data_4TYO # _model_server_result.job_id CKVuGwDTH05Wpas5Je9aTQ _model_server_result.datetime_utc '2025-02-05 15:49:27' _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":"E","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 . . . E 2 -1.549 26.149 26.939 1 25.27 ? O3 39X 201 B 1 HETATM 2 C C21 39X . . . E 2 -1.294 26.32 25.732 1 24.7 ? C21 39X 201 B 1 HETATM 3 O O2 39X . . . E 2 -1.026 25.418 24.909 1 23.44 ? O2 39X 201 B 1 HETATM 4 C C20 39X . . . E 2 -1.308 27.761 25.197 1 22.02 ? C20 39X 201 B 1 HETATM 5 C C12 39X . . . E 2 0.02 28.431 25.578 1 20.53 ? C12 39X 201 B 1 HETATM 6 C C13 39X . . . E 2 0.165 29.761 24.978 1 23.45 ? C13 39X 201 B 1 HETATM 7 N N3 39X . . . E 2 0.57 29.987 23.742 1 23.26 ? N3 39X 201 B 1 HETATM 8 C C15 39X . . . E 2 0.485 31.366 23.582 1 23.5 ? C15 39X 201 B 1 HETATM 9 C C19 39X . . . E 2 0.811 32.173 22.496 1 24.02 ? C19 39X 201 B 1 HETATM 10 C C18 39X . . . E 2 0.666 33.549 22.605 1 24.83 ? C18 39X 201 B 1 HETATM 11 C C17 39X . . . E 2 0.222 34.073 23.799 1 24.17 ? C17 39X 201 B 1 HETATM 12 F F1 39X . . . E 2 0.126 35.419 23.915 1 26.11 ? F1 39X 201 B 1 HETATM 13 C C16 39X . . . E 2 -0.115 33.313 24.898 1 25.11 ? C16 39X 201 B 1 HETATM 14 C C14 39X . . . E 2 0.02 31.941 24.766 1 24.17 ? C14 39X 201 B 1 HETATM 15 N N2 39X . . . E 2 -0.194 30.89 25.627 1 23.55 ? N2 39X 201 B 1 HETATM 16 N N1 39X . . . E 2 -1.49 27.763 23.749 1 22.97 ? N1 39X 201 B 1 HETATM 17 C C1 39X . . . E 2 -2.147 28.736 23.097 1 24.61 ? C1 39X 201 B 1 HETATM 18 O O1 39X . . . E 2 -2.698 29.659 23.693 1 23.95 ? O1 39X 201 B 1 HETATM 19 C C2 39X . . . E 2 -2.114 28.696 21.596 1 25.71 ? C2 39X 201 B 1 HETATM 20 C C7 39X . . . E 2 -2.155 29.907 20.896 1 26.11 ? C7 39X 201 B 1 HETATM 21 C C6 39X . . . E 2 -2.191 29.929 19.534 1 26.41 ? C6 39X 201 B 1 HETATM 22 C C5 39X . . . E 2 -2.124 28.73 18.779 1 26.39 ? C5 39X 201 B 1 HETATM 23 C C11 39X . . . E 2 -2.057 28.715 17.36 1 26.62 ? C11 39X 201 B 1 HETATM 24 C C10 39X . . . E 2 -1.892 27.542 16.679 1 27.86 ? C10 39X 201 B 1 HETATM 25 C C9 39X . . . E 2 -1.798 26.337 17.364 1 28.96 ? C9 39X 201 B 1 HETATM 26 C C8 39X . . . E 2 -1.88 26.305 18.727 1 28.6 ? C8 39X 201 B 1 HETATM 27 C C4 39X . . . E 2 -2.046 27.499 19.474 1 27.41 ? C4 39X 201 B 1 HETATM 28 C C3 39X . . . E 2 -2.058 27.514 20.893 1 25.6 ? C3 39X 201 B 1 HETATM 29 H H15 39X . . . E 2 -2.133 28.273 25.691 1 20.89 ? H15 39X 201 B 1 HETATM 30 H H9 39X . . . E 2 0.826 27.769 25.266 1 18.65 ? H9 39X 201 B 1 HETATM 31 H H10 39X . . . E 2 0.138 28.586 26.649 1 19.27 ? H10 39X 201 B 1 HETATM 32 H H14 39X . . . E 2 1.167 31.742 21.562 1 23.29 ? H14 39X 201 B 1 HETATM 33 H H13 39X . . . E 2 0.905 34.197 21.763 1 24.31 ? H13 39X 201 B 1 HETATM 34 H H12 39X . . . E 2 -0.479 33.763 25.82 1 26.15 ? H12 39X 201 B 1 HETATM 35 H H11 39X . . . E 2 -0.622 30.987 26.541 1 24.17 ? H11 39X 201 B 1 HETATM 36 H H1 39X . . . E 2 -1.625 26.832 23.37 1 22.04 ? H1 39X 201 B 1 HETATM 37 H H4 39X . . . E 2 -2.067 30.837 21.455 1 25.82 ? H4 39X 201 B 1 HETATM 38 H H3 39X . . . E 2 -2.272 30.869 18.991 1 26.79 ? H3 39X 201 B 1 HETATM 39 H H8 39X . . . E 2 -2.125 29.664 16.833 1 26.44 ? H8 39X 201 B 1 HETATM 40 H H7 39X . . . E 2 -1.835 27.572 15.592 1 27.61 ? H7 39X 201 B 1 HETATM 41 H H6 39X . . . E 2 -1.665 25.414 16.802 1 28.65 ? H6 39X 201 B 1 HETATM 42 H H5 39X . . . E 2 -1.813 25.358 19.259 1 28.81 ? H5 39X 201 B 1 HETATM 43 H H2 39X . . . E 2 -2.014 26.56 21.411 1 25.89 ? H2 39X 201 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 43 #