data_6VL3 # _model_server_result.job_id LL5tOYC3kXrtSeSu1AGjqA _model_server_result.datetime_utc '2024-11-24 08:36:02' _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 6vl3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 6VL3 # _exptl.entry_id 6VL3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 449.38 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-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 90 _cell.entry_id 6VL3 _cell.length_a 89.804 _cell.length_b 89.804 _cell.length_c 132.729 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VL3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 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 _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 61 A HIS 41 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc2 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc3 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc4 A OE2 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc5 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc6 B MN MN . A MN 201 1_555 D O13 R1D . A R1D 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc7 B MN MN . A MN 201 1_555 D O15 R1D . A R1D 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc8 C MN MN . A MN 202 1_555 D O13 R1D . A R1D 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc9 C MN MN . A MN 202 1_555 D O10 R1D . A R1D 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.723 ? metalc ? metalc10 C MN MN . A MN 202 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc11 C MN MN . A MN 202 1_555 G O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? # _chem_comp.formula 'C21 H18 F3 N3 O5' _chem_comp.formula_weight 449.38 _chem_comp.id R1D _chem_comp.mon_nstd_flag . _chem_comp.name 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-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 O15 C14 R1D doub 386 n n O13 C12 R1D sing 387 n n C14 C12 R1D sing 388 n n C14 N16 R1D sing 389 n n C12 C11 R1D doub 390 n n N16 C17 R1D sing 391 n n F26 C25 R1D sing 392 n n C11 C09 R1D sing 393 n n C11 N18 R1D sing 394 n n O10 C09 R1D doub 395 n n C17 N18 R1D doub 396 n n C17 C19 R1D sing 397 n n C09 N08 R1D sing 398 n n C19 C20 R1D doub 399 n y C19 C24 R1D sing 400 n y C25 C24 R1D sing 401 n n C25 F27 R1D sing 402 n n C25 F28 R1D sing 403 n n N08 C07 R1D sing 404 n n C20 C21 R1D sing 405 n y C24 C23 R1D doub 406 n y C07 C06 R1D sing 407 n n C21 C22 R1D doub 408 n y C23 C22 R1D sing 409 n y C06 C05 R1D sing 410 n n C04 C05 R1D doub 411 n y C04 C03 R1D sing 412 n y C05 C29 R1D sing 413 n y O02 C03 R1D sing 414 n n O02 C01 R1D sing 415 n n C03 C31 R1D doub 416 n y C29 C30 R1D doub 417 n y C31 C30 R1D sing 418 n y C31 O32 R1D sing 419 n n C01 H1 R1D sing 420 n n C01 H2 R1D sing 421 n n C01 H3 R1D sing 422 n n C04 H4 R1D sing 423 n n C06 H5 R1D sing 424 n n C06 H6 R1D sing 425 n n C07 H7 R1D sing 426 n n C07 H8 R1D sing 427 n n C20 H9 R1D sing 428 n n C21 H10 R1D sing 429 n n C22 H11 R1D sing 430 n n C23 H12 R1D sing 431 n n C29 H13 R1D sing 432 n n C30 H14 R1D sing 433 n n N08 H15 R1D sing 434 n n N16 H16 R1D sing 435 n n O13 H17 R1D sing 436 n n O32 H18 R1D sing 437 n n # _atom_sites.entry_id 6VL3 _atom_sites.fract_transf_matrix[1][1] 0.011135 _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] 0.011135 _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] 0.007534 _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 1 201 