data_5W3I # _model_server_result.job_id DuBuaFRtCPVUndOyJ5SSqg _model_server_result.datetime_utc '2024-11-28 13:24:08' _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 5w3i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 5W3I # _exptl.entry_id 5W3I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 416.428 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-hydroxy-N-(2-methoxyethyl)-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-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 5W3I _cell.length_a 61.162 _cell.length_b 61.162 _cell.length_c 94.813 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W3I _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 _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 4 _struct_asym.id E _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc2 A OE2 GLU 61 A GLU 80 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc3 A OD1 ASP 89 A ASP 108 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc4 A OD2 ASP 89 A ASP 108 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc5 A OE1 GLU 100 A GLU 119 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc6 A O ILE 101 A ILE 120 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc7 B MN MN . A MN 301 1_555 E O02 GY5 . A GY5 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc8 B MN MN . A MN 301 1_555 E O01 GY5 . A GY5 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc9 C MN MN . A MN 302 1_555 E O01 GY5 . A GY5 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc10 C MN MN . A MN 302 1_555 E O03 GY5 . A GY5 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc11 C MN MN . A MN 302 1_555 F O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc12 C MN MN . A MN 302 1_555 F O HOH . A HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? # _chem_comp.formula 'C20 H24 N4 O6' _chem_comp.formula_weight 416.428 _chem_comp.id GY5 _chem_comp.mon_nstd_flag . _chem_comp.name 5-hydroxy-N-(2-methoxyethyl)-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-1,6-dihydropyrimidine-4-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SRI-29685 # 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 O02 C04 GY5 doub 142 n n C C17 GY5 doub 143 n y C C13 GY5 sing 144 n y C17 C16 GY5 sing 145 n y O01 C03 GY5 sing 146 n n C04 C03 GY5 sing 147 n n C04 N02 GY5 sing 148 n n C13 C14 GY5 doub 149 n y C03 C02 GY5 doub 150 n n C16 O1 GY5 sing 151 n n C16 C15 GY5 doub 152 n y O1 C12 GY5 sing 153 n n N02 C01 GY5 sing 154 n n C14 C15 GY5 sing 155 n y C12 C11 GY5 sing 156 n n C02 N01 GY5 sing 157 n n C02 C05 GY5 sing 158 n n C01 N01 GY5 doub 159 n n C01 C09 GY5 sing 160 n n O03 C05 GY5 doub 