data_3EEK # _model_server_result.job_id ieHUsNQEXWypxRRFSmjrUQ _model_server_result.datetime_utc '2024-11-27 23:06:46' _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 3eek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":229}' # _entry.id 3EEK # _exptl.entry_id 3EEK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 372.463 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-[(3R)-3-(5-methoxy-4'-methylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine" _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 3EEK _cell.length_a 42.753 _cell.length_b 42.753 _cell.length_c 230.448 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EEK _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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 ? 3 D N N ? 3 F N N # _chem_comp.formula 'C23 H24 N4 O' _chem_comp.formula_weight 372.463 _chem_comp.id 53S _chem_comp.mon_nstd_flag . _chem_comp.name "5-[(3R)-3-(5-methoxy-4'-methylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine" _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 C6 C5 53S doub 1 n y C6 C10 53S sing 2 n n C6 C1 53S sing 3 n y C5 C8 53S sing 4 n n C5 N4 53S sing 5 n y C2 O17 53S sing 6 n n C20 C21 53S doub 7 n y C20 C25 53S sing 8 n y C21 C22 53S sing 9 n y C22 C26 53S sing 10 n n C22 C23 53S doub 11 n y C23 C24 53S sing 12 n y C24 C25 53S doub 13 n y C25 C18 53S sing 14 n y C18 C19 53S doub 15 n y C18 C17 53S sing 16 n y C19 C14 53S sing 17 n y C17 C16 53S doub 18 n y C16 O17 53S sing 19 n n C16 C15 53S sing 20 n y C15 C14 53S doub 21 n y C14 C12 53S sing 22 n n C12 C13 53S sing 23 n n C12 C11 53S sing 24 n n C11 C10 53S trip 25 n n N4 C3 53S doub 26 n y C3 N7 53S sing 27 n n C3 N2 53S sing 28 n y N2 C1 53S doub 29 n y C1 N9 53S sing 30 n n C2 H2 53S sing 31 n n C2 H2A 53S sing 32 n n C2 H2B 53S sing 33 n n C20 H20 53S sing 34 n n C21 H21 53S sing 35 n n C26 H26 53S sing 36 n n C26 H26A 53S sing 37 n n C26 H26B 53S sing 38 n n C23 H23 53S sing 39 n n C24 H24 53S sing 40 n n C19 H19 53S sing 41 n n C17 H17 53S sing 42 n n C15 H15 53S sing 43 n n C12 H12 53S sing 44 n n C13 H13 53S sing 45 n n C13 H13A 53S sing 46 n n C13 H13B 53S sing 47 n n C8 H8 53S sing 48 n n C8 H8A 53S sing 49 n n C8 H8B 53S sing 50 n n N7 HN7 53S sing 51 n n N7 HN7A 53S sing 52 n n N9 HN9 53S sing 53 n n N9 HN9A 53S sing 54 n n # _atom_sites.entry_id 3EEK _atom_sites.fract_transf_matrix[1][1] 0.02339 _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] 0.02339 _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] 0.004339 _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 NDP A 1 228 207 NDP NAP . D 3 53S A 1 229 1 53S 53S . E 2 NDP B 1 228 207 NDP NAP . F 3 53S B 1 229 1 53S 53S . G 4 HOH A 1 230 1 HOH HOH . G 4 HOH A 2 231 2 HOH HOH . G 4 HOH A 3 232 4 HOH HOH . G 4 HOH A 4 233 5 HOH HOH . G 4 HOH A 5 234 8 HOH HOH . G 4 HOH A 6 235 11 HOH HOH . G 4 HOH A 7 236 12 HOH HOH . G 4 HOH A 8 237 13 HOH HOH . G 4 HOH A 9 238 14 HOH HOH . G 4 HOH A 10 239 16 HOH HOH . G 4 HOH A 11 240 17 HOH HOH . G 4 HOH A 12 241 18 HOH HOH . G 4 HOH A 13 242 21 HOH HOH . G 4 HOH A 14 243 23 HOH HOH . G 4 HOH A 15 244 24 HOH HOH . G 4 HOH A 16 245 25 HOH HOH . G 4 HOH A 17 246 26 HOH HOH . G 4 HOH A 18 247 35 HOH HOH . G 4 HOH A 19 248 36 HOH HOH . G 4 HOH A 20 249 40 HOH HOH . G 4 HOH A 21 250 42 HOH HOH . G 4 HOH A 22 251 44 HOH HOH . G 4 HOH A 23 252 45 HOH HOH . G 4 HOH A 24 253 46 HOH HOH . G 4 HOH A 25 254 47 HOH HOH . G 4 HOH A 26 255 48 HOH HOH . G 4 HOH A 27 256 51 HOH HOH . G 4 HOH A 28 257 52 HOH HOH . G 4 HOH A 29 258 53 HOH HOH . G 4 HOH A 30 259 54 HOH HOH . G 4 HOH A 31 260 55 HOH HOH . G 4 HOH A 32 261 57 HOH HOH . G 4 HOH A 33 262 60 HOH HOH . G 4 HOH A 34 263 61 HOH HOH . G 4 HOH A 35 264 64 HOH HOH . G 4 HOH A 36 265 66 HOH HOH . G 4 HOH A 37 266 74 HOH HOH . G 4 HOH A 38 267 75 HOH HOH . G 4 HOH A 39 268 76 HOH HOH . G 4 HOH A 40 269 79 HOH HOH . G 4 HOH A 41 270 80 HOH HOH . G 4 HOH A 42 271 81 HOH HOH . G 4 HOH A 43 272 82 HOH HOH . G 4 HOH A 44 273 84 HOH HOH . G 4 HOH A 45 274 85 HOH HOH . G 4 HOH A 46 275 86 HOH HOH . G 4 HOH A 47 276 88 HOH HOH . G 4 HOH A 48 277 89 HOH HOH . G 4 HOH A 49 278 90 HOH HOH . G 4 HOH A 50 279 91 HOH HOH . G 4 HOH A 51 280 93 HOH HOH . G 4 HOH A 52 281 96 HOH HOH . G 4 HOH A 53 282 98 HOH HOH . G 4 HOH A 54 283 101 HOH HOH . G 4 HOH A 55 284 103 HOH HOH . G 4 HOH A 56 285 108 HOH HOH . G 4 HOH A 57 286 112 HOH HOH . G 4 HOH A 58 287 114 HOH HOH . G 4 HOH A 59 288 115 HOH HOH . G 4 HOH A 60 289 117 HOH HOH . G 4 HOH A 61 290 119 HOH HOH . G 4 HOH A 62 291 120 HOH HOH . G 4 HOH A 63 292 121 HOH HOH . G 4 HOH A 64 293 124 HOH HOH . G 4 HOH A 65 294 127 HOH HOH . G 4 HOH A 66 295 130 HOH HOH . G 4 HOH A 67 296 131 HOH HOH . G 4 HOH A 68 297 132 HOH HOH . G 4 HOH A 69 298 133 HOH HOH . G 4 HOH A 70 299 137 HOH HOH . G 4 HOH A 71 300 138 HOH HOH . H 4 HOH B 1 230 3 HOH HOH . H 4 HOH B 2 231 6 HOH HOH . H 4 HOH B 3 232 7 HOH HOH . H 4 HOH B 4 233 9 HOH HOH . H 4 HOH B 5 234 10 HOH HOH . H 4 HOH B 6 235 15 HOH HOH . H 4 HOH B 7 236 19 HOH HOH . H 4 HOH B 8 237 20 HOH HOH . H 4 HOH B 9 238 22 HOH HOH . H 4 HOH B 10 239 27 HOH HOH . H 4 HOH B 11 240 28 HOH HOH . H 4 HOH B 12 241 29 HOH HOH . H 4 HOH B 13 242 30 HOH HOH . H 4 HOH B 14 243 31 HOH HOH . H 4 HOH B 15 244 32 HOH HOH . H 4 HOH B 16 245 33 HOH HOH . H 4 HOH B 17 246 34 HOH HOH . H 4 HOH B 18 247 37 HOH HOH . H 4 HOH B 19 248 38 HOH HOH . H 4 HOH B 20 249 39 HOH HOH . H 4 HOH B 21 250 41 HOH HOH . H 4 HOH B 22 251 43 HOH HOH . H 4 HOH B 23 252 49 HOH HOH . H 4 HOH B 24 253 50 HOH HOH . H 4 HOH B 25 254 56 HOH HOH . H 4 HOH B 26 255 58 HOH HOH . H 4 HOH B 27 256 59 HOH HOH . H 4 HOH B 28 257 62 HOH HOH . H 4 HOH B 29 258 63 HOH HOH . H 4 HOH B 30 259 65 HOH HOH . H 4 HOH B 31 260 67 HOH HOH . H 4 HOH B 32 261 69 HOH HOH . H 4 HOH B 33 262 70 HOH HOH . H 4 HOH B 34 263 71 HOH HOH . H 4 HOH B 35 264 72 HOH HOH . H 4 HOH B 36 265 73 HOH HOH . H 4 HOH B 37 266 77 HOH HOH . H 4 HOH B 38 267 78 HOH HOH . H 4 HOH B 39 268 83 HOH HOH . H 4 HOH B 40 269 87 HOH HOH . H 4 HOH B 41 270 92 HOH HOH . H 4 HOH B 42 271 95 HOH HOH . H 4 HOH B 43 272 97 HOH HOH . H 4 HOH B 44 273 99 HOH HOH . H 4 HOH B 45 274 100 HOH HOH . H 4 HOH B 46 275 102 HOH HOH . H 4 HOH B 47 276 104 HOH HOH . H 4 HOH B 48 277 105 HOH HOH . H 4 HOH B 49 278 106 HOH HOH . H 4 HOH B 50 279 107 HOH HOH . H 4 HOH B 51 280 109 HOH HOH . H 4 HOH B 52 281 110 HOH HOH . H 4 HOH B 53 282 111 HOH HOH . H 4 HOH B 54 283 113 HOH HOH . H 4 HOH B 55 284 118 HOH HOH . H 4 HOH B 56 285 122 HOH HOH . H 4 HOH B 57 286 123 HOH HOH . H 4 HOH B 58 287 125 HOH HOH . H 4 HOH B 59 288 126 HOH HOH . H 4 HOH B 60 289 128 HOH HOH . H 4 HOH B 61 290 129 HOH HOH . H 4 HOH B 62 291 134 HOH HOH . H 4 HOH B 63 292 135 HOH HOH . H 4 HOH B 64 293 136 HOH HOH . H 4 HOH B 65 294 139 HOH HOH . H 4 HOH B 66 295 140 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 C6 53S . . . D 3 15.043 -8.455 -3.016 1 15.6 ? C6 53S 229 A 1 HETATM 2 C C5 53S . . . D 3 15.135 -9.161 -4.235 1 15.11 ? C5 53S 229 A 1 HETATM 3 C C2 53S . . . D 3 14.771 -1.192 -4.965 1 18.59 ? C2 53S 229 A 1 HETATM 4 C C20 53S . . . D 3 8.875 -5.187 -6.303 1 29 ? C20 53S 229 A 1 HETATM 5 C C21 53S . . . D 3 7.958 -5.575 -7.291 1 30.84 ? C21 53S 229 A 1 HETATM 6 C C22 53S . . . D 3 8.165 -5.325 -8.669 1 31.63 ? C22 53S 229 A 1 HETATM 7 C C26 53S . . . D 3 7.102 -5.804 -9.719 1 31.66 ? C26 53S 229 A 1 HETATM 8 C C23 53S . . . D 3 9.335 -4.681 -9.104 1 27.42 ? C23 53S 229 A 1 HETATM 9 C C24 53S . . . D 3 10.255 -4.301 -8.114 1 27.87 ? C24 53S 229 A 1 HETATM 10 C C25 53S . . . D 3 10.04 -4.536 -6.725 1 26.68 ? C25 53S 229 A 1 HETATM 11 C C18 53S . . . D 3 11.032 -4.114 -5.812 1 25.3 ? C18 53S 229 A 1 HETATM 12 C C19 53S . . . D 3 11.401 -4.891 -4.667 1 22.48 ? C19 53S 229 A 1 HETATM 13 C C17 53S . . . D 3 11.712 -2.892 -6.121 1 24.8 ? C17 53S 229 A 1 HETATM 14 C C16 53S . . . D 3 12.731 -2.406 -5.29 1 25.22 ? C16 53S 229 A 1 HETATM 15 O O17 53S . . . D 3 13.41 -1.213 -5.563 1 26.74 ? O17 53S 229 A 1 HETATM 16 C C15 53S . . . D 3 13.068 -3.174 -4.164 1 24.92 ? C15 53S 229 A 1 HETATM 17 C C14 53S . . . D 3 12.431 -4.379 -3.851 1 21.05 ? C14 53S 229 A 1 HETATM 18 C C12 53S . . . D 3 12.941 -5.013 -2.575 1 19.47 ? C12 53S 229 A 1 HETATM 19 C C13 53S . . . D 3 11.852 -5.095 -1.473 1 22.79 ? C13 53S 229 A 1 HETATM 20 C C11 53S . . . D 3 13.635 -6.291 -2.821 1 16.94 ? C11 53S 229 A 1 HETATM 21 C C10 53S . . . D 3 14.273 -7.27 -2.93 1 13.71 ? C10 53S 229 A 1 HETATM 22 C C8 53S . . . D 3 14.464 -8.699 -5.58 1 13.59 ? C8 53S 229 A 1 HETATM 23 N N4 53S . . . D 3 15.878 -10.283 -4.235 1 13.68 ? N4 53S 229 A 1 HETATM 24 C C3 53S . . . D 3 16.499 -10.759 -3.123 1 14.14 ? C3 53S 229 A 1 HETATM 25 N N7 53S . . . D 3 17.17 -11.926 -3.198 1 14.44 ? N7 53S 229 A 1 HETATM 26 N N2 53S . . . D 3 16.367 -10.121 -1.963 1 13.27 ? N2 53S 229 A 1 HETATM 27 C C1 53S . . . D 3 15.704 -8.963 -1.855 1 12.73 ? C1 53S 229 A 1 HETATM 28 N N9 53S . . . D 3 15.616 -8.358 -0.676 1 10.9 ? N9 53S 229 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 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #