data_3EFJ
#
_model_server_result.job_id            zWbDrQQkJsOOtKw0SQZcEg 
_model_server_result.datetime_utc      '2024-10-18 16:29:38' 
_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          3efj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2}' 
#
_entry.id    3EFJ 
#
_exptl.entry_id    3EFJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              497.517 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-benzyl-5-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]-3-fluorophenyl}-3-methylpyrimidin-4(3H)-one 
_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            3EFJ 
_cell.length_a            74.741 
_cell.length_b            78.648 
_cell.length_c            129.257 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EFJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 software_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F 1 1 
A,C,E 2 1 
B,D,F 3 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
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C29 H24 F N3 O4' 
_chem_comp.formula_weight    497.517 
_chem_comp.id                MT3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-benzyl-5-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]-3-fluorophenyl}-3-methylpyrimidin-4(3H)-one 
_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
N1 C8 MT3 sing 237 n n 
N1 C29 MT3 sing 238 n n 
N1 C9 MT3 sing 239 n n 
N3 C22 MT3 doub 240 n y 
N3 C23 MT3 sing 241 n y 
C4 C5 MT3 doub 242 n y 
C4 C3 MT3 sing 243 n y 
C5 C6 MT3 sing 244 n y 
C6 C1 MT3 doub 245 n y 
C7 C8 MT3 sing 246 n n 
C7 C10 MT3 doub 247 n n 
C7 C14 MT3 sing 248 n n 
C8 O4 MT3 doub 249 n n 
C10 N2 MT3 sing 250 n n 
C13 C12 MT3 doub 251 n y 
C13 C14 MT3 sing 252 n y 
C15 C16 MT3 sing 253 n y 
C15 C14 MT3 doub 254 n y 
C17 C22 MT3 sing 255 n y 
C17 C18 MT3 sing 256 n y 
C17 C25 MT3 doub 257 n y 
C20 C21 MT3 doub 258 n y 
C20 O2 MT3 sing 259 n n 
C20 C19 MT3 sing 260 n y 
C21 C22 MT3 sing 261 n y 
C24 C23 MT3 doub 262 n y 
C24 C25 MT3 sing 263 n y 
C26 O1 MT3 sing 264 n n 
C28 C9 MT3 sing 265 n n 
C28 C1 MT3 sing 266 n n 
C27 O2 MT3 sing 267 n n 
C19 O1 MT3 sing 268 n n 
C19 C18 MT3 doub 269 n y 
C25 O3 MT3 sing 270 n n 
O3 C11 MT3 sing 271 n n 
C11 C12 MT3 sing 272 n y 
C11 C16 MT3 doub 273 n y 
C12 F1 MT3 sing 274 n n 
N2 C9 MT3 doub 275 n n 
C1 C2 MT3 sing 276 n y 
C2 C3 MT3 doub 277 n y 
C4 H4 MT3 sing 278 n n 
C5 H5 MT3 sing 279 n n 
C6 H6 MT3 sing 280 n n 
C10 H10 MT3 sing 281 n n 
C13 H13 MT3 sing 282 n n 
C15 H15 MT3 sing 283 n n 
C21 H21 MT3 sing 284 n n 
C24 H24 MT3 sing 285 n n 
C26 H26 MT3 sing 286 n n 
C26 H26A MT3 sing 287 n n 
C26 H26B MT3 sing 288 n n 
C28 H28 MT3 sing 289 n n 
C28 H28A MT3 sing 290 n n 
C27 H27 MT3 sing 291 n n 
C27 H27A MT3 sing 292 n n 
C27 H27B MT3 sing 293 n n 
C18 H18 MT3 sing 294 n n 
C23 H23 MT3 sing 295 n n 
C16 H16 MT3 sing 296 n n 
C29 H29 MT3 sing 297 n n 
C29 H29A MT3 sing 298 n n 
C29 H29B MT3 sing 299 n n 
C2 H2 MT3 sing 300 n n 
C3 H3 MT3 sing 301 n n 
#
_atom_sites.entry_id                     3EFJ 
_atom_sites.fract_transf_matrix[1][1]    0.01338 
_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]    0.012715 
_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]    0.007737 
_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
C 2 MT3 A 1 1 1 MT3 MT3 . 
D 2 MT3 B 1 2 2 MT3 MT3 . 
E 3 HOH A 1 1357 1 HOH HOH . 
E 3 HOH A 2 1359 5 HOH HOH . 
E 3 HOH A 3 1360 6 HOH HOH . 
E 3 HOH A 4 1361 9 HOH HOH . 
E 3 HOH A 5 1362 10 HOH HOH . 
E 3 HOH A 6 1363 11 HOH HOH . 
E 3 HOH A 7 1364 12 HOH HOH . 
E 3 HOH A 8 1365 14 HOH HOH . 
E 3 HOH A 9 1366 16 HOH HOH . 
E 3 HOH A 10 1367 18 HOH HOH . 
E 3 HOH A 11 1368 21 HOH HOH . 
E 3 HOH A 12 1369 23 HOH HOH . 
E 3 HOH A 13 1370 26 HOH HOH . 
E 3 HOH A 14 1371 27 HOH HOH . 
E 3 HOH A 15 1372 28 HOH HOH . 
E 3 HOH A 16 1373 30 HOH HOH . 
E 3 HOH A 17 1375 33 HOH HOH . 
E 3 HOH A 18 1376 40 HOH HOH . 
E 3 HOH A 19 1377 41 HOH HOH . 
E 3 HOH A 20 1378 42 HOH HOH . 
E 3 HOH A 21 1379 43 HOH HOH . 
E 3 HOH A 22 1380 45 HOH HOH . 
E 3 HOH A 23 1381 47 HOH HOH . 
E 3 HOH A 24 1382 52 HOH HOH . 
E 3 HOH A 25 1383 53 HOH HOH . 
E 3 HOH A 26 1384 54 HOH HOH . 
E 3 HOH A 27 1385 58 HOH HOH . 
E 3 HOH A 28 1386 60 HOH HOH . 
E 3 HOH A 29 1387 61 HOH HOH . 
E 3 HOH A 30 1388 62 HOH HOH . 
E 3 HOH A 31 1389 64 HOH HOH . 
E 3 HOH A 32 1390 68 HOH HOH . 
E 3 HOH A 33 1391 69 HOH HOH . 
E 3 HOH A 34 1392 70 HOH HOH . 
E 3 HOH A 35 1393 74 HOH HOH . 
E 3 HOH A 36 1394 76 HOH HOH . 
E 3 HOH A 37 1395 78 HOH HOH . 
E 3 HOH A 38 1396 79 HOH HOH . 
E 3 HOH A 39 1397 80 HOH HOH . 
E 3 HOH A 40 1398 81 HOH HOH . 
E 3 HOH A 41 1399 82 HOH HOH . 
F 3 HOH B 1 1358 3 HOH HOH . 
F 3 HOH B 2 1359 31 HOH HOH . 
F 3 HOH B 3 1360 2 HOH HOH . 
F 3 HOH B 4 1361 4 HOH HOH . 
F 3 HOH B 5 1362 7 HOH HOH . 
F 3 HOH B 6 1363 8 HOH HOH . 
F 3 HOH B 7 1364 13 HOH HOH . 
F 3 HOH B 8 1365 15 HOH HOH . 
F 3 HOH B 9 1366 17 HOH HOH . 
F 3 HOH B 10 1367 19 HOH HOH . 
F 3 HOH B 11 1368 20 HOH HOH . 
F 3 HOH B 12 1369 22 HOH HOH . 
F 3 HOH B 13 1370 24 HOH HOH . 
F 3 HOH B 14 1371 25 HOH HOH . 
F 3 HOH B 15 1372 29 HOH HOH . 
F 3 HOH B 16 1373 32 HOH HOH . 
F 3 HOH B 17 1374 34 HOH HOH . 
F 3 HOH B 18 1375 35 HOH HOH . 
F 3 HOH B 19 1376 36 HOH HOH . 
F 3 HOH B 20 1377 37 HOH HOH . 
F 3 HOH B 21 1378 38 HOH HOH . 
F 3 HOH B 22 1379 39 HOH HOH . 
F 3 HOH B 23 1380 44 HOH HOH . 
F 3 HOH B 24 1381 46 HOH HOH . 
F 3 HOH B 25 1382 48 HOH HOH . 
F 3 HOH B 26 1383 49 HOH HOH . 
F 3 HOH B 27 1384 50 HOH HOH . 
F 3 HOH B 28 1385 51 HOH HOH . 
F 3 HOH B 29 1386 55 HOH HOH . 
F 3 HOH B 30 1387 56 HOH HOH . 
F 3 HOH B 31 1388 57 HOH HOH . 
F 3 HOH B 32 1389 59 HOH HOH . 
F 3 HOH B 33 1390 63 HOH HOH . 
F 3 HOH B 34 1391 65 HOH HOH . 
F 3 HOH B 35 1392 66 HOH HOH . 
F 3 HOH B 36 1393 67 HOH HOH . 
F 3 HOH B 37 1394 71 HOH HOH . 
F 3 HOH B 38 1395 72 HOH HOH . 
F 3 HOH B 39 1396 73 HOH HOH . 
F 3 HOH B 40 1397 75 HOH HOH . 