161 n n C05 N03 GY5 sing 162 n n C09 N GY5 sing 163 n n C09 C08 GY5 sing 164 n n C11 N GY5 sing 165 n n C11 O GY5 doub 166 n n N C10 GY5 sing 167 n n C08 C07 GY5 sing 168 n n N03 C06 GY5 sing 169 n n C06 C1 GY5 sing 170 n n C18 O11 GY5 sing 171 n n C10 C07 GY5 sing 172 n n C1 O11 GY5 sing 173 n n C H GY5 sing 174 n n C06 H10 GY5 sing 175 n n C06 H03 GY5 sing 176 n n C07 H05 GY5 sing 177 n n C07 H11 GY5 sing 178 n n C08 H07 GY5 sing 179 n n C08 H06 GY5 sing 180 n n C09 H08 GY5 sing 181 n n C1 H13 GY5 sing 182 n n C1 H12 GY5 sing 183 n n C10 H1 GY5 sing 184 n n C10 H09 GY5 sing 185 n n C12 H2 GY5 sing 186 n n C12 H3 GY5 sing 187 n n C13 H120 GY5 sing 188 n n C14 H130 GY5 sing 189 n n C15 H14 GY5 sing 190 n n C17 H15 GY5 sing 191 n n N02 H01 GY5 sing 192 n n N03 H04 GY5 sing 193 n n O01 H02 GY5 sing 194 n n C18 H112 GY5 sing 195 n n C18 H111 GY5 sing 196 n n C18 H113 GY5 sing 197 n n # _atom_sites.entry_id 5W3I _atom_sites.fract_transf_matrix[1][1] 0.01635 _atom_sites.fract_transf_matrix[1][2] 0.00944 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018879 _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] 0.010547 _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 1 301 201 MN MN . C 2 MN A 1 302 202 MN MN . D 3 GOL A 1 303 1 GOL GOL . E 4 GY5 A 1 304 1 GY5 GY5 . F 5 HOH A 1 401 3 HOH HOH . F 5 HOH A 2 402 177 HOH HOH . F 5 HOH A 3 403 171 HOH HOH . F 5 HOH A 4 404 29 HOH HOH . F 5 HOH A 5 405 110 HOH HOH . F 5 HOH A 6 406 34 HOH HOH . F 5 HOH A 7 407 13 HOH HOH . F 5 HOH A 8 408 39 HOH HOH . F 5 HOH A 9 409 4 HOH HOH . F 5 HOH A 10 410 176 HOH HOH . F 5 HOH A 11 411 5 HOH HOH . F 5 HOH A 12 412 37 HOH HOH . F 5 HOH A 13 413 21 HOH HOH . F 5 HOH A 14 414 123 HOH HOH . F 5 HOH A 15 415 64 HOH HOH . F 5 HOH A 16 416 168 HOH HOH . F 5 HOH A 17 417 19 HOH HOH . F 5 HOH A 18 418 65 HOH HOH . F 5 HOH A 19 419 57 HOH HOH . F 5 HOH A 20 420 6 HOH HOH . F 5 HOH A 21 421 8 HOH HOH . F 5 HOH A 22 422 41 HOH HOH . F 5 HOH A 23 423 11 HOH HOH . F 5 HOH A 24 424 18 HOH HOH . F 5 HOH A 25 425 66 HOH HOH . F 5 HOH A 26 426 10 HOH HOH . F 5 HOH A 27 427 169 HOH HOH . F 5 HOH A 28 428 9 HOH HOH . F 5 HOH A 29 429 15 HOH HOH . F 5 HOH A 30 430 174 HOH HOH . F 5 HOH A 31 431 1 HOH HOH . F 5 HOH A 32 432 23 HOH HOH . F 5 HOH A 33 433 62 HOH HOH . F 5 HOH A 34 434 38 HOH HOH . F 5 HOH A 35 435 181 HOH HOH . F 5 HOH A 36 436 175 HOH HOH . F 5 HOH A 37 437 61 HOH HOH . F 5 HOH A 38 438 97 HOH HOH . F 5 HOH A 39 439 22 HOH HOH . F 5 HOH A 40 440 167 HOH HOH . F 5 HOH A 41 441 173 HOH HOH . F 5 HOH A 42 442 84 HOH HOH . F 5 HOH A 43 443 51 HOH HOH . F 5 HOH A 44 444 16 HOH HOH . F 5 HOH A 45 445 170 HOH HOH . F 5 HOH A 46 446 26 HOH HOH . F 5 HOH A 47 447 27 HOH HOH . F 5 HOH A 48 448 25 HOH HOH . F 5 HOH A 49 449 35 HOH HOH . F 5 HOH A 50 450 172 HOH HOH . F 5 HOH A 51 451 20 HOH HOH . F 5 HOH A 52 452 45 HOH HOH . F 5 HOH A 53 453 72 HOH HOH . F 5 HOH A 54 454 178 HOH HOH . F 5 HOH A 55 455 2 HOH HOH . F 5 HOH A 56 456 125 HOH HOH . F 5 HOH A 57 457 166 HOH HOH . F 5 HOH A 58 458 12 HOH HOH . F 5 HOH A 59 459 14 HOH HOH . F 5 HOH A 60 460 179 HOH HOH . F 5 HOH A 61 461 17 HOH HOH . F 5 HOH A 62 462 99 HOH HOH . F 5 HOH A 63 463 180 HOH HOH . F 5 HOH A 64 464 148 HOH HOH . F 5 HOH A 65 465 56 HOH HOH . F 5 HOH A 66 466 52 HOH HOH . F 5 HOH A 67 467 42 HOH HOH . F 5 HOH A 68 468 48 HOH HOH . F 5 HOH A 69 469 50 HOH HOH . F 5 HOH A 70 470 33 HOH HOH . F 5 HOH A 71 471 28 HOH HOH . F 5 HOH A 72 472 96 HOH HOH . F 5 HOH A 73 473 49 HOH HOH . F 5 HOH A 74 474 157 HOH HOH . F 5 HOH A 75 475 164 HOH HOH . F 5 HOH A 76 476 156 HOH HOH . F 5 HOH A 77 477 165 HOH HOH . F 5 HOH A 78 478 75 HOH HOH . F 5 HOH A 79 479 154 HOH HOH . F 5 HOH A 80 480 152 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 N N GY5 . . . E 4 24.234 -20.893 9.432 1 40.92 ? N GY5 304 A 1 HETATM 2 C C GY5 . . . E 4 25.371 -17.558 5.243 1 52.7 ? C GY5 304 A 1 HETATM 3 O O GY5 . . . E 4 26.474 -21.144 9.678 1 53.14 ? O GY5 304 A 1 HETATM 4 C C01 GY5 . . . E 4 22.705 -19.519 7.863 1 26.56 ? C01 GY5 304 A 1 HETATM 5 C C02 GY5 . . . E 4 22.702 -17.142 7.711 1 19.49 ? C02 GY5 304 A 1 HETATM 6 C C03 GY5 . . . E 4 22.08 -17.201 6.483 1 12.57 ? C03 GY5 304 A 1 HETATM 7 C C04 GY5 . . . E 4 21.722 -18.535 5.854 1 13.09 ? C04 GY5 304 A 1 HETATM 8 C C05 GY5 . . . E 4 23.107 -15.826 8.443 1 20.98 ? C05 GY5 304 A 1 HETATM 9 C C06 GY5 . . . E 4 24.232 -14.875 10.596 1 38.32 ? C06 GY5 304 A 1 HETATM 10 C C07 GY5 . . . E 4 22.285 -20.649 10.914 1 36.39 ? C07 GY5 304 A 1 HETATM 11 C C08 GY5 . . . E 4 21.849 -21.174 9.549 1 33.68 ? C08 GY5 304 A 1 HETATM 12 C C09 GY5 . . . E 4 23.019 -20.879 8.569 1 34.99 ? C09 GY5 304 A 1 HETATM 13 C C1 GY5 . . . E 4 25.575 -15.253 11.362 1 45.34 ? C1 GY5 304 A 1 HETATM 14 C C10 GY5 . . . E 4 23.828 -20.533 10.816 1 38.38 ? C10 GY5 304 A 1 HETATM 15 C C11 GY5 . . . E 4 25.573 -21.176 8.91 1 49.6 ? C11 GY5 304 A 1 HETATM 16 C C12 GY5 . . . E 4 25.791 -21.551 7.319 1 51.76 ? C12 GY5 304 A 1 HETATM 17 C C13 GY5 . . . E 4 25.815 -16.595 6.153 1 58.22 ? C13 GY5 304 A 1 HETATM 18 C C14 GY5 . . . E 4 26.577 -17.016 7.235 1 58.34 ? C14 GY5 304 A 1 HETATM 19 C C15 GY5 . . . E 4 26.887 -18.373 7.398 1 61.64 ? C15 GY5 304 A 1 HETATM 20 C C16 GY5 . . . E 4 26.448 -19.36 6.486 1 56.17 ? C16 GY5 304 A 1 HETATM 21 C C17 GY5 . . . E 4 25.677 -18.912 5.403 1 55.31 ? C17 GY5 304 A 1 HETATM 22 N N01 GY5 . . . E 4 23.012 -18.359 8.401 1 22.04 ? N01 GY5 304 A 1 HETATM 23 N N02 GY5 . . . E 4 22.087 -19.662 6.65 1 19.84 ? N02 GY5 304 A 1 HETATM 24 N N03 GY5 . . . E 4 23.742 -15.974 9.707 1 31.1 ? N03 GY5 304 A 1 HETATM 25 O O01 GY5 . . . E 4 21.749 -16.151 5.779 1 13.06 ? O01 GY5 304 A 1 HETATM 26 O O02 GY5 . . . E 4 21.173 -18.686 4.792 1 12.01 ? O02 GY5 304 A 1 HETATM 27 O O03 GY5 . . . E 4 22.891 -14.75 7.981 1 12.5 ? O03 GY5 304 A 1 HETATM 28 O O1 GY5 . . . E 4 26.751 -20.715 6.64 1 54.03 ? O1 GY5 304 A 1 HETATM 29 O O11 GY5 . . . E 4 25.635 -16.653 11.69 1 50.09 ? O11 GY5 304 A 1 HETATM 30 C C18 GY5 . . . E 4 26.292 -17.491 10.74 1 49.26 ? C18 GY5 304 A 1 HETATM 31 H H GY5 . . . E 4 24.86 -17.273 4.52 1 63.25 ? H GY5 304 A 1 HETATM 32 H H10 GY5 . . . E 4 23.552 -14.615 11.237 1 45.99 ? H10 GY5 304 A 1 HETATM 33 H H03 GY5 . . . E 4 24.408 -14.082 10.065 1 45.99 ? H03 GY5 304 A 1 HETATM 34 H H05 GY5 . . . E 4 21.984 -21.236 11.625 1 43.69 ? H05 GY5 304 A 1 HETATM 35 H H11 GY5 . . . E 4 21.844 -19.821 11.159 1 43.69 ? H11 GY5 304 A 1 HETATM 36 H H07 GY5 . . . E 4 21.609 -22.113 9.579 1 40.43 ? H07 GY5 304 A 1 HETATM 37 H H06 GY5 . . . E 4 21.012 -20.77 9.271 1 40.43 ? H06 GY5 304 A 1 HETATM 38 H H08 GY5 . . . E 4 22.988 -21.61 7.932 1 42 ? H08 GY5 304 A 1 HETATM 39 H H13 GY5 . . . E 4 25.644 -14.723 12.172 1 54.42 ? H13 GY5 304 A 1 HETATM 40 H H12 GY5 . . . E 4 26.346 -15.037 10.815 1 54.42 ? H12 GY5 304 A 1 HETATM 41 H H1 GY5 . . . E 4 24.11 -19.637 11.06 1 46.07 ? H1 GY5 304 A 1 HETATM 42 H H09 GY5 . . . E 4 24.24 -21.085 11.498 1 46.07 ? H09 GY5 304 A 1 HETATM 43 H H2 GY5 . . . E 4 26.138 -22.457 7.323 1 62.13 ? H2 GY5 304 A 1 HETATM 44 H H3 GY5 . . . E 4 24.935 -21.502 6.866 1 62.13 ? H3 GY5 304 A 1 HETATM 45 H H120 GY5 . . . E 4 25.604 -15.696 6.038 1 69.88 ? H120 GY5 304 A 1 HETATM 46 H H130 GY5 . . . E 4 26.873 -16.376 7.841 1 70.02 ? H130 GY5 304 A 1 HETATM 47 H H14 GY5 . . . E 4 27.401 -18.617 8.134 1 73.98 ? H14 GY5 304 A 1 HETATM 48 H H15 GY5 . . . E 4 25.368 -19.529 4.779 1 66.39 ? H15 GY5 304 A 1 HETATM 49 H H01 GY5 . . . E 4 21.873 -20.403 6.269 1 23.82 ? H01 GY5 304 A 1 HETATM 50 H H04 GY5 . . . E 4 23.886 -16.755 10.035 1 37.33 ? H04 GY5 304 A 1 HETATM 51 H H02 GY5 . . . E 4 20.907 -16.089 5.681 1 15.69 ? H02 GY5 304 A 1 HETATM 52 H H112 GY5 . . . E 4 26.441 -18.374 11.112 1 59.13 ? H112 GY5 304 A 1 HETATM 53 H H111 GY5 . . . E 4 27.152 -17.168 10.427 1 59.13 ? H111 GY5 304 A 1 HETATM 54 H H113 GY5 . . . E 4 25.77 -17.696 9.949 1 59.13 ? H113 GY5 304 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 54 #