data_6YBG # _model_server_result.job_id DS4X-57BcCycXqExadF3fQ _model_server_result.datetime_utc '2025-08-31 00:25:33' _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 6ybg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6YBG # _exptl.entry_id 6YBG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 707.666 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(3-chlorophenyl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-(2-methoxyphenyl)propanoic acid' _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 98.86 _cell.angle_gamma 90 _cell.entry_id 6YBG _cell.length_a 126.749 _cell.length_b 79.061 _cell.length_c 42.294 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,F 1 1 B,E,G 2 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 E N N # _chem_comp.formula 'C36 H36 Cl2 N4 O5 S' _chem_comp.formula_weight 707.666 _chem_comp.id OJT _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(3-chlorophenyl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-(2-methoxyphenyl)propanoic 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 O5 C36 OJT doub 237 n n C20 C21 OJT doub 238 n y C20 C19 OJT sing 239 n y C21 C16 OJT sing 240 n y S1 C12 OJT sing 241 n y S1 C15 OJT sing 242 n y C19 C18 OJT doub 243 n y N2 C12 OJT doub 244 n y N2 C11 OJT sing 245 n y O4 C36 OJT sing 246 n n C36 C1 OJT sing 247 n n C12 C13 OJT sing 248 n y C16 C15 OJT sing 249 n n C16 C17 OJT doub 250 n y C11 N1 OJT doub 251 n y C15 C14 OJT doub 252 n y C18 C17 OJT sing 253 n y C18 CL1 OJT sing 254 n n C35 C34 OJT doub 255 n y C35 C22 OJT sing 256 n y C13 C14 OJT sing 257 n y C13 C10 OJT doub 258 n y N1 C10 OJT sing 259 n y C14 C22 OJT sing 260 n n C10 O2 OJT sing 261 n n C34 C26 OJT sing 262 n y C22 C23 OJT doub 263 n y O2 C1 OJT sing 264 n n C1 C2 OJT sing 265 n n C2 C3 OJT sing 266 n n C27 O3 OJT sing 267 n n C27 C28 OJT sing 268 n n C26 O3 OJT sing 269 n n C26 C25 OJT doub 270 n y C23 C25 OJT sing 271 n y C23 C24 OJT sing 272 n n C25 CL2 OJT sing 273 n n C28 N3 OJT sing 274 n n N3 C29 OJT sing 275 n n N3 C33 OJT sing 276 n n C29 C30 OJT sing 277 n n C30 N4 OJT sing 278 n n C3 C9 OJT doub 279 n y C3 C4 OJT sing 280 n y C9 C8 OJT sing 281 n y O1 C4 OJT sing 282 n n O1 C5 OJT sing 283 n n C33 C32 OJT sing 284 n n C4 C6 OJT doub 285 n y C32 N4 OJT sing 286 n n N4 C31 OJT sing 287 n n C8 C7 OJT doub 288 n y C6 C7 OJT sing 289 n y C1 H1 OJT sing 290 n n C2 H2 OJT sing 291 n n C2 H3 OJT sing 292 n n C5 H4 OJT sing 293 n n C5 H5 OJT sing 294 n n C5 H6 OJT sing 295 n n C6 H7 OJT sing 296 n n C7 H8 OJT sing 297 n n C8 H9 OJT sing 298 n n C9 H10 OJT sing 299 n n C11 H11 OJT sing 300 n n C17 H12 OJT sing 301 n n C19 H13 OJT sing 302 n n C20 H14 OJT sing 303 n n C21 H15 OJT sing 304 n n C24 H16 OJT sing 305 n n C24 H17 OJT sing 306 n n C24 H18 OJT sing 307 n n C27 H19 OJT sing 308 n n C27 H20 OJT sing 309 n n C28 H21 OJT sing 310 n n C28 H22 OJT sing 311 n n C29 H24 OJT sing 312 n n C29 H25 OJT sing 313 n n C30 H26 OJT sing 314 n n C30 H27 OJT sing 315 n n C31 H29 OJT sing 316 n n C31 H30 OJT sing 317 n n C31 H31 OJT sing 318 n n C32 H32 OJT sing 319 n n C32 H33 OJT sing 320 n n C33 H34 OJT sing 321 n n C33 H35 OJT sing 322 n n C34 H36 OJT sing 323 n n C35 H37 OJT sing 324 n n O4 H38 OJT sing 325 n n # _atom_sites.entry_id 6YBG _atom_sites.fract_transf_matrix[1][1] 0.00789 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001229 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012648 _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] 0.023929 _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 OJT A 1 401 401 OJT UNL . D 3 CL A 1 402 1 CL CL . E 2 OJT B 1 401 401 OJT UNL . F 4 HOH A 1 501 11 HOH HOH . F 4 HOH A 2 502 24 HOH HOH . F 4 HOH A 3 503 5 HOH HOH . F 4 HOH A 4 504 57 HOH HOH . F 4 HOH A 5 505 1 HOH HOH . F 4 HOH A 6 506 22 HOH HOH . F 4 HOH A 7 507 38 HOH HOH . F 4 HOH A 8 508 10 HOH HOH . F 4 HOH A 9 509 37 HOH HOH . F 4 HOH A 10 510 45 HOH HOH . F 4 HOH A 11 511 4 HOH HOH . F 4 HOH A 12 512 12 HOH HOH . F 4 HOH A 13 513 9 HOH HOH . F 4 HOH A 14 514 29 HOH HOH . F 4 HOH A 15 515 20 HOH HOH . F 4 HOH A 16 516 65 HOH HOH . F 4 HOH A 17 517 36 HOH HOH . F 4 HOH A 18 518 16 HOH HOH . F 4 HOH A 19 519 50 HOH HOH . F 4 HOH A 20 520 51 HOH HOH . F 4 HOH A 21 521 7 HOH HOH . F 4 HOH A 22 522 15 HOH HOH . F 4 HOH A 23 523 35 HOH HOH . F 4 HOH A 24 524 46 HOH HOH . F 4 HOH A 25 525 14 HOH HOH . F 4 HOH A 26 526 30 HOH HOH . F 4 HOH A 27 527 66 HOH HOH . G 4 HOH B 1 501 69 HOH HOH . G 4 HOH B 2 502 26 HOH HOH . G 4 HOH B 3 503 58 HOH HOH . G 4 HOH B 4 504 25 HOH HOH . G 4 HOH B 5 505 68 HOH HOH . G 4 HOH B 6 506 62 HOH HOH . G 4 HOH B 7 507 17 HOH HOH . G 4 HOH B 8 508 8 HOH HOH . G 4 HOH B 9 509 49 HOH HOH . G 4 HOH B 10 510 67 HOH HOH . G 4 HOH B 11 511 3 HOH HOH . G 4 HOH B 12 512 33 HOH HOH . G 4 HOH B 13 513 53 HOH HOH . G 4 HOH B 14 514 60 HOH HOH . G 4 HOH B 15 515 41 HOH HOH . G 4 HOH B 16 516 64 HOH HOH . G 4 HOH B 17 517 18 HOH HOH . G 4 HOH B 18 518 13 HOH HOH . G 4 HOH B 19 519 32 HOH HOH . G 4 HOH B 20 520 34 HOH HOH . G 4 HOH B 21 521 2 HOH HOH . G 4 HOH B 22 522 28 HOH HOH . G 4 HOH B 23 523 48 HOH HOH . G 4 HOH B 24 524 23 HOH HOH . G 4 HOH B 25 525 55 HOH HOH . G 4 HOH B 26 526 59 HOH HOH . G 4 HOH B 27 527 6 HOH HOH . G 4 HOH B 28 528 56 HOH HOH . G 4 HOH B 29 529 27 HOH HOH . G 4 HOH B 30 530 21 HOH HOH . G 4 HOH B 31 531 40 HOH HOH . G 4 HOH B 32 532 47 HOH HOH . G 4 HOH B 33 533 43 HOH HOH . G 4 HOH B 34 534 19 HOH HOH . G 4 HOH B 35 535 63 HOH HOH . G 4 HOH B 36 536 54 HOH HOH . G 4 HOH B 37 537 39 HOH HOH . G 4 HOH B 38 538 61 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 C1 OJT . . . C 2 27.218 0.063 8.926 1 40.72 ? C1 OJT 401 A 1 HETATM 2 C C2 OJT . . . C 2 27.828 1.318 9.505 1 42.19 ? C2 OJT 401 A 1 HETATM 3 C C3 OJT . . . C 2 27.335 1.54 10.911 1 41.33 ? C3 OJT 401 A 1 HETATM 4 C C4 OJT . . . C 2 27.834 0.752 11.959 1 40.48 ? C4 OJT 401 A 1 HETATM 5 O O1 OJT . . . C 2 28.765 -0.158 11.578 1 40.72 ? O1 OJT 401 A 1 HETATM 6 C C5 OJT . . . C 2 29.406 -0.947 12.581 1 45.74 ? C5 OJT 401 A 1 HETATM 7 C C6 OJT . . . C 2 27.367 0.917 13.252 1 44.31 ? C6 OJT 401 A 1 HETATM 8 C C7 OJT . . . C 2 26.411 1.886 13.509 