data_4TYO # _model_server_result.job_id AVRq51ovb4ySJ8pWchkRGg _model_server_result.datetime_utc '2025-02-05 15:50:57' _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 4tyo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 4TYO # _exptl.entry_id 4TYO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 377.368 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(6-fluoro-1H-benzimidazol-2-yl)-N-(naphthalen-2-ylcarbonyl)-D-alanine _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 100.82 _cell.angle_gamma 90 _cell.entry_id 4TYO _cell.length_a 117.559 _cell.length_b 36.525 _cell.length_c 51.251 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4TYO _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,G 1 1 B,E,F,H 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 'C21 H16 F N3 O3' _chem_comp.formula_weight 377.368 _chem_comp.id 39X _chem_comp.mon_nstd_flag . _chem_comp.name 3-(6-fluoro-1H-benzimidazol-2-yl)-N-(naphthalen-2-ylcarbonyl)-D-alanine _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 C9 C8 39X doub 1 n y C9 C10 39X sing 2 n y C8 C4 39X sing 3 n y C10 C11 39X doub 4 n y O2 C21 39X doub 5 n n C4 C3 39X doub 6 n y C4 C5 39X sing 7 n y C11 C5 39X sing 8 n y C3 C2 39X sing 9 n y C21 O3 39X sing 10 n n C21 C20 39X sing 11 n n C5 C6 39X doub 12 n y N3 C13 39X doub 13 n y N3 C15 39X sing 14 n y C12 C20 39X sing 15 n n C12 C13 39X sing 16 n n N1 C20 39X sing 17 n n N1 C1 39X sing 18 n n C2 C1 39X sing 19 n n C2 C7 39X doub 20 n y C13 N2 39X sing 21 n y C19 C15 39X doub 22 n y C19 C18 39X sing 23 n y C15 C14 39X sing 24 n y C6 C7 39X sing 25 n y C1 O1 39X doub 26 n n N2 C14 39X sing 27 n y C18 C17 39X doub 28 n y C14 C16 39X doub 29 n y C17 C16 39X sing 30 n y C17 F1 39X sing 31 n n O3 H16 39X sing 32 n n C20 H15 39X sing 33 n n C12 H9 39X sing 34 n n C12 H10 39X sing 35 n n C19 H14 39X sing 36 n n C18 H13 39X sing 37 n n C16 H12 39X sing 38 n n N2 H11 39X sing 39 n n N1 H1 39X sing 40 n n C7 H4 39X sing 41 n n C6 H3 39X sing 42 n n C11 H8 39X sing 43 n n C10 H7 39X sing 44 n n C9 H6 39X sing 45 n n C8 H5 39X sing 46 n n C3 H2 39X sing 47 n n # _atom_sites.entry_id 4TYO _atom_sites.fract_transf_matrix[1][1] 0.008506 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001626 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.027379 _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] 0.019865 _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 39X A 1 201 1 39X AGI . D 3 GOL A 1 202 1 GOL GOL . E 2 39X B 1 201 1 39X AGI . F 3 GOL B 1 202 1 GOL GOL . G 4 HOH A 1 301 162 HOH HOH . G 4 HOH A 2 302 126 HOH HOH . G 4 HOH A 3 303 40 HOH HOH . G 4 HOH A 4 304 69 HOH HOH . G 4 HOH A 5 305 122 HOH HOH . G 4 HOH A 6 306 140 HOH HOH . G 4 HOH A 7 307 143 HOH HOH . G 4 HOH A 8 308 61 HOH HOH . G 4 HOH A 9 309 92 HOH HOH . G 4 HOH A 10 310 94 HOH HOH . G 4 HOH A 11 311 6 HOH HOH . G 4 HOH A 12 312 157 HOH HOH . G 4 HOH A 13 313 45 HOH HOH . G 4 HOH A 14 314 30 HOH HOH . G 4 HOH A 15 315 116 HOH HOH . G 4 HOH A 16 316 107 HOH HOH . G 4 HOH A 17 317 14 HOH HOH . G 4 HOH A 18 318 88 HOH HOH . G 4 HOH A 19 319 31 HOH HOH . G 4 HOH A 20 320 98 HOH HOH . G 4 HOH A 21 321 86 HOH HOH . G 4 HOH A 22 322 11 HOH HOH . G 4 HOH A 23 323 115 HOH HOH . G 4 HOH A 24 324 5 HOH HOH . G 4 HOH A 25 325 153 HOH HOH . G 4 HOH A 26 326 10 HOH HOH . G 4 HOH A 27 327 23 HOH HOH . G 4 HOH A 28 328 27 HOH HOH . G 4 HOH A 29 329 70 HOH HOH . G 4 HOH A 30 330 141 HOH HOH . G 4 HOH A 31 331 71 HOH HOH . G 4 HOH A 32 332 54 HOH HOH . G 4 HOH A 33 333 125 HOH HOH . G 4 HOH A 34 334 9 HOH HOH . G 4 HOH A 35 335 8 HOH HOH . G 4 HOH A 36 336 112 HOH HOH . G 4 HOH A 37 337 84 HOH HOH . G 4 HOH A 38 338 22 HOH HOH . G 4 HOH A 39 339 82 HOH HOH . G 4 HOH A 40 340 106 HOH HOH . G 4 HOH A 41 341 74 HOH HOH . G 4 HOH A 42 342 3 HOH HOH . G 4 HOH A 43 343 114 HOH HOH . G 4 HOH A 44 344 20 HOH HOH . G 4 HOH A 45 345 37 HOH HOH . G 4 HOH A 46 346 156 HOH HOH . G 4 HOH A 47 347 132 HOH HOH . G 4 HOH A 48 348 1 HOH HOH . G 4 HOH A 49 349 16 HOH HOH . G 4 HOH A 50 350 111 HOH HOH . G 4 HOH A 51 351 110 HOH HOH . G 4 HOH A 52 352 142 HOH HOH . G 4 HOH A 53 353 165 HOH HOH . G 4 HOH A 54 354 144 HOH HOH . G 4 HOH A 55 355 41 HOH HOH . G 4 HOH A 56 356 170 HOH HOH . G 4 HOH A 57 357 131 HOH HOH . G 4 HOH A 58 358 128 HOH HOH . G 4 HOH A 59 359 26 HOH HOH . G 4 HOH A 60 360 130 HOH HOH . G 4 HOH A 61 361 148 HOH HOH . G 4 HOH A 62 362 47 HOH HOH . G 4 HOH A 63 363 56 HOH HOH . G 4 HOH A 64 364 4 HOH HOH . G 4 HOH A 65 365 13 HOH HOH . G 4 HOH A 66 366 19 HOH HOH . G 4 HOH A 67 367 28 HOH HOH . G 4 HOH A 68 368 38 HOH HOH . G 4 HOH A 69 369 39 HOH HOH . G 4 HOH A 70 370 42 HOH HOH . G 4 HOH A 71 371 46 HOH HOH . G 4 HOH A 72 372 52 HOH HOH . G 4 HOH A 73 373 62 HOH HOH . G 4 HOH A 74 374 73 HOH HOH . G 4 HOH A 75 375 75 HOH HOH . G 4 HOH A 76 376 99 HOH HOH . G 4 HOH A 77 377 103 HOH HOH . G 4 HOH A 78 378 113 HOH HOH . G 4 HOH A 79 379 123 HOH HOH . G 4 HOH A 80 380 124 HOH HOH . G 4 HOH A 81 381 127 HOH HOH . G 4 HOH A 82 382 129 HOH HOH . G 4 HOH A 83 383 137 HOH HOH . G 4 HOH A 84 384 149 HOH HOH . G 4 HOH A 85 385 154 HOH HOH . G 4 HOH A 86 386 155 HOH HOH . G 4 HOH A 87 387 159 HOH HOH . G 4 HOH A 88 388 160 HOH HOH . G 4 HOH A 89 389 161 HOH HOH . G 4 HOH A 90 390 163 HOH HOH . G 4 HOH A 91 391 164 HOH HOH . G 4 HOH A 92 392 169 HOH HOH . G 4 HOH A 93 393 174 HOH HOH . H 4 HOH B 1 301 166 HOH HOH . H 4 HOH B 2 302 89 HOH HOH . H 4 HOH B 3 303 168 HOH HOH . H 4 HOH B 4 304 25 HOH HOH . H 4 HOH B 5 305 104 HOH HOH . H 4 HOH B 6 306 63 HOH HOH . H 4 HOH B 7 307 150 HOH HOH . H 4 HOH B 8 308 49 HOH HOH . H 4 HOH B 9 309 172 HOH HOH . H 4 HOH B 10 310 2 HOH HOH . H 4 HOH B 11 311 167 HOH HOH . H 4 HOH B 12 312 177 HOH HOH . H 4 HOH B 13 313 65 HOH HOH . H 4 HOH B 14 314 68 HOH HOH . H 4 HOH B 15 315 102 HOH HOH . H 4 HOH B 16 316 152 HOH HOH . H 4 HOH B 17 317 90 HOH HOH . H 4 HOH B 18 318 33 HOH HOH . H 4 HOH B 19 319 85 HOH HOH . H 4 HOH B 20 320 81 HOH HOH . H 4 HOH B 21 321 100 HOH HOH . H 4 HOH B 22 322 15 HOH HOH . H 4 HOH B 23 323 79 HOH HOH . H 4 HOH B 24 324 78 HOH HOH . H 4 HOH B 25 325 119 HOH HOH . H 4 HOH B 26 326 29 HOH HOH . H 4 HOH B 27 327 77 HOH HOH . H 4 HOH B 28 328 12 HOH HOH . H 4 HOH B 29 329 53 HOH HOH . H 4 HOH B 30 330 43 HOH HOH . H 4 HOH B 31 331 145 HOH HOH . H 4 HOH B 32 332 175 HOH HOH . H 4 HOH B 33 333 57 HOH HOH . H 4 HOH B 34 334 83 HOH HOH . H 4 HOH B 35 335 117 HOH HOH . H 4 HOH B 36 336 133 HOH HOH . H 4 HOH B 37 337 93 HOH HOH . H 4 HOH B 38 338 173 HOH HOH . H 4 HOH B 39 339 21 HOH HOH . H 4 HOH B 40 340 32 HOH HOH . H 4 HOH B 41 341 34 HOH HOH . H 4 HOH B 42 342 48 HOH HOH . H 4 HOH B 43 343 50 HOH HOH . H 4 HOH B 44 344 55 HOH HOH . H 4 HOH B 45 345 58 HOH HOH . H 4 HOH B 46 346 60 HOH HOH . H 4 HOH B 47 347 64 HOH HOH . H 4 HOH B 48 348 67 HOH HOH . H 4 HOH B 49 349 72 HOH HOH . H 4 HOH B 50 350 76 HOH HOH . H 4 HOH B 51 351 80 HOH HOH . H 4 HOH B 52 352 87 HOH HOH . H 4 HOH B 53 353 91 HOH HOH . H 4 HOH B 54 354 95 HOH HOH . H 4 HOH B 55 355 97 HOH HOH . H 4 HOH B 56 356 101 HOH HOH . H 4 HOH B 57 357 108 HOH HOH . H 4 HOH B 58 358 109 HOH HOH . H 4 HOH B 59 359 118 HOH HOH . H 4 HOH B 60 360 121 HOH HOH . H 4 HOH B 61 361 135 HOH HOH . H 4 HOH B 62 362 136 HOH HOH . H 4 HOH B 63 363 138 HOH HOH . H 4 HOH B 64 364 139 HOH HOH . H 4 HOH B 65 365 146 HOH HOH . H 4 HOH B 66 366 147 HOH HOH . H 4 HOH B 67 367 151 HOH HOH . H 4 HOH B 68 368 176 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 O O3 39X . . . C 2 16.195 -0.442 0.493 1 34.49 ? O3 39X 201 A 1 HETATM 2 C C21 39X . . . C 2 15.271 0.261 0.019 1 31.23 ? C21 39X 201 A 1 HETATM 3 O O2 39X . . . C 2 14.649 0.045 -1.056 1 30.45 ? O2 39X 201 A 1 HETATM 4 C C20 39X . . . C 2 14.886 1.52 0.808 1 27.02 ? C20 39X 201 A 1 HETATM 5 C C12 39X . . . C 2 15.907 2.612 0.472 1 26.81 ? C12 39X 201 A 1 HETATM 6 C C13 39X . . . C 2 15.595 3.963 1.002 1 25.41 ? C13 39X 201 A 1 HETATM 7 N N3 39X . . . C 2 14.758 4.818 0.445 1 21.63 ? N3 39X 201 A 1 HETATM 8 C C15 39X . . . C 2 14.749 5.925 1.298 1 24.66 ? C15 39X 201 A 1 HETATM 9 C C19 39X . . . C 2 14.016 7.112 1.248 1 24.11 ? C19 39X 201 A 1 HETATM 10 C C18 39X . . . C 2 14.188 8.063 2.245 1 25.87 ? C18 39X 201 A 1 HETATM 11 C C17 39X . . . C 2 15.087 7.803 3.259 1 27.77 ? C17 39X 201 A 1 HETATM 12 F F1 39X . . . C 2 15.217 8.715 4.262 1 26.84 ? F1 39X 201 A 1 HETATM 13 C C16 39X . . . C 2 15.823 6.639 3.352 1 28.06 ? C16 39X 201 A 1 HETATM 14 C C14 39X . . . C 2 15.624 5.695 2.359 1 27 ? C14 39X 201 A 1 HETATM 15 N N2 39X . . . C 2 16.124 4.425 2.154 1 26.54 ? N2 39X 201 A 1 HETATM 16 N N1 39X . . . C 2 13.522 1.939 0.501 1 24.84 ? N1 39X 201 A 1 HETATM 17 C C1 39X . . . C 2 12.739 2.501 1.434 1 28.29 ? C1 39X 201 A 1 HETATM 18 O O1 39X . . . C 2 13.102 2.604 2.606 1 28.87 ? O1 39X 201 A 1 HETATM 19 C C2 39X . . . C 2 11.434 3.085 0.975 1 31.73 ? C2 39X 201 A 1 HETATM 20 C C7 39X . . . C 2 10.823 4.03 1.804 1 34.08 ? C7 39X 201 A 1 HETATM 21 C C6 39X . . . C 2 9.664 4.646 1.432 1 35.13 ? C6 39X 201 A 1 HETATM 22 C C5 39X . . . C 2 9.056 4.367 0.189 1 35.18 ? C5 39X 201 A 1 HETATM 23 C C11 39X . . . C 2 7.897 5.044 -0.266 1 38.38 ? C11 39X 201 A 1 HETATM 24 C C10 39X . . . C 2 7.369 4.771 -1.491 1 41.08 ? C10 39X 201 A 1 HETATM 25 C C9 39X . . . C 2 7.95 3.822 -2.315 1 40.61 ? C9 39X 201 A 1 HETATM 26 C C8 39X . . . C 2 9.067 3.144 -1.916 1 39.81 ? C8 39X 201 A 1 HETATM 27 C C4 39X . . . C 2 9.656 3.402 -0.656 1 35.32 ? C4 39X 201 A 1 HETATM 28 C C3 39X . . . C 2 10.846 2.766 -0.229 1 32.97 ? C3 39X 201 A 1 HETATM 29 H H15 39X . . . C 2 14.984 1.269 1.863 1 27.11 ? H15 39X 201 A 1 HETATM 30 H H9 39X . . . C 2 16 2.641 -0.613 1 26.16 ? H9 39X 201 A 1 HETATM 31 H H10 39X . . . C 2 16.897 2.382 0.862 1 25.37 ? H10 39X 201 A 1 HETATM 32 H H14 39X . . . C 2 13.305 7.301 0.445 1 23.5 ? H14 39X 201 A 1 HETATM 33 H H13 39X . . . C 2 13.609 8.985 2.231 1 24.96 ? H13 39X 201 A 1 HETATM 34 H H12 39X . . . C 2 16.542 6.475 4.153 1 28.59 ? H12 39X 201 A 1 HETATM 35 H H11 39X . . . C 2 16.697 3.932 2.831 1 26.41 ? H11 39X 201 A 1 HETATM 36 H H1 39X . . . C 2 13.036 1.272 -0.089 1 24.18 ? H1 39X 201 A 1 HETATM 37 H H4 39X . . . C 2 11.286 4.277 2.758 1 33.16 ? H4 39X 201 A 1 HETATM 38 H H3 39X . . . C 2 9.164 5.359 2.085 1 34.99 ? H3 39X 201 A 1 HETATM 39 H H8 39X . . . C 2 7.443 5.787 0.388 1 37.5 ? H8 39X 201 A 1 HETATM 40 H H7 39X . . . C 2 6.483 5.318 -1.811 1 42.04 ? H7 39X 201 A 1 HETATM 41 H H6 39X . . . C 2 7.503 3.626 -3.289 1 40.55 ? H6 39X 201 A 1 HETATM 42 H H5 39X . . . C 2 9.523 2.394 -2.561 1 39.81 ? H5 39X 201 A 1 HETATM 43 H H2 39X . . . C 2 11.273 2.011 -0.887 1 32.27 ? H2 39X 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #