data_6D88 # _model_server_result.job_id lIr3CSV744Vv204D6h-9hA _model_server_result.datetime_utc '2025-07-08 06:01:03' _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 6d88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":502}' # _entry.id 6D88 # _exptl.entry_id 6D88 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 373.362 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[2-(1H-indol-3-yl)-1H-imidazol-4-yl](8-methoxy-1,4-benzodioxin-6-yl)methanone' _entity.pdbx_number_of_molecules 2 _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 6D88 _cell.length_a 105.536 _cell.length_b 157.894 _cell.length_c 182.025 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D88 _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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,T,U,V,W,X,Y,Z _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 ? 10 N N N ? 10 S 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 A OD1 ASP 39 A ASP 39 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc7 G O2G GTP . A GTP 501 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc8 G O2B GTP . A GTP 501 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc9 I MG MG . A MG 503 1_555 U O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc10 I MG MG . A MG 503 1_555 U O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc11 B OE1 GLN 11 B GLN 11 1_555 M MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc12 B OD2 ASP 177 B ASP 177 1_555 M MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc13 J O2A GDP . B GDP 501 1_555 M MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc14 M MG MG . B MG 504 1_555 V O HOH . B HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc15 M MG MG . B MG 504 1_555 W O HOH . C HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc16 C OD1 ASP 39 C ASP 39 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc17 C OD2 ASP 39 C ASP 39 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc18 C O THR 41 C THR 41 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc19 C OG1 THR 41 C THR 41 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc20 C O GLY 44 C GLY 44 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc21 C OE1 GLU 55 C GLU 55 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc22 C OE2 GLU 55 C GLU 55 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc23 O O3G GTP . C GTP 501 1_555 Q MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc24 O O2B GTP . C GTP 501 1_555 Q MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc25 Q MG MG . C MG 503 1_555 W O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc26 Q MG MG . C MG 503 1_555 W O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? # _chem_comp.formula 'C21 H15 N3 O4' _chem_comp.formula_weight 373.362 _chem_comp.id G9K _chem_comp.mon_nstd_flag . _chem_comp.name '[2-(1H-indol-3-yl)-1H-imidazol-4-yl](8-methoxy-1,4-benzodioxin-6-yl)methanone' _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 N2 C14 G9K sing 134 n y N2 C15 G9K sing 135 n y C20 C15 G9K doub 136 n y C20 C19 G9K sing 137 n y C14 C13 G9K doub 138 n y C15 C16 G9K sing 139 n y C19 C18 G9K doub 140 n y C13 C16 G9K sing 141 n y C13 C12 G9K sing 142 n n C16 C17 G9K doub 143 n y C18 C17 G9K sing 144 n y N1 C12 G9K sing 145 n y N1 C11 G9K sing 146 n y C12 N3 G9K doub 147 n y C11 C10 G9K doub 148 n y N3 C10 G9K sing 149 n y C10 C9 G9K sing 150 n n C1 O1 G9K sing 151 n n C9 O4 G9K doub 152 n n C9 C8 G9K sing 153 n n C21 C8 G9K doub 154 n y C21 C2 G9K sing 155 n y O1 C2 G9K sing 156 n n C8 C7 G9K sing 157 n y C2 C3 G9K doub 158 n y C7 C4 G9K doub 159 n y C3 C4 G9K sing 160 n y C3 O3 G9K sing 161 n n C4 O2 G9K sing 162 n n O3 C6 G9K sing 163 n n O2 C5 G9K sing 164 n n C6 C5 G9K doub 165 n n C1 H1 G9K sing 166 n n C1 H2 G9K sing 167 n n C1 H3 G9K sing 168 n n C11 H4 G9K sing 169 n n C14 H5 G9K sing 170 n n C17 H6 G9K sing 171 n n C18 H7 G9K sing 172 n n C19 H8 G9K sing 173 n n C20 H9 G9K sing 174 n n C21 H10 G9K sing 175 n n C5 H11 G9K sing 176 n n C6 H12 G9K sing 177 n n C7 H13 G9K sing 178 n n N1 H14 G9K sing 179 n n N2 H15 G9K sing 180 n n # _atom_sites.entry_id 6D88 _atom_sites.fract_transf_matrix[1][1] 0.009475 _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] 0.006333 _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] 0.005494 _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 5 GTP A 1 501 501 GTP GTP . H 6 CA A 1 502 1 CA CA . I 7 MG A 1 503 1 MG MG . J 8 GDP B 1 501 501 GDP GDP . K 9 MES B 1 502 1 MES MES . L 9 MES B 1 503 2 MES MES . M 7 MG B 1 504 2 MG MG . N 10 G9K B 1 505 1 G9K G9K . O 5 GTP C 1 501 501 GTP GTP . P 6 CA C 1 502 2 CA CA . Q 7 MG C 1 503 3 MG MG . R 8 GDP D 1 501 1 GDP GDP . S 10 G9K D 1 502 2 G9K G9K . T 11 ACP F 1 401 1 ACP ACP . U 12 HOH A 1 601 98 HOH HOH . U 12 HOH A 2 602 27 HOH HOH . U 12 HOH A 3 603 119 HOH HOH . U 12 HOH A 4 604 99 HOH HOH . U 12 HOH A 5 605 95 HOH HOH . U 12 HOH A 6 606 115 HOH HOH . U 12 HOH A 7 607 25 HOH HOH . U 12 HOH A 8 608 13 HOH HOH . U 12 HOH A 9 609 63 HOH HOH . U 12 HOH A 10 610 56 HOH HOH . U 12 HOH A 11 611 60 HOH HOH . U 12 HOH A 12 612 33 HOH HOH . U 12 HOH A 13 613 50 HOH HOH . U 12 HOH A 14 614 8 HOH HOH . U 12 HOH A 15 615 30 HOH HOH . U 12 HOH A 16 616 75 HOH HOH . U 12 HOH A 17 617 22 HOH HOH . V 12 HOH B 1 601 53 HOH HOH . V 12 HOH B 2 602 44 HOH HOH . V 12 HOH B 3 603 112 HOH HOH . V 12 HOH B 4 604 89 HOH HOH . V 12 HOH B 5 605 24 HOH HOH . V 12 HOH B 6 606 107 HOH HOH . V 12 HOH B 7 607 18 HOH HOH . V 12 HOH B 8 608 116 HOH HOH . V 12 HOH B 9 609 125 HOH HOH . V 12 HOH B 10 610 85 HOH HOH . V 12 HOH B 11 611 108 HOH HOH . V 12 HOH B 12 612 109 HOH HOH . V 12 HOH B 13 613 126 HOH HOH . V 12 HOH B 14 614 92 HOH HOH . V 12 HOH B 15 615 96 HOH HOH . V 12 HOH B 16 616 70 HOH HOH . V 12 HOH B 17 617 124 HOH HOH . V 12 HOH B 18 618 21 HOH HOH . V 12 HOH B 19 619 101 HOH HOH . W 12 HOH C 1 601 103 HOH HOH . W 12 HOH C 2 602 102 HOH HOH . W 12 HOH C 3 603 121 HOH HOH . W 12 HOH C 4 604 114 HOH HOH . W 12 HOH C 5 605 104 HOH HOH . W 12 HOH C 6 606 97 HOH HOH . W 12 HOH C 7 607 123 HOH HOH . W 12 HOH C 8 608 19 HOH HOH . W 12 HOH C 9 609 72 HOH HOH . W 12 HOH C 10 610 1 HOH HOH . W 12 HOH C 11 611 20 HOH HOH . W 12 HOH C 12 612 106 HOH HOH . W 12 HOH C 13 613 111 HOH HOH . W 12 HOH C 14 614 105 HOH HOH . W 12 HOH C 15 615 23 HOH HOH . W 12 HOH C 16 616 6 HOH HOH . W 12 HOH C 17 617 83 HOH HOH . W 12 HOH C 18 618 65 HOH HOH . W 12 HOH C 19 619 100 HOH HOH . W 12 HOH C 20 620 87 HOH HOH . W 12 HOH C 21 621 122 HOH HOH . W 12 HOH C 22 622 42 HOH HOH . W 12 HOH C 23 623 29 HOH HOH . W 12 HOH C 24 624 71 HOH HOH . W 12 HOH C 25 625 110 HOH HOH . W 12 HOH C 26 626 7 HOH HOH . W 12 HOH C 27 627 41 HOH HOH . W 12 HOH C 28 628 86 HOH HOH . W 12 HOH C 29 629 88 HOH HOH . X 12 HOH D 1 601 118 HOH HOH . X 12 HOH D 2 602 74 HOH HOH . X 12 HOH D 3 603 54 HOH HOH . X 12 HOH D 4 604 90 HOH HOH . X 12 HOH D 5 605 12 HOH HOH . X 12 HOH D 6 606 5 HOH HOH . X 12 HOH D 7 607 32 HOH HOH . X 12 HOH D 8 608 80 HOH HOH . X 12 HOH D 9 609 57 HOH HOH . X 12 HOH D 10 610 76 HOH HOH . X 12 HOH D 11 611 77 HOH HOH . X 12 HOH D 12 612 82 HOH HOH . X 12 HOH D 13 613 69 HOH HOH . X 12 HOH D 14 614 94 HOH HOH . Y 12 HOH E 1 201 40 HOH HOH . Y 12 HOH E 2 202 93 HOH HOH . Y 12 HOH E 3 203 17 HOH HOH . Y 12 HOH E 4 204 67 HOH HOH . Y 12 HOH E 5 205 78 HOH HOH . Z 12 HOH F 1 501 59 HOH HOH . Z 12 HOH F 2 502 117 HOH HOH . Z 12 HOH F 3 503 79 HOH HOH . Z 12 HOH F 4 504 11 HOH HOH . Z 12 HOH F 5 505 81 HOH HOH . Z 12 HOH F 6 506 46 HOH HOH . Z 12 HOH F 7 507 38 HOH HOH . Z 12 HOH F 8 508 64 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 C1 G9K . . . S 10 10.769 -7.192 21.859 1 72.17 ? C1 G9K 502 D 1 HETATM 2 C C10 G9K . . . S 10 14.875 -9.921 20.279 1 62.65 ? C10 G9K 502 D 1 HETATM 3 C C11 G9K . . . S 10 15.117 -10.935 19.391 1 61.97 ? C11 G9K 502 D 1 HETATM 4 C C12 G9K . . . S 10 14.306 -9.234 18.294 1 62.06 ? C12 G9K 502 D 1 HETATM 5 C C13 G9K . . . S 10 13.806 -8.434 17.186 1 56.61 ? C13 G9K 502 D 1 HETATM 6 C C14 G9K . . . S 10 13.444 -8.896 15.935 1 53.23 ? C14 G9K 502 D 1 HETATM 7 C C15 G9K . . . S 10 13.106 -6.694 15.887 1 51.43 ? C15 G9K 502 D 1 HETATM 8 C C16 G9K . . . S 10 13.597 -7.019 17.164 1 52.56 ? C16 G9K 502 D 1 HETATM 9 C C17 G9K . . . S 10 13.777 -6.005 18.113 1 47.21 ? C17 G9K 502 D 1 HETATM 10 C C18 G9K . . . S 10 13.471 -4.711 17.754 1 50.5 ? C18 G9K 502 D 1 HETATM 11 C C19 G9K . . . S 10 12.987 -4.407 16.482 1 50.34 ? C19 G9K 502 D 1 HETATM 12 C C2 G9K . . . S 10 12.719 -7.4 23.206 1 72.45 ? C2 G9K 502 D 1 HETATM 13 C C20 G9K . . . S 10 12.795 -5.385 15.532 1 52.09 ? C20 G9K 502 D 1 HETATM 14 C C21 G9K . . . S 10 13.291 -8.304 22.324 1 70.44 ? C21 G9K 502 D 1 HETATM 15 C C3 G9K . . . S 10 13.363 -7.104 24.421 1 76.92 ? C3 G9K 502 D 1 HETATM 16 C C4 G9K . . . S 10 14.563 -7.725 24.736 1 76.39 ? C4 G9K 502 D 1 HETATM 17 C C5 G9K . . . S 10 14.648 -6.559 26.787 1 81.32 ? C5 G9K 502 D 1 HETATM 18 C C6 G9K . . . S 10 13.424 -5.93 26.469 1 81.9 ? C6 G9K 502 D 1 HETATM 19 C C7 G9K . . . S 10 15.123 -8.634 23.852 1 74.22 ? C7 G9K 502 D 1 HETATM 20 C C8 G9K . . . S 10 14.506 -8.911 22.633 1 68.94 ? C8 G9K 502 D 1 HETATM 21 C C9 G9K . . . S 10 15.131 -9.914 21.735 1 63.24 ? C9 G9K 502 D 1 HETATM 22 N N1 G9K . . . S 10 14.746 -10.52 18.153 1 61.87 ? N1 G9K 502 D 1 HETATM 23 N N2 G9K . . . S 10 13.021 -7.864 15.166 1 49.07 ? N2 G9K 502 D 1 HETATM 24 N N3 G9K . . . S 10 14.373 -8.842 19.594 1 63.81 ? N3 G9K 502 D 1 HETATM 25 O O1 G9K . . . S 10 11.542 -6.752 22.978 1 71.53 ? O1 G9K 502 D 1 HETATM 26 O O2 G9K . . . S 10 15.22 -7.461 25.927 1 79.03 ? O2 G9K 502 D 1 HETATM 27 O O3 G9K . . . S 10 12.773 -6.2 25.291 1 81.81 ? O3 G9K 502 D 1 HETATM 28 O O4 G9K . . . S 10 15.869 -10.765 22.217 1 62.05 ? O4 G9K 502 D 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #