data_5WEF # _model_server_result.job_id 21cCUiSrBvoF3inGl2uC1Q _model_server_result.datetime_utc '2024-11-25 03:07:17' _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 5wef # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5WEF # _exptl.entry_id 5WEF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 501.362 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[(2S)-1-(2,6-dichlorobenzene-1-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-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 120 _cell.entry_id 5WEF _cell.length_a 73.878 _cell.length_b 73.878 _cell.length_c 127.282 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WEF _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id D _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 metalc ? metalc1 A NE2 HIS 41 A HIS 41 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc2 A OE1 GLU 61 A GLU 80 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc3 A OD2 ASP 89 A ASP 108 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc4 A OD1 ASP 89 A ASP 108 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc5 A OE1 GLU 100 A GLU 119 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc6 A O ILE 101 A ILE 120 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc7 B MN MN . A MN 301 1_555 D O08 GY6 . A GY6 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc8 B MN MN . A MN 301 1_555 D O05 GY6 . A GY6 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc9 C MN MN . A MN 302 1_555 D O05 GY6 . A GY6 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc10 C MN MN . A MN 302 1_555 D O12 GY6 . A GY6 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc11 C MN MN . A MN 302 1_555 I O HOH . A HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc12 C MN MN . A MN 302 1_555 I O HOH . A HOH 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? # _chem_comp.formula 'C24 H22 Cl2 N4 O4' _chem_comp.formula_weight 501.362 _chem_comp.id GY6 _chem_comp.mon_nstd_flag . _chem_comp.name 2-[(2S)-1-(2,6-dichlorobenzene-1-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-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 CL C42 GY6 sing 138 n n C44 C42 GY6 doub 139 n y C44 C35 GY6 sing 140 n y C42 C41 GY6 sing 141 n y O34 C33 GY6 doub 142 n n C35 C37 GY6 doub 143 n y C41 C33 GY6 sing 144 n n C41 C39 GY6 doub 145 n y C33 N29 GY6 sing 146 n n C37 C39 GY6 sing 147 n y N29 C27 GY6 sing 148 n n N29 C30 GY6 sing 149 n n C39 CL2 GY6 sing 150 n n C27 C24 GY6 sing 151 n n C27 C01 GY6 sing 152 n n C24 C21 GY6 sing 153 n n C30 C21 GY6 sing 154 n n N09 C01 GY6 sing 155 n n N09 C07 GY6 sing 156 n n C01 N02 GY6 doub 157 n n O08 C07 GY6 doub 158 n n C07 C04 GY6 sing 159 n n N02 C03 GY6 sing 160 n n C04 C03 GY6 doub 161 n n C04 O05 GY6 sing 162 n n C03 C11 GY6 sing 163 n n C55 C46 GY6 doub 164 n y C55 C53 GY6 sing 165 n y C46 C48 GY6 sing 166 n y C53 C52 GY6 doub 167 n y N13 C11 GY6 sing 168 n n N13 C14 GY6 sing 169 n n C11 O12 GY6 doub 170 n n C48 C50 GY6 doub 171 n y C52 C50 GY6 sing 172 n y C52 C17 GY6 sing 173 n n C14 C17 GY6 sing 174 n n C14 H15 GY6 sing 175 n n C14 H16 GY6 sing 176 n n C17 H18 GY6 sing 177 n n C17 H19 GY6 sing 178 n n C21 H23 GY6 sing 179 n n C21 H22 GY6 sing 180 n n C24 H26 GY6 sing 181 n n C24 H25 GY6 sing 182 n n C27 H28 GY6 sing 183 n n C30 H31 GY6 sing 184 n n C30 H32 GY6 sing 185 n n C35 H36 GY6 sing 186 n n C37 H38 GY6 sing 187 n n C44 H45 GY6 sing 188 n n C46 H47 GY6 sing 189 n n C48 H49 GY6 sing 190 n n C50 H51 GY6 sing 191 n n C53 H54 GY6 sing 192 n n C55 H56 GY6 sing 193 n n N09 H10 GY6 sing 194 n n N13 H20 GY6 sing 195 n n O05 H06 GY6 sing 196 n n # _atom_sites.entry_id 5WEF _atom_sites.fract_transf_matrix[1][1] 0.013536 _atom_sites.fract_transf_matrix[1][2] 0.007815 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01563 _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] 0.007857 _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 B 2 MN A 1 301 1 MN MN . C 2 MN A 1 302 2 MN MN . D 3 GY6 A 1 303 1 GY6 GY6 . E 4 EDO A 1 304 1 EDO EDO . F 4 EDO A 1 305 2 EDO EDO . G 4 EDO A 1 306 3 EDO EDO . H 5 NA A 1 307 1 NA NA . I 6 HOH A 1 401 62 HOH HOH . I 6 HOH A 2 402 10 HOH HOH . I 6 HOH A 3 403 63 HOH HOH . I 6 HOH A 4 404 17 HOH HOH . I 6 HOH A 5 405 59 HOH HOH . I 6 HOH A 6 406 52 HOH HOH . I 6 HOH A 7 407 6 HOH HOH . I 6 HOH A 8 408 61 HOH HOH . I 6 HOH A 9 409 46 HOH HOH . I 6 HOH A 10 410 7 HOH HOH . I 6 HOH A 11 411 65 HOH HOH . I 6 HOH A 12 412 2 HOH HOH . I 6 HOH A 13 413 54 HOH HOH . I 6 HOH A 14 414 24 HOH HOH . I 6 HOH A 15 415 20 HOH HOH . I 6 HOH A 16 416 69 HOH HOH . I 6 HOH A 17 417 71 HOH HOH . I 6 HOH A 18 418 3 HOH HOH . I 6 HOH A 19 419 15 HOH HOH . I 6 HOH A 20 420 21 HOH HOH . I 6 HOH A 21 421 18 HOH HOH . I 6 HOH A 22 422 44 HOH HOH . I 6 HOH A 23 423 5 HOH HOH . I 6 HOH A 24 424 4 HOH HOH . I 6 HOH A 25 425 51 HOH HOH . I 6 HOH A 26 426 29 HOH HOH . I 6 HOH A 27 427 50 HOH HOH . I 6 HOH A 28 428 39 HOH HOH . I 6 HOH A 29 429 14 HOH HOH . I 6 HOH A 30 430 68 HOH HOH . I 6 HOH A 31 431 73 HOH HOH . I 6 HOH A 32 432 70 HOH HOH . I 6 HOH A 33 433 64 HOH HOH . I 6 HOH A 34 434 1 HOH HOH . I 6 HOH A 35 435 28 HOH HOH . I 6 HOH A 36 436 72 HOH HOH . I 6 HOH A 37 437 45 HOH HOH . I 6 HOH A 38 438 9 HOH HOH . I 6 HOH A 39 439 8 HOH HOH . I 6 HOH A 40 440 16 HOH HOH . I 6 HOH A 41 441 19 HOH HOH . I 6 HOH A 42 442 11 HOH HOH . I 6 HOH A 43 443 35 HOH HOH . I 6 HOH A 44 444 58 HOH HOH . I 6 HOH A 45 445 40 HOH HOH . I 6 HOH A 46 446 13 HOH HOH . I 6 HOH A 47 447 26 HOH HOH . I 6 HOH A 48 448 25 HOH HOH . I 6 HOH A 49 449 42 HOH HOH . I 6 HOH A 50 450 57 HOH HOH . I 6 HOH A 51 451 55 HOH HOH . I 6 HOH A 52 452 47 HOH HOH . I 6 HOH A 53 453 66 HOH HOH . I 6 HOH A 54 454 12 HOH HOH . I 6 HOH A 55 455 27 HOH HOH . I 6 HOH A 56 456 67 HOH HOH . I 6 HOH A 57 457 53 HOH HOH . I 6 HOH A 58 458 22 HOH HOH . I 6 HOH A 59 459 23 HOH HOH . I 6 HOH A 60 460 36 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 C01 GY6 . . . D 3 -8.48 79.71 14.923 1 60.29 ? C01 GY6 303 A 1 HETATM 2 C C03 GY6 . . . D 3 -9.842 79.984 16.809 1 51.63 ? C03 GY6 303 A 1 HETATM 3 C C04 GY6 . . . D 3 -10.25 78.678 16.752 1 48.28 ? C04 GY6 303 A 1 HETATM 4 C C07 GY6 . . . D 3 -9.698 77.835 15.763 1 50 ? C07 GY6 303 A 1 HETATM 5 C C11 GY6 . . . D 3 -10.298 80.925 17.9 1 49.8 ? C11 GY6 303 A 1 HETATM 6 C C14 GY6 . . . D 3 -9.917 83.067 18.997 1 62.67 ? C14 GY6 303 A 1 HETATM 7 C C17 GY6 . . . D 3 -9.211 84.39 18.814 1 71.5 ? C17 GY6 303 A 1 HETATM 8 C C21 GY6 . . . D 3 -5.747 81.25 15.248 1 63.92 ? C21 GY6 303 A 1 HETATM 9 C C24 GY6 . . . D 3 -6.03 80.046 14.363 1 67.1 ? C24 GY6 303 A 1 HETATM 10 C C27 GY6 . . . D 3 -7.485 80.285 13.927 1 65.27 ? C27 GY6 303 A 1 HETATM 11 C C30 GY6 . . . D 3 -6.357 82.395 14.448 1 64.79 ? C30 GY6 303 A 1 HETATM 12 C C33 GY6 . . . D 3 -8.557 82.41 13.213 1 77.63 ? C33 GY6 303 A 1 HETATM 13 C C35 GY6 . . . D 3 -8.302 86.667 12.599 1 93.6 ? C35 GY6 303 A 1 HETATM 14 C C37 GY6 . . . D 3 -9.152 86.185 13.566 1 91.63 ? C37 GY6 303 A 1 HETATM 15 C C39 GY6 . . . D 3 -9.25 84.821 13.782 1 91.08 ? C39 GY6 303 A 1 HETATM 16 C C41 GY6 . . . D 3 -8.488 83.906 13.042 1 92.85 ? C41 GY6 303 A 1 HETATM 17 C C42 GY6 . . . D 3 -7.639 84.44 12.071 1 104.61 ? C42 GY6 303 A 1 HETATM 18 C C44 GY6 . . . D 3 -7.546 85.803 11.846 1 99.3 ? C44 GY6 303 A 1 HETATM 19 C C46 GY6 . . . D 3 -5.126 83.822 17.631 1 84.52 ? C46 GY6 303 A 1 HETATM 20 C C48 GY6 . . . D 3 -5.876 84.828 17.062 1 82.31 ? C48 GY6 303 A 1 HETATM 21 C C50 GY6 . . . D 3 -7.194 85.028 17.448 1 79.46 ? C50 GY6 303 A 1 HETATM 22 C C52 GY6 . . . D 3 -7.77 84.21 18.41 1 77.12 ? C52 GY6 303 A 1 HETATM 23 C C53 GY6 . . . D 3 -7.002 83.196 18.967 1 82.07 ? C53 GY6 303 A 1 HETATM 24 C C55 GY6 . . . D 3 -5.683 83.008 18.587 1 83.37 ? C55 GY6 303 A 1 HETATM 25 N N02 GY6 . . . D 3 -8.961 80.488 15.915 1 56.94 ? N02 GY6 303 A 1 HETATM 26 N N09 GY6 . . . D 3 -8.817 78.398 14.866 1 56.44 ? N09 GY6 303 A 1 HETATM 27 N N13 GY6 . . . D 3 -9.755 82.151 17.866 1 54.37 ? N13 GY6 303 A 1 HETATM 28 N N29 GY6 . . . D 3 -7.529 81.772 13.805 1 65.06 ? N29 GY6 303 A 1 HETATM 29 O O05 GY6 . . . D 3 -11.097 78.091 17.622 1 42.96 ? O05 GY6 303 A 1 HETATM 30 O O08 GY6 . . . D 3 -10.01 76.651 15.615 1 43.18 ? O08 GY6 303 A 1 HETATM 31 O O12 GY6 . . . D 3 -11.007 80.528 18.829 1 43.29 ? O12 GY6 303 A 1 HETATM 32 O O34 GY6 . . . D 3 -9.567 81.799 12.847 1 74.53 ? O34 GY6 303 A 1 HETATM 33 CL CL2 GY6 . . . D 3 -10.349 84.296 15.025 1 88.5 ? CL2 GY6 303 A 1 HETATM 34 CL CL GY6 . . . D 3 -6.659 83.391 11.091 1 120.74 ? CL GY6 303 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #