data_3GJJ # _model_server_result.job_id K-jCtW3h6yTig5z3ifunZQ _model_server_result.datetime_utc '2025-08-30 23:49:09' _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 3gjj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":25}' # _entry.id 3GJJ # _exptl.entry_id 3GJJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 424.498 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" _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 3GJJ _cell.length_a 25.03 _cell.length_b 41.659 _cell.length_c 64.569 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GJJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,E _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 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 covale ? covale1 A O3' DT 7 A DT 7 1_555 A P B7C 8 A B7C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? covale ? covale2 A O3' B7C 8 A B7C 8 1_555 A P DC 9 A DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? covale ? covale3 B O3' DT 7 B DT 19 1_555 B P B7C 8 B B7C 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? covale ? covale4 B O3' B7C 8 B B7C 20 1_555 B P DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 6 A DA 6 1_555 B N3 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 6 A DA 6 1_555 B O4 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DT 7 A DT 7 1_555 B N1 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O4 DT 7 A DT 7 1_555 B N6 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 DC 9 A DC 9 1_555 B N1 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N4 DC 9 A DC 9 1_555 B O6 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O2 DC 9 A DC 9 1_555 B N2 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N3 DC 11 A DC 11 1_555 B N1 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N4 DC 11 A DC 11 1_555 B O6 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A O2 DC 11 A DC 11 1_555 B N2 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N1 DG 12 A DG 12 1_555 B N3 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N2 DG 12 A DG 12 1_555 B O2 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O6 DG 12 A DG 12 1_555 B N4 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C25 H24 N6 O' _chem_comp.formula_weight 424.498 _chem_comp.id HT _chem_comp.mon_nstd_flag . _chem_comp.name "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'HOECHST 33258' # 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 O1 C1 HT sing 193 n n O1 HO1 HT sing 194 n n C1 C2 HT doub 195 n y C1 C6 HT sing 196 n y C2 C3 HT sing 197 n y C2 H2 HT sing 198 n n C3 C4 HT doub 199 n y C3 H3 HT sing 200 n n C4 C5 HT sing 201 n y C4 C7 HT sing 202 n y C5 C6 HT doub 203 n y C5 H5 HT sing 204 n n C6 H6 HT sing 205 n n C7 N1 HT sing 206 n y C7 N2 HT doub 207 n y N1 C8 HT sing 208 n y N1 HN1 HT sing 209 n n C8 C9 HT doub 210 n y C8 C13 HT sing 211 n y C9 N2 HT sing 212 n y C9 C10 HT sing 213 n y C10 C11 HT doub 214 n y C10 H10 HT sing 215 n n C11 C12 HT sing 216 n y C11 H11 HT sing 217 n n C12 C13 HT doub 218 n y C12 C14 HT sing 219 n y C13 H13 HT sing 220 n n C14 N3 HT sing 221 n y C14 N4 HT doub 222 n y N3 C15 HT sing 223 n y N3 HN3 HT sing 224 n n C15 C16 HT doub 225 n y C15 C20 HT sing 226 n y C16 N4 HT sing 227 n y C16 C17 HT sing 228 n y C17 C18 HT doub 229 n y C17 H17 HT sing 230 n n C18 C19 HT sing 231 n y C18 H18 HT sing 232 n n C19 C20 HT doub 233 n y C19 N5 HT sing 234 n n C20 H20 HT sing 235 n n N5 C21 HT sing 236 n n N5 C24 HT sing 237 n n C21 C22 HT sing 238 n n C21 H211 HT sing 239 n n C21 H212 HT sing 240 n n C22 N6 HT sing 241 n n C22 H221 HT sing 242 n n C22 H222 HT sing 243 n n N6 C23 HT sing 244 n n N6 C25 HT sing 245 n n C23 C24 HT sing 246 n n C23 H231 HT sing 247 n n C23 H232 HT sing 248 n n C24 H241 HT sing 249 n n C24 H242 HT sing 250 n n C25 H253 HT sing 251 n n C25 H252 HT sing 252 n n C25 H251 HT sing 253 n n # _atom_sites.entry_id 3GJJ _atom_sites.fract_transf_matrix[1][1] 0.039952 _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] 0.024004 _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] 0.015487 _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 C 2 HT B 1 25 25 HT HT . D 3 HOH A 1 13 13 HOH HOH . D 3 HOH A 2 14 1 HOH HOH . D 3 HOH A 3 15 15 HOH HOH . D 3 HOH A 4 16 16 HOH HOH . D 3 HOH A 5 17 2 HOH HOH . D 3 HOH A 6 18 3 HOH HOH . D 3 HOH A 7 19 4 HOH HOH . D 3 HOH A 8 20 20 HOH HOH . D 3 HOH A 9 21 6 HOH HOH . D 3 HOH A 10 22 22 HOH HOH . D 3 HOH A 11 23 11 HOH HOH . D 3 HOH A 12 24 14 HOH HOH . D 3 HOH A 13 25 25 HOH HOH . D 3 HOH A 14 26 26 HOH HOH . D 3 HOH A 15 27 27 HOH HOH . D 3 HOH A 16 28 28 HOH HOH . D 3 HOH A 17 34 34 HOH HOH . D 3 HOH A 18 35 35 HOH HOH . D 3 HOH A 19 40 40 HOH HOH . D 3 HOH A 20 42 42 HOH HOH . D 3 HOH A 21 43 43 HOH HOH . D 3 HOH A 22 47 47 HOH HOH . D 3 HOH A 23 49 49 HOH HOH . D 3 HOH A 24 51 51 HOH HOH . E 3 HOH B 1 5 5 HOH HOH . E 3 HOH B 2 7 7 HOH HOH . E 3 HOH B 3 8 8 HOH HOH . E 3 HOH B 4 9 9 HOH HOH . E 3 HOH B 5 10 10 HOH HOH . E 3 HOH B 6 12 12 HOH HOH . E 3 HOH B 7 27 17 HOH HOH . E 3 HOH B 8 28 18 HOH HOH . E 3 HOH B 9 29 29 HOH HOH . E 3 HOH B 10 30 30 HOH HOH . E 3 HOH B 11 31 31 HOH HOH . E 3 HOH B 12 32 32 HOH HOH . E 3 HOH B 13 33 33 HOH HOH . E 3 HOH B 14 34 21 HOH HOH . E 3 HOH B 15 35 23 HOH HOH . E 3 HOH B 16 36 36 HOH HOH . E 3 HOH B 17 37 37 HOH HOH . E 3 HOH B 18 38 38 HOH HOH . E 3 HOH B 19 39 39 HOH HOH . E 3 HOH B 20 40 24 HOH HOH . E 3 HOH B 21 41 41 HOH HOH . E 3 HOH B 22 42 19 HOH HOH . E 3 HOH B 23 44 44 HOH HOH . E 3 HOH B 24 45 45 HOH HOH . E 3 HOH B 25 46 46 HOH HOH . E 3 HOH B 26 48 48 HOH HOH . E 3 HOH B 27 50 50 HOH HOH . E 3 HOH B 28 52 52 HOH HOH . E 3 HOH B 29 53 53 HOH HOH . E 3 HOH B 30 54 54 HOH HOH . E 3 HOH B 31 55 55 HOH HOH . E 3 HOH B 32 56 56 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 O O1 HT . . . C 2 15.076 -2.871 13.866 1 79.67 ? O1 HT 25 B 1 HETATM 2 C C1 HT . . . C 2 15.448 -2.341 15.077 1 78.57 ? C1 HT 25 B 1 HETATM 3 C C4 HT . . . C 2 16.203 -1.3 17.608 1 74.92 ? C4 HT 25 B 1 HETATM 4 C C2 HT . . . C 2 16.819 -2.37 15.49 1 77.81 ? C2 HT 25 B 1 HETATM 5 C C3 HT . . . C 2 17.193 -1.88 16.765 1 76.08 ? C3 HT 25 B 1 HETATM 6 C C6 HT . . . C 2 14.461 -1.802 15.947 1 77.73 ? C6 HT 25 B 1 HETATM 7 C C5 HT . . . C 2 14.834 -1.275 17.192 1 76.33 ? C5 HT 25 B 1 HETATM 8 C C7 HT . . . C 2 16.589 -0.626 18.871 1 72.71 ? C7 HT 25 B 1 HETATM 9 N N1 HT . . . C 2 15.694 -0.084 19.766 1 71.31 ? N1 HT 25 B 1 HETATM 10 C C8 HT . . . C 2 16.414 0.566 20.742 1 69.4 ? C8 HT 25 B 1 HETATM 11 C C9 HT . . . C 2 17.794 0.382 20.399 1 69.97 ? C9 HT 25 B 1 HETATM 12 N N2 HT . . . C 2 17.824 -0.368 19.274 1 71.59 ? N2 HT 25 B 1 HETATM 13 C C10 HT . . . C 2 18.81 0.927 21.228 1 69.08 ? C10 HT 25 B 1 HETATM 14 C C11 HT . . . C 2 18.457 1.617 22.371 1 67.87 ? C11 HT 25 B 1 HETATM 15 C C12 HT . . . C 2 17.082 1.768 22.749 1 66.47 ? C12 HT 25 B 1 HETATM 16 C C13 HT . . . C 2 16.062 1.239 21.926 1 67.63 ? C13 HT 25 B 1 HETATM 17 C C14 HT . . . C 2 16.749 2.606 23.91 1 64.14 ? C14 HT 25 B 1 HETATM 18 N N3 HT . . . C 2 15.514 2.74 24.486 1 62.61 ? N3 HT 25 B 1 HETATM 19 C C15 HT . . . C 2 15.645 3.69 25.475 1 63.6 ? C15 HT 25 B 1 HETATM 20 C C16 HT . . . C 2 16.99 4.147 25.405 1 63.66 ? C16 HT 25 B 1 HETATM 21 N N4 HT . . . C 2 17.605 3.393 24.489 1 63.47 ? N4 HT 25 B 1 HETATM 22 C C17 HT . . . C 2 17.444 5.182 26.275 1 63.67 ? C17 HT 25 B 1 HETATM 23 C C18 HT . . . C 2 16.581 5.746 27.203 1 64.46 ? C18 HT 25 B 1 HETATM 24 C C19 HT . . . C 2 15.242 5.233 27.356 1 65.25 ? C19 HT 25 B 1 HETATM 25 C C20 HT . . . C 2 14.792 4.191 26.473 1 64.54 ? C20 HT 25 B 1 HETATM 26 N N5 HT . . . C 2 14.343 5.793 28.334 1 66.08 ? N5 HT 25 B 1 HETATM 27 C C21 HT . . . C 2 15.118 6.339 29.503 1 66 ? C21 HT 25 B 1 HETATM 28 C C22 HT . . . C 2 14.17 6.803 30.635 1 66.53 ? C22 HT 25 B 1 HETATM 29 N N6 HT . . . C 2 13.255 5.708 31.028 1 67.6 ? N6 HT 25 B 1 HETATM 30 C C23 HT . . . C 2 12.456 5.309 29.849 1 67.29 ? C23 HT 25 B 1 HETATM 31 C C24 HT . . . C 2 13.415 4.727 28.806 1 66.29 ? C24 HT 25 B 1 HETATM 32 C C25 HT . . . C 2 12.34 6.253 32.05 1 67.66 ? C25 HT 25 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 706 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #