data_9EMA # _model_server_result.job_id HSvTt69dMogAWHpw5I9Hzw _model_server_result.datetime_utc '2025-07-07 20:03:28' _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 9ema # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 9EMA # _exptl.entry_id 9EMA _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 573.055 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 J N N ? 4 L N 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 G O3G ATP . A ATP 501 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc2 G O3B ATP . A ATP 501 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc3 G O1A ATP . A ATP 501 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc4 D OG1 THR 102 D THR 84 1_555 N MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc5 M O1G ATP . D ATP 801 1_555 N MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc6 M O2B ATP . D ATP 801 1_555 N MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc7 E OG1 THR 102 E THR 84 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc8 O O1G ATP . E ATP 801 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc9 O O2B ATP . E ATP 801 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc10 O O1A ATP . E ATP 801 1_555 P MG MG . E MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc11 F OG1 THR 102 F THR 84 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc12 F OE2 GLU 335 F GLU 317 1_555 Q MG MG . F MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc13 R O1G ATP . F ATP 802 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc14 R O2B ATP . F ATP 802 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc15 R O1A ATP . F ATP 802 1_555 S MG MG . F MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? # _chem_comp.formula 'C29 H34 Cl F N4 O5' _chem_comp.formula_weight 573.055 _chem_comp.id A1H5V _chem_comp.mon_nstd_flag . _chem_comp.name 5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]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 C37 C38 A1H5V doub 1 n y C37 C36 A1H5V sing 2 n y C38 C39 A1H5V sing 3 n y C36 C35 A1H5V doub 4 n y C39 C34 A1H5V doub 5 n y C35 C34 A1H5V sing 6 n y C35 C33 A1H5V sing 7 n n C34 N29 A1H5V sing 8 n n O40 C28 A1H5V doub 9 n n C33 C32 A1H5V sing 10 n n N29 C28 A1H5V sing 11 n n N29 N30 A1H5V sing 12 n n C19 C18 A1H5V sing 13 n n C28 C05 A1H5V sing 14 n n C32 C31 A1H5V sing 15 n n F22 C21 A1H5V sing 16 n n N30 C31 A1H5V sing 17 n n N30 C04 A1H5V sing 18 n n C20 C21 A1H5V doub 19 n y C20 C16 A1H5V sing 20 n y C18 O17 A1H5V sing 21 n n C21 C23 A1H5V sing 22 n y O17 C16 A1H5V sing 23 n n C05 C04 A1H5V doub 24 n n C05 N06 A1H5V sing 25 n n C16 C15 A1H5V doub 26 n y C04 C03 A1H5V sing 27 n n O27 C07 A1H5V doub 28 n n N06 C07 A1H5V sing 29 n n C07 C08 A1H5V sing 30 n n C23 CL24 A1H5V sing 31 n n C23 C25 A1H5V doub 32 n y C15 C25 A1H5V sing 33 n y C15 C14 A1H5V sing 34 n n C03 O02 A1H5V sing 35 n n C08 C09 A1H5V sing 36 n n O02 C01 A1H5V sing 37 n n N13 C14 A1H5V sing 38 n n N13 C12 A1H5V sing 39 n n C14 O26 A1H5V doub 40 n n C12 C09 A1H5V sing 41 n n C09 C11 A1H5V sing 42 n n C09 C10 A1H5V sing 43 n n C01 H1 A1H5V sing 44 n n C01 H2 A1H5V sing 45 n n C01 H3 A1H5V sing 46 n n C03 H4 A1H5V sing 47 n n C03 H5 A1H5V sing 48 n n N06 H6 A1H5V sing 49 n n C08 H7 A1H5V sing 50 n n C08 H8 A1H5V sing 51 n n C10 H9 A1H5V sing 52 n n C10 H10 A1H5V sing 53 n n C10 H11 A1H5V sing 54 n n C11 H12 A1H5V sing 55 n n C11 H13 A1H5V sing 56 n n C11 H14 A1H5V sing 57 n n C12 H15 A1H5V sing 58 n n C12 H16 A1H5V sing 59 n n N13 H17 A1H5V sing 60 n n C18 H18 A1H5V sing 61 n n C18 H19 A1H5V sing 62 n n C19 H20 A1H5V sing 63 n n C19 H21 A1H5V sing 64 n n C19 H22 A1H5V sing 65 n n C20 H23 A1H5V sing 66 n n C25 H24 A1H5V sing 67 n n C31 H25 A1H5V sing 68 n n C31 H26 A1H5V sing 69 n n C32 H27 A1H5V sing 70 n n C32 H28 A1H5V sing 71 n n C33 H29 A1H5V sing 72 n n C33 H30 A1H5V sing 73 n n C36 H31 A1H5V sing 74 n n C37 H32 A1H5V sing 75 n n C38 H33 A1H5V sing 76 n n C39 H34 A1H5V sing 77 n n # _atom_sites.entry_id 9EMA _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 G 3 ATP A 1 501 500 ATP ATP . H 4 A1H5V A 1 502 503 A1H5V CB6 . I 3 ATP B 1 500 500 ATP ATP . J 4 A1H5V B 1 501 501 A1H5V CB6 . K 3 ATP C 1 501 500 ATP ATP . L 4 A1H5V C 1 502 502 A1H5V CB6 . M 3 ATP D 1 801 500 ATP ATP . N 5 MG D 1 802 501 MG MG . O 3 ATP E 1 801 500 ATP ATP . P 5 MG E 1 802 501 MG MG . Q 5 MG F 1 801 501 MG MG . R 3 ATP F 1 802 500 ATP ATP . S 5 MG F 1 803 501 MG MG . # 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 CL CL24 A1H5V . . . J 4 112.597 149.4 119.689 1 25.86 ? CL24 A1H5V 501 B 1 HETATM 2 C C01 A1H5V . . . J 4 101.523 146.931 121.366 1 26.79 ? C01 A1H5V 501 B 1 HETATM 3 O O02 A1H5V . . . J 4 101.633 146.492 120.037 1 30.48 ? O02 A1H5V 501 B 1 HETATM 4 C C03 A1H5V . . . J 4 100.669 145.551 119.673 1 24.09 ? C03 A1H5V 501 B 1 HETATM 5 C C04 A1H5V . . . J 4 101.084 144.938 118.334 1 15.3 ? C04 A1H5V 501 B 1 HETATM 6 C C05 A1H5V . . . J 4 102.338 144.07 118.028 1 18.34 ? C05 A1H5V 501 B 1 HETATM 7 N N06 A1H5V . . . J 4 103.374 143.656 118.937 1 16.57 ? N06 A1H5V 501 B 1 HETATM 8 C C07 A1H5V . . . J 4 104.573 144.44 119.053 1 20.05 ? C07 A1H5V 501 B 1 HETATM 9 C C08 A1H5V . . . J 4 105.675 144.005 120.006 1 18 ? C08 A1H5V 501 B 1 HETATM 10 C C09 A1H5V . . . J 4 105.6 144.694 121.354 1 20.82 ? C09 A1H5V 501 B 1 HETATM 11 C C10 A1H5V . . . J 4 106.718 144.164 122.251 1 18.2 ? C10 A1H5V 501 B 1 HETATM 12 C C11 A1H5V . . . J 4 104.257 144.38 122.006 1 17.05 ? C11 A1H5V 501 B 1 HETATM 13 C C12 A1H5V . . . J 4 105.714 146.21 121.173 1 22.47 ? C12 A1H5V 501 B 1 HETATM 14 N N13 A1H5V . . . J 4 106.738 146.56 120.216 1 10.79 ? N13 A1H5V 501 B 1 HETATM 15 C C14 A1H5V . . . J 4 108.03 147.024 120.655 1 17.68 ? C14 A1H5V 501 B 1 HETATM 16 C C15 A1H5V . . . J 4 109.098 147.396 119.637 1 19.79 ? C15 A1H5V 501 B 1 HETATM 17 C C16 A1H5V . . . J 4 108.973 147.021 118.309 1 23.22 ? C16 A1H5V 501 B 1 HETATM 18 O O17 A1H5V . . . J 4 107.86 146.298 117.874 1 29.27 ? O17 A1H5V 501 B 1 HETATM 19 C C18 A1H5V . . . J 4 108.103 144.943 117.625 1 21.19 ? C18 A1H5V 501 B 1 HETATM 20 C C19 A1H5V . . . J 4 108.175 144.744 116.117 1 15.03 ? C19 A1H5V 501 B 1 HETATM 21 C C20 A1H5V . . . J 4 109.947 147.38 117.4 1 16.29 ? C20 A1H5V 501 B 1 HETATM 22 C C21 A1H5V . . . J 4 111.053 148.097 117.815 1 16.9 ? C21 A1H5V 501 B 1 HETATM 23 C C23 A1H5V . . . J 4 111.179 148.471 119.139 1 16.05 ? C23 A1H5V 501 B 1 HETATM 24 C C25 A1H5V . . . J 4 110.204 148.117 120.05 1 14.22 ? C25 A1H5V 501 B 1 HETATM 25 O O26 A1H5V . . . J 4 108.264 147.123 121.808 1 27.09 ? O26 A1H5V 501 B 1 HETATM 26 O O27 A1H5V . . . J 4 104.695 145.419 118.402 1 24.67 ? O27 A1H5V 501 B 1 HETATM 27 C C28 A1H5V . . . J 4 102.243 143.728 116.508 1 19.15 ? C28 A1H5V 501 B 1 HETATM 28 N N29 A1H5V . . . J 4 101.038 144.373 116.05 1 25.83 ? N29 A1H5V 501 B 1 HETATM 29 N N30 A1H5V . . . J 4 100.401 145.032 117.059 1 25.05 ? N30 A1H5V 501 B 1 HETATM 30 C C31 A1H5V . . . J 4 99.151 145.819 117.079 1 19.44 ? C31 A1H5V 501 B 1 HETATM 31 C C32 A1H5V . . . J 4 97.93 144.964 116.776 1 16.97 ? C32 A1H5V 501 B 1 HETATM 32 C C33 A1H5V . . . J 4 98.253 143.755 115.914 1 15.38 ? C33 A1H5V 501 B 1 HETATM 33 C C34 A1H5V . . . J 4 100.367 144.426 114.723 1 22.29 ? C34 A1H5V 501 B 1 HETATM 34 C C35 A1H5V . . . J 4 99.037 144.127 114.636 1 20.53 ? C35 A1H5V 501 B 1 HETATM 35 C C36 A1H5V . . . J 4 98.389 144.167 113.378 1 14.42 ? C36 A1H5V 501 B 1 HETATM 36 C C37 A1H5V . . . J 4 99.12 144.509 112.241 1 16.87 ? C37 A1H5V 501 B 1 HETATM 37 C C38 A1H5V . . . J 4 100.484 144.809 112.337 1 22.14 ? C38 A1H5V 501 B 1 HETATM 38 C C39 A1H5V . . . J 4 101.124 144.772 113.569 1 17.99 ? C39 A1H5V 501 B 1 HETATM 39 O O40 A1H5V . . . J 4 103 143.081 115.865 1 22.46 ? O40 A1H5V 501 B 1 HETATM 40 F F22 A1H5V . . . J 4 112.005 148.432 116.907 1 30.37 ? F22 A1H5V 501 B 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 40 #