data_6YID # _model_server_result.job_id 7NNyf-W56olrCqr4u7MZcg _model_server_result.datetime_utc '2024-11-22 03:19:24' _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 6yid # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":301}' # _entry.id 6YID # _exptl.entry_id 6YID _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 489.319 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-({5-bromo-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}oxy)-N-methylbenzene-1-carboximidic acid' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.03 _cell.angle_gamma 90 _cell.entry_id 6YID _cell.length_a 75.968 _cell.length_b 76.526 _cell.length_c 95.244 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YID _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I,J 1 1 C,G,K 2 1 D,H,L 2 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 1_565 x,y+1,z 1 0 0 0 1 0 0 0 1 0 76.526 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C21 H21 Br N4 O5' _chem_comp.formula_weight 489.319 _chem_comp.id EDJ _chem_comp.mon_nstd_flag . _chem_comp.name '2-({5-bromo-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}oxy)-N-methylbenzene-1-carboximidic acid' _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 CAD OAT EDJ sing 83 n n CAB OAR EDJ sing 84 n n OAS CBB EDJ sing 85 n n OAS CAC EDJ sing 86 n n CAM CBB EDJ doub 87 n y CAM CAW EDJ sing 88 n y CBB CBE EDJ sing 89 n y NAQ CAW EDJ sing 90 n n NAQ C2 EDJ sing 91 n n CAW CAL EDJ doub 92 n y CBE OAT EDJ sing 93 n n CBE CBA EDJ doub 94 n y CAL CBA EDJ sing 95 n y CBA OAR EDJ sing 96 n n CAH CAG EDJ doub 97 n y CAH CAJ EDJ sing 98 n y CAG CAI EDJ sing 99 n y C2 N1 EDJ doub 100 n y C2 N3 EDJ sing 101 n y N1 C6 EDJ sing 102 n y CAJ CBC EDJ doub 103 n y CAI CAZ EDJ doub 104 n y N3 C4 EDJ doub 105 n y C6 C5 EDJ doub 106 n y CBC CAZ EDJ sing 107 n y CBC CAV EDJ sing 108 n n CAZ OAU EDJ sing 109 n n C4 C5 EDJ sing 110 n y C4 OAU EDJ sing 111 n n C5 BR5 EDJ sing 112 n n CAV OAE EDJ doub 113 n n CAV NAP EDJ sing 114 n n NAP CAA EDJ sing 115 n n C6 H1 EDJ sing 116 n n CAB H2 EDJ sing 117 n n CAB H3 EDJ sing 118 n n CAB H4 EDJ sing 119 n n CAL H5 EDJ sing 120 n n CAD H6 EDJ sing 121 n n CAD H7 EDJ sing 122 n n CAD H8 EDJ sing 123 n n CAC H9 EDJ sing 124 n n CAC H10 EDJ sing 125 n n CAC H11 EDJ sing 126 n n CAM H12 EDJ sing 127 n n NAQ H13 EDJ sing 128 n n CAI H14 EDJ sing 129 n n CAG H15 EDJ sing 130 n n CAH H16 EDJ sing 131 n n CAJ H17 EDJ sing 132 n n CAA H19 EDJ sing 133 n n CAA H20 EDJ sing 134 n n CAA H21 EDJ sing 135 n n NAP H18 EDJ sing 136 n n # _atom_sites.entry_id 6YID _atom_sites.fract_transf_matrix[1][1] 0.013163 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001622 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013067 _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] 0.010579 _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 2 EDJ A 1 301 1 EDJ ZZZ . F 2 EDJ B 1 301 2 EDJ ZZZ . G 2 EDJ C 1 301 3 EDJ ZZZ . H 2 EDJ D 1 301 4 EDJ ZZZ . I 3 HOH A 1 401 33 HOH HOH . I 3 HOH A 2 402 62 HOH HOH . I 3 HOH A 3 403 8 HOH HOH . I 3 HOH A 4 404 3 HOH HOH . I 3 HOH A 5 405 48 HOH HOH . I 3 HOH A 6 406 26 HOH HOH . I 3 HOH A 7 407 1 HOH HOH . I 3 HOH A 8 408 60 HOH HOH . I 3 HOH A 9 409 31 HOH HOH . I 3 HOH A 10 410 55 HOH HOH . I 3 HOH A 11 411 56 HOH HOH . I 3 HOH A 12 412 12 HOH HOH . I 3 HOH A 13 413 6 HOH HOH . I 3 HOH A 14 414 63 HOH HOH . I 3 HOH A 15 415 61 HOH HOH . I 3 HOH A 16 416 58 HOH HOH . I 3 HOH A 17 417 59 HOH HOH . J 3 HOH B 1 401 69 HOH HOH . J 3 HOH B 2 402 30 HOH HOH . J 3 HOH B 3 403 42 HOH HOH . J 3 HOH B 4 404 57 HOH HOH . J 3 HOH B 5 405 21 HOH HOH . J 3 HOH B 6 406 38 HOH HOH . J 3 HOH B 7 407 13 HOH HOH . J 3 HOH B 8 408 14 HOH HOH . J 3 HOH B 9 409 68 HOH HOH . J 3 HOH B 10 410 37 HOH HOH . J 3 HOH B 11 411 40 HOH HOH . J 3 HOH B 12 412 66 HOH HOH . J 3 HOH B 13 413 43 HOH HOH . J 3 HOH B 14 414 54 HOH HOH . J 3 HOH B 15 415 27 HOH HOH . J 3 HOH B 16 416 65 HOH HOH . J 3 HOH B 17 417 16 HOH HOH . J 3 HOH B 18 418 53 HOH HOH . J 3 HOH B 19 419 4 HOH HOH . J 3 HOH B 20 420 10 HOH HOH . J 3 HOH B 21 421 19 HOH HOH . J 3 HOH B 22 422 64 HOH HOH . J 3 HOH B 23 423 5 HOH HOH . J 3 HOH B 24 424 34 HOH HOH . K 3 HOH C 1 401 32 HOH HOH . K 3 HOH C 2 402 70 HOH HOH . K 3 HOH C 3 403 71 HOH HOH . K 3 HOH C 4 404 72 HOH HOH . K 3 HOH C 5 405 17 HOH HOH . L 3 HOH D 1 401 47 HOH HOH . L 3 HOH D 2 402 24 HOH HOH . L 3 HOH D 3 403 22 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 EDJ . . . H 2 39.536 -12.653 6.206 1 69.02 ? C4 EDJ 301 D 1 HETATM 2 C C5 EDJ . . . H 2 38.16 -12.673 6.269 1 68.93 ? C5 EDJ 301 D 1 HETATM 3 C C6 EDJ . . . H 2 37.507 -11.503 5.949 1 67.33 ? C6 EDJ 301 D 1 HETATM 4 N N1 EDJ . . . H 2 38.157 -10.398 5.577 1 67.6 ? N1 EDJ 301 D 1 HETATM 5 N N3 EDJ . . . H 2 40.227 -11.589 5.842 1 67.06 ? N3 EDJ 301 D 1 HETATM 6 C CAB EDJ . . . H 2 42.87 -6.369 2.099 1 68.55 ? CAB EDJ 301 D 1 HETATM 7 O OAR EDJ . . . H 2 43.703 -6.788 3.181 1 68.09 ? OAR EDJ 301 D 1 HETATM 8 C CBA EDJ . . . H 2 43.241 -7.788 3.989 1 64.17 ? CBA EDJ 301 D 1 HETATM 9 C CAL EDJ . . . H 2 41.906 -8.11 4.14 1 66.82 ? CAL EDJ 301 D 1 HETATM 10 C CBE EDJ . . . H 2 44.211 -8.448 4.745 1 66.23 ? CBE EDJ 301 D 1 HETATM 11 O OAT EDJ . . . H 2 45.548 -8.16 4.563 1 69.73 ? OAT EDJ 301 D 1 HETATM 12 C CAD EDJ . . . H 2 46.152 -8.727 3.401 1 74.52 ? CAD EDJ 301 D 1 HETATM 13 C CBB EDJ . . . H 2 43.82 -9.405 5.687 1 68.48 ? CBB EDJ 301 D 1 HETATM 14 O OAS EDJ . . . H 2 44.837 -9.979 6.401 1 69.14 ? OAS EDJ 301 D 1 HETATM 15 C CAC EDJ . . . H 2 44.486 -10.828 7.494 1 68.08 ? CAC EDJ 301 D 1 HETATM 16 C CAM EDJ . . . H 2 42.478 -9.706 5.856 1 66.46 ? CAM EDJ 301 D 1 HETATM 17 C CAW EDJ . . . H 2 41.52 -9.067 5.075 1 65.17 ? CAW EDJ 301 D 1 HETATM 18 N NAQ EDJ . . . H 2 40.147 -9.351 5.207 1 65.17 ? NAQ EDJ 301 D 1 HETATM 19 C C2 EDJ . . . H 2 39.495 -10.497 5.548 1 66.95 ? C2 EDJ 301 D 1 HETATM 20 BR BR5 EDJ . . . H 2 37.144 -14.209 6.707 1 84.14 ? BR5 EDJ 301 D 1 HETATM 21 O OAU EDJ . . . H 2 40.148 -13.819 6.571 1 67.69 ? OAU EDJ 301 D 1 HETATM 22 C CAZ EDJ . . . H 2 41.525 -13.949 6.598 1 68.28 ? CAZ EDJ 301 D 1 HETATM 23 C CAI EDJ . . . H 2 42.312 -13.802 5.466 1 67.76 ? CAI EDJ 301 D 1 HETATM 24 C CAG EDJ . . . H 2 43.674 -14.047 5.551 1 64.27 ? CAG EDJ 301 D 1 HETATM 25 C CAH EDJ . . . H 2 44.237 -14.434 6.747 1 62.83 ? CAH EDJ 301 D 1 HETATM 26 C CAJ EDJ . . . H 2 43.449 -14.576 7.877 1 67.63 ? CAJ EDJ 301 D 1 HETATM 27 C CBC EDJ . . . H 2 42.074 -14.333 7.819 1 72.23 ? CBC EDJ 301 D 1 HETATM 28 C CAV EDJ . . . H 2 41.28 -14.551 9.069 1 76.13 ? CAV EDJ 301 D 1 HETATM 29 O OAE EDJ . . . H 2 40.4 -15.41 9.113 1 84.56 ? OAE EDJ 301 D 1 HETATM 30 N NAP EDJ . . . H 2 41.569 -13.757 10.101 1 72.99 ? NAP EDJ 301 D 1 HETATM 31 C CAA EDJ . . . H 2 40.752 -13.725 11.301 1 69.74 ? CAA EDJ 301 D 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 57 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #