data_5ZKB # _model_server_result.job_id 5WPSE0ssOKGcP7GInbz8gQ _model_server_result.datetime_utc '2024-11-04 22:40:10' _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 5zkb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1201}' # _entry.id 5ZKB # _exptl.entry_id 5ZKB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 478.63 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[2-[(2S)-2-[(dipropylamino)methyl]piperidin-1-yl]ethyl]-6-oxidanylidene-5H-pyrido[2,3-b][1,4]benzodiazepine-11-carboxamide _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 92.66 _cell.angle_gamma 90 _cell.entry_id 5ZKB _cell.length_a 213.01 _cell.length_b 60.09 _cell.length_c 48.75 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZKB _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 # 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 98 A CYS 96 1_555 A SG CYS 178 A CYS 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 362 A CYS 413 1_555 A SG CYS 365 A CYS 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C27 H38 N6 O2' _chem_comp.formula_weight 478.63 _chem_comp.id 82F _chem_comp.mon_nstd_flag . _chem_comp.name N-[2-[(2S)-2-[(dipropylamino)methyl]piperidin-1-yl]ethyl]-6-oxidanylidene-5H-pyrido[2,3-b][1,4]benzodiazepine-11-carboxamide _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 C17 C18 82F sing 1 n n C17 C16 82F sing 2 n n C20 C19 82F sing 3 n n C20 N5 82F sing 4 n n C18 C19 82F sing 5 n n C16 C15 82F sing 6 n n C24 N5 82F sing 7 n n C24 C25 82F sing 8 n n C19 N4 82F sing 9 n n N5 C21 82F sing 10 n n C15 N4 82F sing 11 n n C26 C25 82F sing 12 n n C21 C22 82F sing 13 n n N4 C14 82F sing 14 n n C22 C23 82F sing 15 n n C14 C13 82F sing 16 n n C13 N3 82F sing 17 n n O1 C12 82F doub 18 n n O C 82F doub 19 n n N3 C12 82F sing 20 n n C12 N2 82F sing 21 n n N C 82F sing 22 n n N C1 82F sing 23 n n C C11 82F sing 24 n n C1 C2 82F doub 25 n y C1 C5 82F sing 26 n y N2 C5 82F sing 27 n n N2 C6 82F sing 28 n n C2 C3 82F sing 29 n y C5 N1 82F doub 30 n y C11 C6 82F doub 31 n y C11 C10 82F sing 32 n y C6 C7 82F sing 33 n y C3 C4 82F doub 34 n y N1 C4 82F sing 35 n y C10 C9 82F doub 36 n y C7 C8 82F doub 37 n y C9 C8 82F sing 38 n y C4 H1 82F sing 39 n n C7 H2 82F sing 40 n n C8 H3 82F sing 41 n n C9 H4 82F sing 42 n n C10 H5 82F sing 43 n n N3 H6 82F sing 44 n n C13 H7 82F sing 45 n n C13 H8 82F sing 46 n n C14 H9 82F sing 47 n n C14 H10 82F sing 48 n n C15 H11 82F sing 49 n n C15 H12 82F sing 50 n n N H14 82F sing 51 n n C16 H15 82F sing 52 n n C16 H16 82F sing 53 n n C17 H17 82F sing 54 n n C17 H18 82F sing 55 n n C18 H19 82F sing 56 n n C18 H20 82F sing 57 n n C19 H21 82F sing 58 n n C2 H22 82F sing 59 n n C20 H23 82F sing 60 n n C20 H24 82F sing 61 n n C21 H25 82F sing 62 n n C21 H26 82F sing 63 n n C22 H27 82F sing 64 n n C22 H28 82F sing 65 n n C23 H29 82F sing 66 n n C23 H30 82F sing 67 n n C23 H31 82F sing 68 n n C24 H32 82F sing 69 n n C24 H33 82F sing 70 n n C25 H34 82F sing 71 n n C25 H35 82F sing 72 n n C26 H36 82F sing 73 n n C26 H37 82F sing 74 n n C26 H38 82F sing 75 n n C3 H39 82F sing 76 n n # _atom_sites.entry_id 5ZKB _atom_sites.fract_transf_matrix[1][1] 0.004695 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000218 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016642 _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] 0.020535 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id 82F _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1201 _pdbx_nonpoly_scheme.auth_seq_num 1201 _pdbx_nonpoly_scheme.pdb_mon_id 82F _pdbx_nonpoly_scheme.auth_mon_id 82F _pdbx_nonpoly_scheme.pdb_ins_code . # 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 C4 82F . . . B 2 -60.758 -12.798 12.588 1 10 ? C4 82F 1201 A 1 HETATM 2 C C5 82F . . . B 2 -58.813 -13.642 11.741 1 11.76 ? C5 82F 1201 A 1 HETATM 3 C C6 82F . . . B 2 -56.729 -14.838 12.173 1 37.39 ? C6 82F 1201 A 1 HETATM 4 N N1 82F . . . B 2 -59.997 -13.87 12.321 1 8.68 ? N1 82F 1201 A 1 HETATM 5 C C7 82F . . . B 2 -56.49 -15.835 13.115 1 34.15 ? C7 82F 1201 A 1 HETATM 6 C C8 82F . . . B 2 -55.269 -15.881 13.765 1 25.47 ? C8 82F 1201 A 1 HETATM 7 N N2 82F . . . B 2 -57.994 -14.776 11.503 1 16.69 ? N2 82F 1201 A 1 HETATM 8 C C9 82F . . . B 2 -54.292 -14.948 13.485 1 28.05 ? C9 82F 1201 A 1 HETATM 9 C C10 82F . . . B 2 -54.52 -13.951 12.552 1 30.53 ? C10 82F 1201 A 1 HETATM 10 C C11 82F . . . B 2 -55.742 -13.882 11.885 1 29.67 ? C11 82F 1201 A 1 HETATM 11 C C12 82F . . . B 2 -58.398 -15.793 10.59 1 10.05 ? C12 82F 1201 A 1 HETATM 12 N N3 82F . . . B 2 -57.457 -16.7 10.313 1 1 ? N3 82F 1201 A 1 HETATM 13 C C13 82F . . . B 2 -57.775 -17.792 9.406 1 1.75 ? C13 82F 1201 A 1 HETATM 14 C C14 82F . . . B 2 -57.364 -17.472 7.984 1 6.47 ? C14 82F 1201 A 1 HETATM 15 C C15 82F . . . B 2 -56.38 -18.752 6.171 1 11 ? C15 82F 1201 A 1 HETATM 16 N N4 82F . . . B 2 -57.626 -18.352 6.839 1 9.18 ? N4 82F 1201 A 1 HETATM 17 N N 82F . . . B 2 -57.1 -12.154 10.777 1 22.79 ? N 82F 1201 A 1 HETATM 18 C C 82F . . . B 2 -55.909 -12.768 10.907 1 19.08 ? C 82F 1201 A 1 HETATM 19 O O 82F . . . B 2 -54.957 -12.431 10.208 1 21.45 ? O 82F 1201 A 1 HETATM 20 C C1 82F . . . B 2 -58.352 -12.363 11.404 1 15.53 ? C1 82F 1201 A 1 HETATM 21 C C16 82F . . . B 2 -55.764 -17.606 5.405 1 10.11 ? C16 82F 1201 A 1 HETATM 22 C C17 82F . . . B 2 -56.739 -17.052 4.392 1 5.84 ? C17 82F 1201 A 1 HETATM 23 C C18 82F . . . B 2 -58.05 -16.657 5.059 1 6.04 ? C18 82F 1201 A 1 HETATM 24 C C19 82F . . . B 2 -58.61 -17.812 5.877 1 7.95 ? C19 82F 1201 A 1 HETATM 25 C C2 82F . . . B 2 -59.165 -11.273 11.695 1 16.31 ? C2 82F 1201 A 1 HETATM 26 C C20 82F . . . B 2 -59.248 -18.934 5.053 1 13.4 ? C20 82F 1201 A 1 HETATM 27 C C21 82F . . . B 2 -61.341 -18.646 6.284 1 21.74 ? C21 82F 1201 A 1 HETATM 28 C C22 82F . . . B 2 -61.719 -18.581 7.749 1 23.06 ? C22 82F 1201 A 1 HETATM 29 C C23 82F . . . B 2 -62.906 -17.684 7.98 1 36.72 ? C23 82F 1201 A 1 HETATM 30 C C24 82F . . . B 2 -60.632 -20.869 5.598 1 11.94 ? C24 82F 1201 A 1 HETATM 31 C C25 82F . . . B 2 -60.659 -21.864 6.733 1 16.3 ? C25 82F 1201 A 1 HETATM 32 C C26 82F . . . B 2 -61.109 -23.205 6.276 1 13.49 ? C26 82F 1201 A 1 HETATM 33 C C3 82F . . . B 2 -60.389 -11.502 12.299 1 11.09 ? C3 82F 1201 A 1 HETATM 34 N N5 82F . . . B 2 -60.2 -19.526 6 1 17.85 ? N5 82F 1201 A 1 HETATM 35 O O1 82F . . . B 2 -59.526 -15.785 10.119 1 25.74 ? O1 82F 1201 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 35 #