data_3DDP # _model_server_result.job_id myJ9rVQplAnGowHzkm18mg _model_server_result.datetime_utc '2024-11-26 12:41:09' _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 3ddp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":299}' # _entry.id 3DDP # _exptl.entry_id 3DDP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 431.533 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol _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 3DDP _cell.length_a 74.318 _cell.length_b 135.159 _cell.length_c 168.952 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DDP _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 author_and_software_defined_assembly 1 PISA dimeric 2 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 C,D,F,I,J 1 1 A,B,E,G,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 E N N ? 3 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C TYR 160 A TYR 159 1_555 A N TPO 161 A TPO 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C TPO 161 A TPO 160 1_555 A N HIS 162 A HIS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 C C TYR 160 C TYR 159 1_555 C N TPO 161 C TPO 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 C C TPO 161 C TPO 160 1_555 C N HIS 162 C HIS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? # _chem_comp.formula 'C24 H29 N7 O' _chem_comp.formula_weight 431.533 _chem_comp.id RC8 _chem_comp.mon_nstd_flag . _chem_comp.name (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol _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 N2 C2 RC8 sing 277 n n N3 C2 RC8 doub 278 n y C2 N1 RC8 sing 279 n y N3 C4 RC8 sing 280 n y N9 C4 RC8 sing 281 n y C4 C5 RC8 doub 282 n y C5 C6 RC8 sing 283 n y C5 N7 RC8 sing 284 n y N1 C6 RC8 doub 285 n y C6 N6 RC8 sing 286 n n N9 C8 RC8 sing 287 n y C8 N7 RC8 doub 288 n y C8 H8 RC8 sing 289 n n C10 C9 RC8 sing 290 n n C9 N9 RC8 sing 291 n n C9 C11 RC8 sing 292 n n C9 H9 RC8 sing 293 n n C10 H10 RC8 sing 294 n n C10 H10A RC8 sing 295 n n C10 H10B RC8 sing 296 n n C13 C12 RC8 sing 297 n n C12 C15 RC8 sing 298 n n C12 N2 RC8 sing 299 n n C12 H12 RC8 sing 300 n n C14 C13 RC8 sing 301 n n C14 H14 RC8 sing 302 n n C14 H14A RC8 sing 303 n n C14 H14B RC8 sing 304 n n C15 O1 RC8 sing 305 n n O1 HO1 RC8 sing 306 n n C15 H15 RC8 sing 307 n n C15 H15A RC8 sing 308 n n C13 H13 RC8 sing 309 n n C13 H13A RC8 sing 310 n n N2 HN2 RC8 sing 311 n n C11 H11 RC8 sing 312 n n C11 H11A RC8 sing 313 n n C11 H11B RC8 sing 314 n n CA' N6 RC8 sing 315 n n N6 HN6 RC8 sing 316 n n CA' C1' RC8 sing 317 n n CA' HA' RC8 sing 318 n n CA' "HA'A" RC8 sing 319 n n C6' C1' RC8 doub 320 n y C1' C2' RC8 sing 321 n y C6' C5' RC8 sing 322 n y C6' H6' RC8 sing 323 n n C5' C4' RC8 doub 324 n y C5' H5' RC8 sing 325 n n C4' C3' RC8 sing 326 n y C4' C1B RC8 sing 327 n y C2' C3' RC8 doub 328 n y C3' H3' RC8 sing 329 n n C2' H2' RC8 sing 330 n n C2B C1B RC8 doub 331 n y C1B N1B RC8 sing 332 n y N1B C5B RC8 doub 333 n y C4B C5B RC8 sing 334 n y C5B H5B RC8 sing 335 n n C3B C4B RC8 doub 336 n y C4B H4B RC8 sing 337 n n C2B C3B RC8 sing 338 n y C3B H3B RC8 sing 339 n n C2B H2B RC8 sing 340 n n # _atom_sites.entry_id 3DDP _atom_sites.fract_transf_matrix[1][1] 0.013456 _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] 0.007399 _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] 0.005919 _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 E 3 RC8 A 1 299 1 RC8 RC8 . F 3 RC8 C 1 299 1 RC8 RC8 . G 4 HOH A 1 300 2 HOH HOH . G 4 HOH A 2 301 4 HOH HOH . G 4 HOH A 3 302 7 HOH HOH . G 4 HOH A 4 303 8 HOH HOH . G 4 HOH A 5 304 9 HOH HOH . G 4 HOH A 6 305 10 HOH HOH . G 4 HOH A 7 306 11 HOH HOH . G 4 HOH A 8 307 12 HOH HOH . G 4 HOH A 9 308 13 HOH HOH . G 4 HOH A 10 309 16 HOH HOH . G 4 HOH A 11 310 18 HOH HOH . G 4 HOH A 12 311 20 HOH HOH . G 4 HOH A 13 312 24 HOH HOH . G 4 HOH A 14 313 30 HOH HOH . G 4 HOH A 15 314 33 HOH HOH . G 4 HOH A 16 315 35 HOH HOH . G 4 HOH A 17 316 36 HOH HOH . G 4 HOH A 18 317 38 HOH HOH . G 4 HOH A 19 318 40 HOH HOH . G 4 HOH A 20 319 50 HOH HOH . G 4 HOH A 21 320 53 HOH HOH . G 4 HOH A 22 321 56 HOH HOH . G 4 HOH A 23 322 66 HOH HOH . G 4 HOH A 24 323 67 HOH HOH . G 4 HOH A 25 324 69 HOH HOH . G 4 HOH A 26 325 70 HOH HOH . G 4 HOH A 27 326 75 HOH HOH . G 4 HOH A 28 327 77 HOH HOH . G 4 HOH A 29 328 84 HOH HOH . G 4 HOH A 30 329 85 HOH HOH . G 4 HOH A 31 330 86 HOH HOH . G 4 HOH A 32 331 89 HOH HOH . G 4 HOH A 33 332 90 HOH HOH . G 4 HOH A 34 333 91 HOH HOH . G 4 HOH A 35 334 93 HOH HOH . G 4 HOH A 36 335 99 HOH HOH . G 4 HOH A 37 336 101 HOH HOH . G 4 HOH A 38 337 103 HOH HOH . G 4 HOH A 39 338 104 HOH HOH . G 4 HOH A 40 339 110 HOH HOH . G 4 HOH A 41 340 113 HOH HOH . G 4 HOH A 42 341 120 HOH HOH . G 4 HOH A 43 342 6 HOH HOH . G 4 HOH A 44 343 9 HOH HOH . G 4 HOH A 45 344 10 HOH HOH . G 4 HOH A 46 345 13 HOH HOH . G 4 HOH A 47 346 14 HOH HOH . G 4 HOH A 48 347 17 HOH HOH . G 4 HOH A 49 348 18 HOH HOH . G 4 HOH A 50 349 19 HOH HOH . G 4 HOH A 51 350 20 HOH HOH . G 4 HOH A 52 351 25 HOH HOH . G 4 HOH A 53 352 26 HOH HOH . H 4 HOH B 1 439 5 HOH HOH . H 4 HOH B 2 440 14 HOH HOH . H 4 HOH B 3 441 19 HOH HOH . H 4 HOH B 4 442 23 HOH HOH . H 4 HOH B 5 443 29 HOH HOH . H 4 HOH B 6 444 42 HOH HOH . H 4 HOH B 7 445 49 HOH HOH . H 4 HOH B 8 446 52 HOH HOH . H 4 HOH B 9 447 59 HOH HOH . H 4 HOH B 10 448 62 HOH HOH . H 4 HOH B 11 449 68 HOH HOH . H 4 HOH B 12 450 74 HOH HOH . H 4 HOH B 13 451 76 HOH HOH . H 4 HOH B 14 452 82 HOH HOH . H 4 HOH B 15 453 88 HOH HOH . H 4 HOH B 16 454 92 HOH HOH . H 4 HOH B 17 455 96 HOH HOH . H 4 HOH B 18 456 107 HOH HOH . H 4 HOH B 19 457 121 HOH HOH . H 4 HOH B 20 458 122 HOH HOH . H 4 HOH B 21 459 5 HOH HOH . H 4 HOH B 22 460 7 HOH HOH . H 4 HOH B 23 461 8 HOH HOH . H 4 HOH B 24 462 15 HOH HOH . H 4 HOH B 25 463 16 HOH HOH . H 4 HOH B 26 464 21 HOH HOH . H 4 HOH B 27 465 22 HOH HOH . H 4 HOH B 28 466 23 HOH HOH . I 4 HOH C 1 300 15 HOH HOH . I 4 HOH C 2 301 21 HOH HOH . I 4 HOH C 3 302 22 HOH HOH . I 4 HOH C 4 303 25 HOH HOH . I 4 HOH C 5 304 32 HOH HOH . I 4 HOH C 6 305 34 HOH HOH . I 4 HOH C 7 306 41 HOH