201 MN MN . C 2 MN A 1 202 202 MN MN . D 3 R1D A 1 203 301 R1D 436 . E 4 QQ4 A 1 204 401 QQ4 PVP . F 5 SO4 A 1 205 1 SO4 SO4 . G 6 HOH A 1 301 1 HOH HOH . G 6 HOH A 2 302 7 HOH HOH . G 6 HOH A 3 303 27 HOH HOH . G 6 HOH A 4 304 2 HOH HOH . G 6 HOH A 5 305 9 HOH HOH . G 6 HOH A 6 306 28 HOH HOH . G 6 HOH A 7 307 6 HOH HOH . G 6 HOH A 8 308 10 HOH HOH . G 6 HOH A 9 309 3 HOH HOH . G 6 HOH A 10 310 5 HOH HOH . G 6 HOH A 11 311 21 HOH HOH . G 6 HOH A 12 312 23 HOH HOH . G 6 HOH A 13 313 15 HOH HOH . G 6 HOH A 14 314 8 HOH HOH . G 6 HOH A 15 315 19 HOH HOH . G 6 HOH A 16 316 11 HOH HOH . G 6 HOH A 17 317 20 HOH HOH . G 6 HOH A 18 318 12 HOH HOH . G 6 HOH A 19 319 18 HOH HOH . G 6 HOH A 20 320 13 HOH HOH . G 6 HOH A 21 321 25 HOH HOH . G 6 HOH A 22 322 29 HOH HOH . G 6 HOH A 23 323 22 HOH HOH . G 6 HOH A 24 324 14 HOH HOH . G 6 HOH A 25 325 16 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 R1D . . . D 3 9.422 40.624 -11.413 1 85.75 ? C01 R1D 203 A 1 HETATM 2 C C03 R1D . . . D 3 11.654 40.715 -12.12 1 100.06 ? C03 R1D 203 A 1 HETATM 3 C C04 R1D . . . D 3 12.018 41.905 -12.731 1 98.17 ? C04 R1D 203 A 1 HETATM 4 C C05 R1D . . . D 3 13.284 42.432 -12.527 1 105.44 ? C05 R1D 203 A 1 HETATM 5 C C06 R1D . . . D 3 13.691 43.749 -13.195 1 112.25 ? C06 R1D 203 A 1 HETATM 6 C C07 R1D . . . D 3 13.767 43.709 -14.721 1 73.68 ? C07 R1D 203 A 1 HETATM 7 C C09 R1D . . . D 3 14.986 41.927 -16.003 1 66.44 ? C09 R1D 203 A 1 HETATM 8 C C11 R1D . . . D 3 15.039 40.487 -16.507 1 65.03 ? C11 R1D 203 A 1 HETATM 9 C C12 R1D . . . D 3 15.738 40.139 -17.777 1 63.17 ? C12 R1D 203 A 1 HETATM 10 C C14 R1D . . . D 3 15.762 38.719 -18.235 1 67.44 ? C14 R1D 203 A 1 HETATM 11 C C17 R1D . . . D 3 14.416 38.045 -16.184 1 67.41 ? C17 R1D 203 A 1 HETATM 12 C C19 R1D . . . D 3 13.72 36.979 -15.338 1 82 ? C19 R1D 203 A 1 HETATM 13 C C20 R1D . . . D 3 12.391 37.159 -14.995 1 93.52 ? C20 R1D 203 A 1 HETATM 14 C C21 R1D . . . D 3 11.737 36.212 -14.225 1 99.35 ? C21 R1D 203 A 1 HETATM 15 C C22 R1D . . . D 3 12.413 35.082 -13.798 1 90.4 ? C22 R1D 203 A 1 HETATM 16 C C23 R1D . . . D 3 13.744 34.9 -14.139 1 86.35 ? C23 R1D 203 A 1 HETATM 17 C C24 R1D . . . D 3 14.402 35.847 -14.907 1 86.13 ? C24 R1D 203 A 1 HETATM 18 C C25 R1D . . . D 3 15.869 35.63 -15.275 1 82.43 ? C25 R1D 203 A 1 HETATM 19 C C29 R1D . . . D 3 14.18 41.771 -11.699 1 89.84 ? C29 R1D 203 A 1 HETATM 20 C C30 R1D . . . D 3 13.815 40.582 -11.087 1 88.33 ? C30 R1D 203 A 1 HETATM 21 C C31 R1D . . . D 3 12.552 40.055 -11.297 1 106.88 ? C31 R1D 203 A 1 HETATM 22 F F26 R1D . . . D 3 16.009 35.633 -16.633 1 88.84 ? F26 R1D 203 A 1 HETATM 23 F F27 R1D . . . D 3 16.289 34.426 -14.796 1 73 ? F27 R1D 203 A 1 HETATM 24 F F28 R1D . . . D 3 16.63 36.624 -14.731 1 76.12 ? F28 R1D 203 A 1 HETATM 25 N N08 R1D . . . D 3 13.843 42.346 -15.211 1 78.88 ? N08 R1D 203 A 1 HETATM 26 N N16 R1D . . . D 3 15.107 37.69 -17.451 1 75.88 ? N16 R1D 203 A 1 HETATM 27 N N18 R1D . . . D 3 14.388 39.454 -15.726 1 66 ? N18 R1D 203 A 1 HETATM 28 O O02 R1D . . . D 3 10.379 40.182 -12.332 1 79.43 ? O02 R1D 203 A 1 HETATM 29 O O10 R1D . . . D 3 15.858 42.689 -16.245 1 61.6 ? O10 R1D 203 A 1 HETATM 30 O O13 R1D . . . D 3 16.366 41.135 -18.534 1 69.48 ? O13 R1D 203 A 1 HETATM 31 O O15 R1D . . . D 3 16.313 38.428 -19.241 1 65.3 ? O15 R1D 203 A 1 HETATM 32 O O32 R1D . . . D 3 12.181 38.853 -10.679 1 106.77 ? O32 R1D 203 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #