data_5ONE # _model_server_result.job_id j4v72jji--XEEWTOvlr6ew _model_server_result.datetime_utc '2024-10-21 23:30:10' _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 5one # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5ONE # _exptl.entry_id 5ONE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 535.596 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-(propanoylamino)-~{N}-[4-[(5,8,11-trimethyl-6-oxidanylidene-pyrimido[4,5-b][1,4]benzodiazepin-2-yl)amino]phenyl]benzamide _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 5ONE _cell.length_a 86.765 _cell.length_b 86.765 _cell.length_c 77.103 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ONE _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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 'C30 H29 N7 O3' _chem_comp.formula_weight 535.596 _chem_comp.id 9YQ _chem_comp.mon_nstd_flag . _chem_comp.name 4-(propanoylamino)-~{N}-[4-[(5,8,11-trimethyl-6-oxidanylidene-pyrimido[4,5-b][1,4]benzodiazepin-2-yl)amino]phenyl]benzamide _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 C5 N 9YQ sing 1 n n C C1 9YQ sing 2 n n O2 C27 9YQ doub 3 n n C29 C28 9YQ doub 4 n y C29 C1 9YQ sing 5 n y C28 C4 9YQ sing 6 n y C1 C2 9YQ doub 7 n y N C4 9YQ sing 8 n n N C6 9YQ sing 9 n n C4 C3 9YQ doub 10 n y C2 C3 9YQ sing 11 n y C3 C27 9YQ sing 12 n n C27 N6 9YQ sing 13 n n N6 C26 9YQ sing 14 n n N6 C25 9YQ sing 15 n n C6 C25 9YQ doub 16 n y C6 N1 9YQ sing 17 n y C25 C24 9YQ sing 18 n y N1 C7 9YQ doub 19 n y C20 C21 9YQ doub 20 n y C20 C16 9YQ sing 21 n y C18 C19 9YQ sing 22 n n C18 C17 9YQ sing 23 n n C21 C13 9YQ sing 24 n y C22 C23 9YQ doub 25 n y C22 C11 9YQ sing 26 n y C23 C8 9YQ sing 27 n y N4 C16 9YQ sing 28 n n N4 C17 9YQ sing 29 n n C16 C15 9YQ doub 30 n y N3 C11 9YQ sing 31 n n N3 C12 9YQ sing 32 n n C17 O 9YQ doub 33 n n C13 C12 9YQ sing 34 n n C13 C14 9YQ doub 35 n y C24 N5 9YQ doub 36 n y C11 C10 9YQ doub 37 n y C7 N5 9YQ sing 38 n y C7 N2 9YQ sing 39 n n C12 O1 9YQ doub 40 n n C8 N2 9YQ sing 41 n n C8 C9 9YQ doub 42 n y C15 C14 9YQ sing 43 n y C10 C9 9YQ sing 44 n y C5 H1 9YQ sing 45 n n C5 H2 9YQ sing 46 n n C5 H3 9YQ sing 47 n n N2 H4 9YQ sing 48 n n C9 H5 9YQ sing 49 n n C10 H6 9YQ sing 50 n n N3 H7 9YQ sing 51 n n C14 H8 9YQ sing 52 n n C15 H9 9YQ sing 53 n n N4 H10 9YQ sing 54 n n C2 H11 9YQ sing 55 n n C26 H12 9YQ sing 56 n n C26 H13 9YQ sing 57 n n C26 H14 9YQ sing 58 n n C28 H15 9YQ sing 59 n n C29 H16 9YQ sing 60 n n C H17 9YQ sing 61 n n C H18 9YQ sing 62 n n C H19 9YQ sing 63 n n C24 H20 9YQ sing 64 n n C23 H21 9YQ sing 65 n n C22 H22 9YQ sing 66 n n C21 H23 9YQ sing 67 n n C20 H24 9YQ sing 68 n n C18 H25 9YQ sing 69 n n C18 H26 9YQ sing 70 n n C19 H27 9YQ sing 71 n n C19 H28 9YQ sing 72 n n C19 H29 9YQ sing 73 n n # _atom_sites.entry_id 5ONE _atom_sites.fract_transf_matrix[1][1] 0.011525 _atom_sites.fract_transf_matrix[1][2] 0.006654 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013308 _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] 0.01297 _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 9YQ A 1 501 1 9YQ XXX . C 3 HOH A 1 601 11 HOH HOH . C 3 HOH A 2 602 8 HOH HOH . C 3 HOH A 3 603 12 HOH HOH . C 3 HOH A 4 604 15 HOH HOH . C 3 HOH A 5 605 4 HOH HOH . C 3 HOH A 6 606 14 HOH HOH . C 3 HOH A 7 607 9 HOH HOH . C 3 HOH A 8 608 1 HOH HOH . C 3 HOH A 9 609 10 HOH HOH . C 3 HOH A 10 610 2 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 C4 9YQ . . . B 2 28.48 -10.438 -4.847 1 67.68 ? C4 9YQ 501 A 1 HETATM 2 C C5 9YQ . . . B 2 30.64 -9.525 -5.694 1 65.8 ? C5 9YQ 501 A 1 HETATM 3 C C6 9YQ . . . B 2 29.515 -8.659 -3.675 1 66.75 ? C6 9YQ 501 A 1 HETATM 4 N N1 9YQ . . . B 2 30.682 -8.672 -3.013 1 64.73 ? N1 9YQ 501 A 1 HETATM 5 C C7 9YQ . . . B 2 30.738 -8.005 -1.849 1 66.63 ? C7 9YQ 501 A 1 HETATM 6 C C8 9YQ . . . B 2 33.207 -8.57 -1.416 1 70.33 ? C8 9YQ 501 A 1 HETATM 7 N N2 9YQ . . . B 2 31.93 -7.987 -1.164 1 68.23 ? N2 9YQ 501 A 1 HETATM 8 C C9 9YQ . . . B 2 34.255 -8.334 -0.529 1 70.33 ? C9 9YQ 501 A 1 HETATM 9 C C10 9YQ . . . B 2 35.502 -8.898 -0.752 1 72.29 ? C10 9YQ 501 A 1 HETATM 10 C C11 9YQ . . . B 2 35.721 -9.701 -1.866 1 78.4 ? C11 9YQ 501 A 1 HETATM 11 C C12 9YQ . . . B 2 38.207 -9.945 -1.84 1 106.74 ? C12 9YQ 501 A 1 HETATM 12 N N3 9YQ . . . B 2 36.947 -10.365 -2.126 1 89.93 ? N3 9YQ 501 A 1 HETATM 13 C C13 9YQ . . . B 2 39.273 -10.987 -1.959 1 116.71 ? C13 9YQ 501 A 1 HETATM 14 C C14 9YQ . . . B 2 39.153 -12.161 -1.222 1 126.06 ? C14 9YQ 501 A 1 HETATM 15 C C15 9YQ . . . B 2 40.062 -13.192 -1.379 1 130.24 ? C15 9YQ 501 A 1 HETATM 16 N N4 9YQ . . . B 2 42.022 -14.137 -2.526 1 124.47 ? N4 9YQ 501 A 1 HETATM 17 O O2 9YQ . . . B 2 25.379 -8.623 -5.032 1 74.53 ? O2 9YQ 501 A 1 HETATM 18 C C27 9YQ . . . B 2 26.478 -8.838 -4.555 1 69.93 ? C27 9YQ 501 A 1 HETATM 19 C C3 9YQ . . . B 2 27.102 -10.192 -4.71 1 66.43 ? C3 9YQ 501 A 1 HETATM 20 C C2 9YQ . . . B 2 26.218 -11.276 -4.747 1 68.04 ? C2 9YQ 501 A 1 HETATM 21 N N6 9YQ . . . B 2 27.132 -7.846 -3.85 1 71.13 ? N6 9YQ 501 A 1 HETATM 22 C C26 9YQ . . . B 2 26.429 -6.563 -3.8 1 71.34 ? C26 9YQ 501 A 1 HETATM 23 C C25 9YQ . . . B 2 28.379 -7.97 -3.169 1 67.75 ? C25 9YQ 501 A 1 HETATM 24 N N 9YQ . . . B 2 29.427 -9.373 -4.884 1 66.3 ? N 9YQ 501 A 1 HETATM 25 C C28 9YQ . . . B 2 28.934 -11.751 -4.975 1 65.75 ? C28 9YQ 501 A 1 HETATM 26 C C29 9YQ . . . B 2 28.031 -12.8 -4.999 1 66.15 ? C29 9YQ 501 A 1 HETATM 27 C C1 9YQ . . . B 2 26.665 -12.583 -4.904 1 69.05 ? C1 9YQ 501 A 1 HETATM 28 C C 9YQ . . . B 2 25.688 -13.725 -5.034 1 68.76 ? C 9YQ 501 A 1 HETATM 29 C C24 9YQ . . . B 2 28.565 -7.343 -1.937 1 67 ? C24 9YQ 501 A 1 HETATM 30 N N5 9YQ . . . B 2 29.729 -7.335 -1.271 1 66.9 ? N5 9YQ 501 A 1 HETATM 31 C C23 9YQ . . . B 2 33.434 -9.368 -2.533 1 69.51 ? C23 9YQ 501 A 1 HETATM 32 C C22 9YQ . . . B 2 34.681 -9.922 -2.758 1 74.63 ? C22 9YQ 501 A 1 HETATM 33 O O1 9YQ . . . B 2 38.481 -8.792 -1.512 1 112.56 ? O1 9YQ 501 A 1 HETATM 34 C C21 9YQ . . . B 2 40.349 -10.855 -2.836 1 119.27 ? C21 9YQ 501 A 1 HETATM 35 C C20 9YQ . . . B 2 41.262 -11.884 -2.996 1 123.89 ? C20 9YQ 501 A 1 HETATM 36 C C16 9YQ . . . B 2 41.114 -13.072 -2.283 1 128.14 ? C16 9YQ 501 A 1 HETATM 37 C C17 9YQ . . . B 2 42.036 -15.377 -1.969 1 121.75 ? C17 9YQ 501 A 1 HETATM 38 O O 9YQ . . . B 2 41.599 -15.637 -0.849 1 112.42 ? O 9YQ 501 A 1 HETATM 39 C C18 9YQ . . . B 2 42.642 -16.427 -2.864 1 121.61 ? C18 9YQ 501 A 1 HETATM 40 C C19 9YQ . . . B 2 44.108 -16.725 -2.539 1 117.66 ? C19 9YQ 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 40 #