F 3 HOH B 41 1398 77 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 N1 MT3 . . . D 2 61.16 24.248 85.134 1 35.32 ? N1 MT3 2 B 1 
HETATM 2 N N3 MT3 . . . D 2 61.29 26.903 74.506 1 30.8 ? N3 MT3 2 B 1 
HETATM 3 C C4 MT3 . . . D 2 65.666 24.085 88.437 1 36.41 ? C4 MT3 2 B 1 
HETATM 4 C C5 MT3 . . . D 2 64.51 23.629 89.08 1 36.78 ? C5 MT3 2 B 1 
HETATM 5 C C6 MT3 . . . D 2 63.48 23.055 88.336 1 36.04 ? C6 MT3 2 B 1 
HETATM 6 C C7 MT3 . . . D 2 61.017 24.404 82.71 1 34.56 ? C7 MT3 2 B 1 
HETATM 7 C C8 MT3 . . . D 2 60.689 24.905 83.979 1 35.25 ? C8 MT3 2 B 1 
HETATM 8 C C10 MT3 . . . D 2 61.79 23.247 82.651 1 35.22 ? C10 MT3 2 B 1 
HETATM 9 C C13 MT3 . . . D 2 60.391 26.353 81.341 1 34.41 ? C13 MT3 2 B 1 
HETATM 10 C C15 MT3 . . . D 2 60.169 24.136 80.464 1 34.03 ? C15 MT3 2 B 1 
HETATM 11 C C17 MT3 . . . D 2 59.234 27.158 75.645 1 30.44 ? C17 MT3 2 B 1 
HETATM 12 C C20 MT3 . . . D 2 58.074 28.141 73.293 1 30.52 ? C20 MT3 2 B 1 
HETATM 13 C C21 MT3 . . . D 2 59.421 27.761 73.314 1 30.62 ? C21 MT3 2 B 1 
HETATM 14 C C22 MT3 . . . D 2 59.998 27.269 74.489 1 30.51 ? C22 MT3 2 B 1 
HETATM 15 C C24 MT3 . . . D 2 61.155 26.298 76.777 1 30.34 ? C24 MT3 2 B 1 
HETATM 16 C C26 MT3 . . . D 2 55.115 27.816 75.359 1 29.88 ? C26 MT3 2 B 1 
HETATM 17 C C28 MT3 . . . D 2 62.486 22.293 86.17 1 35.07 ? C28 MT3 2 B 1 
HETATM 18 C C27 MT3 . . . D 2 58.289 29.012 71.073 1 29.2 ? C27 MT3 2 B 1 
HETATM 19 O O2 MT3 . . . D 2 57.455 28.637 72.173 1 30.56 ? O2 MT3 2 B 1 
HETATM 20 C C19 MT3 . . . D 2 57.303 28.017 74.446 1 30.57 ? C19 MT3 2 B 1 
HETATM 21 O O1 MT3 . . . D 2 55.987 28.403 74.389 1 30.61 ? O1 MT3 2 B 1 
HETATM 22 C C18 MT3 . . . D 2 57.888 27.534 75.62 1 30.68 ? C18 MT3 2 B 1 
HETATM 23 C C23 MT3 . . . D 2 61.87 26.432 75.596 1 30.23 ? C23 MT3 2 B 1 
HETATM 24 C C25 MT3 . . . D 2 59.818 26.66 76.809 1 30.57 ? C25 MT3 2 B 1 
HETATM 25 O O3 MT3 . . . D 2 59.051 26.541 77.938 1 31.9 ? O3 MT3 2 B 1 
HETATM 26 C C11 MT3 . . . D 2 59.548 25.997 79.09 1 33.24 ? C11 MT3 2 B 1 
HETATM 27 C C12 MT3 . . . D 2 59.896 26.847 80.133 1 33.89 ? C12 MT3 2 B 1 
HETATM 28 F F1 MT3 . . . D 2 59.759 28.173 79.963 1 34.7 ? F1 MT3 2 B 1 
HETATM 29 C C16 MT3 . . . D 2 59.673 24.623 79.257 1 32.84 ? C16 MT3 2 B 1 
HETATM 30 C C14 MT3 . . . D 2 60.55 24.981 81.514 1 34.41 ? C14 MT3 2 B 1 
HETATM 31 O O4 MT3 . . . D 2 60.006 25.921 84.102 1 35.91 ? O4 MT3 2 B 1 
HETATM 32 C C29 MT3 . . . D 2 60.822 24.782 86.481 1 35.43 ? C29 MT3 2 B 1 
HETATM 33 N N2 MT3 . . . D 2 62.226 22.64 83.747 1 35.8 ? N2 MT3 2 B 1 
HETATM 34 C C9 MT3 . . . D 2 61.953 23.095 84.98 1 35.22 ? C9 MT3 2 B 1 
HETATM 35 C C1 MT3 . . . D 2 63.613 22.943 86.952 1 35.52 ? C1 MT3 2 B 1 
HETATM 36 C C2 MT3 . . . D 2 64.767 23.388 86.312 1 35.67 ? C2 MT3 2 B 1 
HETATM 37 C C3 MT3 . . . D 2 65.795 23.968 87.053 1 36.15 ? C3 MT3 2 B 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           37 
#