data_9D3E # _model_server_result.job_id nbm5GyW5JXl_zFncbOT8WQ _model_server_result.datetime_utc '2025-01-22 00:29:30' _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 9d3e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":502}' # _entry.id 9D3E # _exptl.entry_id 9D3E _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 426.466 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl)propyl]amino]cyclobuten-1-yl]amino]-~{N},~{N}-dimethyl-3-oxidanyl-pyridine-2-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 90 _cell.angle_gamma 90 _cell.entry_id 9D3E _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9D3E _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 6 _struct_asym.id F _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 139 A CYS 118 1_555 A SG CYS 218 A CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 B SG CYS 44 H CYS 25 1_555 B SG CYS 118 H CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 B SG CYS 173 H CYS 154 1_555 B SG CYS 229 H CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 C SG CYS 42 K CYS 22 1_555 C SG CYS 116 K CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 D SG CYS 43 L CYS 24 1_555 D SG CYS 108 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 D SG CYS 155 L CYS 136 1_555 D SG CYS 215 L CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _chem_comp.formula 'C22 H26 N4 O5' _chem_comp.formula_weight 426.466 _chem_comp.id EBX _chem_comp.mon_nstd_flag . _chem_comp.name 4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl)propyl]amino]cyclobuten-1-yl]amino]-~{N},~{N}-dimethyl-3-oxidanyl-pyridine-2-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 C16 C15 EBX sing 216 n n C15 C13 EBX sing 217 n n C13 N4 EBX sing 218 n n C13 C14 EBX sing 219 n n N4 C10 EBX sing 220 n n C10 C11 EBX sing 221 n n C10 C9 EBX doub 222 n n C11 O4 EBX doub 223 n n C11 C12 EBX sing 224 n n C4 C3 EBX doub 225 n y C4 C5 EBX sing 226 n y N3 C9 EBX sing 227 n n N3 C3 EBX sing 228 n n C9 C12 EBX sing 229 n n C12 O3 EBX doub 230 n n C14 O5 EBX sing 231 n y C14 C19 EBX doub 232 n y C3 C2 EBX sing 233 n y C5 N1 EBX doub 234 n y O5 C17 EBX sing 235 n y C2 O1 EBX sing 236 n n C2 C1 EBX doub 237 n y N1 C1 EBX sing 238 n y C19 C18 EBX sing 239 n y C17 C18 EBX doub 240 n y C1 C6 EBX sing 241 n n O2 C6 EBX doub 242 n n C18 C20 EBX sing 243 n n C6 N2 EBX sing 244 n n C21 C20 EBX sing 245 n n C20 C22 EBX sing 246 n n N2 C7 EBX sing 247 n n N2 C8 EBX sing 248 n n C4 H1 EBX sing 249 n n C5 H2 EBX sing 250 n n C7 H4 EBX sing 251 n n C7 H5 EBX sing 252 n n C7 H6 EBX sing 253 n n C8 H7 EBX sing 254 n n C8 H8 EBX sing 255 n n C8 H9 EBX sing 256 n n C13 H10 EBX sing 257 n n C15 H11 EBX sing 258 n n C15 H12 EBX sing 259 n n C16 H13 EBX sing 260 n n C16 H14 EBX sing 261 n n C16 H15 EBX sing 262 n n C17 H16 EBX sing 263 n n C19 H17 EBX sing 264 n n C20 H18 EBX sing 265 n n C21 H19 EBX sing 266 n n C21 H20 EBX sing 267 n n C21 H21 EBX sing 268 n n C22 H22 EBX sing 269 n n C22 H23 EBX sing 270 n n C22 H24 EBX sing 271 n n N3 H25 EBX sing 272 n n N4 H26 EBX sing 273 n n O1 H3 EBX sing 274 n n # _atom_sites.entry_id 9D3E _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 E 5 CLR A 1 501 501 CLR CLR . F 6 EBX A 1 502 501 EBX PFE . G 7 A1A1W A 1 503 502 A1A1W PFF . # 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 C1 EBX . . . F 6 169.45 187.78 166.124 1 109.73 ? C1 EBX 502 A 1 HETATM 2 C C2 EBX . . . F 6 169.554 187.994 164.734 1 110.97 ? C2 EBX 502 A 1 HETATM 3 C C3 EBX . . . F 6 168.731 187.259 163.867 1 109.59 ? C3 EBX 502 A 1 HETATM 4 C C4 EBX . . . F 6 167.84 186.334 164.393 1 108.68 ? C4 EBX 502 A 1 HETATM 5 C C5 EBX . . . F 6 167.812 186.184 165.763 1 109.39 ? C5 EBX 502 A 1 HETATM 6 C C6 EBX . . . F 6 170.104 188.556 167.244 1 110.55 ? C6 EBX 502 A 1 HETATM 7 C C7 EBX . . . F 6 170.366 190.934 166.225 1 109.86 ? C7 EBX 502 A 1 HETATM 8 C C8 EBX . . . F 6 171.501 190.163 168.212 1 110.71 ? C8 EBX 502 A 1 HETATM 9 C C11 EBX . . . F 6 166.357 188.15 160.231 1 107.71 ? C11 EBX 502 A 1 HETATM 10 C C10 EBX . . . F 6 167.818 187.984 160.24 1 106.75 ? C10 EBX 502 A 1 HETATM 11 C C12 EBX . . . F 6 166.36 187.888 161.703 1 108.75 ? C12 EBX 502 A 1 HETATM 12 C C13 EBX . . . F 6 168.498 188.33 157.909 1 109.99 ? C13 EBX 502 A 1 HETATM 13 C C14 EBX . . . F 6 169.364 189.433 157.469 1 112.14 ? C14 EBX 502 A 1 HETATM 14 C C15 EBX . . . F 6 168.63 187.072 157.051 1 109.84 ? C15 EBX 502 A 1 HETATM 15 C C16 EBX . . . F 6 169.985 186.415 157.164 1 109.43 ? C16 EBX 502 A 1 HETATM 16 C C17 EBX . . . F 6 170.395 190.618 155.944 1 111.89 ? C17 EBX 502 A 1 HETATM 17 C C18 EBX . . . F 6 170.691 191.192 157.125 1 112.15 ? C18 EBX 502 A 1 HETATM 18 C C19 EBX . . . F 6 170.014 190.412 158.106 1 112.19 ? C19 EBX 502 A 1 HETATM 19 C C20 EBX . . . F 6 171.568 192.416 157.366 1 111.79 ? C20 EBX 502 A 1 HETATM 20 C C21 EBX . . . F 6 171.491 192.884 158.809 1 109.91 ? C21 EBX 502 A 1 HETATM 21 C C22 EBX . . . F 6 173.005 192.169 156.963 1 111.62 ? C22 EBX 502 A 1 HETATM 22 C C9 EBX . . . F 6 167.821 187.738 161.632 1 107.98 ? C9 EBX 502 A 1 HETATM 23 N N1 EBX . . . F 6 168.584 186.875 166.615 1 109.33 ? N1 EBX 502 A 1 HETATM 24 N N2 EBX . . . F 6 170.564 189.816 167.147 1 111.61 ? N2 EBX 502 A 1 HETATM 25 N N3 EBX . . . F 6 168.843 187.485 162.476 1 109.96 ? N3 EBX 502 A 1 HETATM 26 N N4 EBX . . . F 6 168.754 188.024 159.307 1 107.61 ? N4 EBX 502 A 1 HETATM 27 O O1 EBX . . . F 6 170.479 188.698 164.033 1 113.13 ? O1 EBX 502 A 1 HETATM 28 O O2 EBX . . . F 6 170.179 187.929 168.285 1 109.76 ? O2 EBX 502 A 1 HETATM 29 O O3 EBX . . . F 6 165.506 187.828 162.582 1 107.8 ? O3 EBX 502 A 1 HETATM 30 O O4 EBX . . . F 6 165.503 188.392 159.388 1 107.52 ? O4 EBX 502 A 1 HETATM 31 O O5 EBX . . . F 6 169.58 189.533 156.123 1 112.28 ? O5 EBX 502 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 31 #