1 42.32 ? C7 OJT 401 A 1 HETATM 9 C C8 OJT . . . C 2 25.918 2.675 12.491 1 46.19 ? C8 OJT 401 A 1 HETATM 10 C C9 OJT . . . C 2 26.389 2.508 11.2 1 41.78 ? C9 OJT 401 A 1 HETATM 11 O O2 OJT . . . C 2 25.793 0.275 8.871 1 39.52 ? O2 OJT 401 A 1 HETATM 12 C C10 OJT . . . C 2 25.042 -0.707 8.376 1 32.55 ? C10 OJT 401 A 1 HETATM 13 N N1 OJT . . . C 2 25.579 -1.879 8.15 1 38.37 ? N1 OJT 401 A 1 HETATM 14 C C11 OJT . . . C 2 24.801 -2.869 7.685 1 36.71 ? C11 OJT 401 A 1 HETATM 15 N N2 OJT . . . C 2 23.523 -2.736 7.366 1 37.53 ? N2 OJT 401 A 1 HETATM 16 C C12 OJT . . . C 2 22.993 -1.522 7.565 1 35.08 ? C12 OJT 401 A 1 HETATM 17 C C13 OJT . . . C 2 23.7 -0.468 8.09 1 33.3 ? C13 OJT 401 A 1 HETATM 18 C C14 OJT . . . C 2 22.842 0.711 8.209 1 32.46 ? C14 OJT 401 A 1 HETATM 19 C C15 OJT . . . C 2 21.576 0.514 7.717 1 32.42 ? C15 OJT 401 A 1 HETATM 20 S S1 OJT . . . C 2 21.352 -1.135 7.24 1 34.61 ? S1 OJT 401 A 1 HETATM 21 C C16 OJT . . . C 2 20.426 1.431 7.566 1 31.75 ? C16 OJT 401 A 1 HETATM 22 C C17 OJT . . . C 2 19.127 0.993 7.842 1 34.94 ? C17 OJT 401 A 1 HETATM 23 C C18 OJT . . . C 2 18.049 1.855 7.734 1 31.45 ? C18 OJT 401 A 1 HETATM 24 CL CL1 OJT . . . C 2 16.453 1.246 8.059 1 37.18 ? CL1 OJT 401 A 1 HETATM 25 C C19 OJT . . . C 2 18.216 3.16 7.356 1 33.27 ? C19 OJT 401 A 1 HETATM 26 C C20 OJT . . . C 2 19.496 3.601 7.081 1 33.19 ? C20 OJT 401 A 1 HETATM 27 C C21 OJT . . . C 2 20.594 2.755 7.171 1 33.33 ? C21 OJT 401 A 1 HETATM 28 C C22 OJT . . . C 2 23.29 2.003 8.754 1 34.02 ? C22 OJT 401 A 1 HETATM 29 C C23 OJT . . . C 2 22.809 2.465 9.986 1 33.71 ? C23 OJT 401 A 1 HETATM 30 C C24 OJT . . . C 2 21.912 1.598 10.83 1 32.52 ? C24 OJT 401 A 1 HETATM 31 C C25 OJT . . . C 2 23.202 3.726 10.43 1 39.81 ? C25 OJT 401 A 1 HETATM 32 CL CL2 OJT . . . C 2 22.667 4.33 11.963 1 39.74 ? CL2 OJT 401 A 1 HETATM 33 C C26 OJT . . . C 2 24.04 4.538 9.679 1 40.05 ? C26 OJT 401 A 1 HETATM 34 O O3 OJT . . . C 2 24.388 5.722 10.261 1 46.83 ? O3 OJT 401 A 1 HETATM 35 C C27 OJT . . . C 2 25.385 6.517 9.612 1 59.35 ? C27 OJT 401 A 1 HETATM 36 C C28 OJT . . . C 2 25.765 7.674 10.505 1 67.8 ? C28 OJT 401 A 1 HETATM 37 N N3 OJT . . . C 2 24.691 8.665 10.677 1 87.47 ? N3 OJT 401 A 1 HETATM 38 C C29 OJT . . . C 2 25.191 10.057 10.695 1 88.1 ? C29 OJT 401 A 1 HETATM 39 C C30 OJT . . . C 2 24.058 11.046 10.879 1 97.63 ? C30 OJT 401 A 1 HETATM 40 N N4 OJT . . . C 2 23.282 10.773 12.093 1 101.71 ? N4 OJT 401 A 1 HETATM 41 C C31 OJT . . . C 2 22.19 11.736 12.266 1 87.88 ? C31 OJT 401 A 1 HETATM 42 C C32 OJT . . . C 2 22.775 9.402 12.058 1 93.59 ? C32 OJT 401 A 1 HETATM 43 C C33 OJT . . . C 2 23.905 8.409 11.906 1 89.09 ? C33 OJT 401 A 1 HETATM 44 C C34 OJT . . . C 2 24.476 4.082 8.441 1 40.24 ? C34 OJT 401 A 1 HETATM 45 C C35 OJT . . . C 2 24.099 2.831 7.984 1 40.99 ? C35 OJT 401 A 1 HETATM 46 C C36 OJT . . . C 2 27.807 -0.182 7.549 1 44.42 ? C36 OJT 401 A 1 HETATM 47 O O4 OJT . . . C 2 28.72 -1.016 7.524 1 41.95 -1 O4 OJT 401 A 1 HETATM 48 O O5 OJT . . . C 2 27.368 0.399 6.515 1 40.7 ? O5 OJT 401 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 48 #