HETATM 13 N N14 49O . . . C 3 -18.314 -9.2 66.068 1 46.34 ? N14 49O 602 A 1 HETATM 14 N N2 49O . . . C 3 -17.507 -10.1 68.631 1 49.12 ? N2 49O 602 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 50 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 37 _model_server_stats.element_count 14 #