HOH . I 4 HOH C 8 307 43 HOH HOH . I 4 HOH C 9 308 45 HOH HOH . I 4 HOH C 10 309 46 HOH HOH . I 4 HOH C 11 310 54 HOH HOH . I 4 HOH C 12 311 57 HOH HOH . I 4 HOH C 13 312 61 HOH HOH . I 4 HOH C 14 313 65 HOH HOH . I 4 HOH C 15 314 71 HOH HOH . I 4 HOH C 16 315 73 HOH HOH . I 4 HOH C 17 316 78 HOH HOH . I 4 HOH C 18 317 80 HOH HOH . I 4 HOH C 19 318 97 HOH HOH . I 4 HOH C 20 319 108 HOH HOH . I 4 HOH C 21 320 112 HOH HOH . I 4 HOH C 22 321 115 HOH HOH . I 4 HOH C 23 322 116 HOH HOH . I 4 HOH C 24 323 118 HOH HOH . I 4 HOH C 25 324 119 HOH HOH . I 4 HOH C 26 325 2 HOH HOH . I 4 HOH C 27 326 3 HOH HOH . I 4 HOH C 28 327 4 HOH HOH . I 4 HOH C 29 328 11 HOH HOH . I 4 HOH C 30 329 12 HOH HOH . I 4 HOH C 31 330 24 HOH HOH . I 4 HOH C 32 331 27 HOH HOH . I 4 HOH C 33 332 48 HOH HOH . J 4 HOH D 1 3 3 HOH HOH . J 4 HOH D 2 26 26 HOH HOH . J 4 HOH D 3 27 27 HOH HOH . J 4 HOH D 4 28 28 HOH HOH . J 4 HOH D 5 31 31 HOH HOH . J 4 HOH D 6 37 37 HOH HOH . J 4 HOH D 7 47 47 HOH HOH . J 4 HOH D 8 51 51 HOH HOH . J 4 HOH D 9 58 58 HOH HOH . J 4 HOH D 10 64 64 HOH HOH . J 4 HOH D 11 72 72 HOH HOH . J 4 HOH D 12 79 79 HOH HOH . J 4 HOH D 13 81 81 HOH HOH . J 4 HOH D 14 83 83 HOH HOH . J 4 HOH D 15 87 87 HOH HOH . J 4 HOH D 16 98 98 HOH HOH . J 4 HOH D 17 102 102 HOH HOH . J 4 HOH D 18 105 105 HOH HOH . J 4 HOH D 19 109 109 HOH HOH . J 4 HOH D 20 114 114 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 C2 RC8 . . . F 3 32.822 -14.668 37.826 1 54.26 ? C2 RC8 299 C 1 HETATM 2 C C4 RC8 . . . F 3 32.482 -13.373 35.902 1 54.64 ? C4 RC8 299 C 1 HETATM 3 C C5 RC8 . . . F 3 32.252 -14.577 35.094 1 54.36 ? C5 RC8 299 C 1 HETATM 4 C C6 RC8 . . . F 3 32.346 -15.879 35.822 1 54.65 ? C6 RC8 299 C 1 HETATM 5 C C8 RC8 . . . F 3 32.08 -12.769 33.854 1 53.94 ? C8 RC8 299 C 1 HETATM 6 C C9 RC8 . . . F 3 32.56 -10.961 35.64 1 53.46 ? C9 RC8 299 C 1 HETATM 7 C C10 RC8 . . . F 3 33.582 -10.202 34.815 1 51.33 ? C10 RC8 299 C 1 HETATM 8 C C12 RC8 . . . F 3 33.669 -13.483 39.772 1 56.64 ? C12 RC8 299 C 1 HETATM 9 C C14 RC8 . . . F 3 35.773 -12.422 38.848 1 55.27 ? C14 RC8 299 C 1 HETATM 10 O O1 RC8 . . . F 3 32.523 -14.597 41.618 1 59.5 ? O1 RC8 299 C 1 HETATM 11 C C15 RC8 . . . F 3 33.197 -13.389 41.223 1 58.19 ? C15 RC8 299 C 1 HETATM 12 C C13 RC8 . . . F 3 35.198 -13.507 39.73 1 56.11 ? C13 RC8 299 C 1 HETATM 13 N N2 RC8 . . . F 3 33.106 -14.674 39.145 1 54.81 ? N2 RC8 299 C 1 HETATM 14 N N1 RC8 . . . F 3 32.625 -15.834 37.152 1 54.47 ? N1 RC8 299 C 1 HETATM 15 N N9 RC8 . . . F 3 32.366 -12.329 35.098 1 54.31 ? N9 RC8 299 C 1 HETATM 16 C C11 RC8 . . . F 3 31.22 -10.274 35.797 1 52.6 ? C11 RC8 299 C 1 HETATM 17 N N7 RC8 . . . F 3 32.007 -14.13 33.842 1 53.45 ? N7 RC8 299 C 1 HETATM 18 N N3 RC8 . . . F 3 32.754 -13.471 37.219 1 53.95 ? N3 RC8 299 C 1 HETATM 19 N N6 RC8 . . . F 3 32.145 -17.057 35.183 1 54.89 ? N6 RC8 299 C 1 HETATM 20 C CA' RC8 . . . F 3 32.639 -18.329 35.674 1 58.11 ? CA' RC8 299 C 1 HETATM 21 C C1' RC8 . . . F 3 31.539 -18.979 36.47 1 58.94 ? C1' RC8 299 C 1 HETATM 22 C C6' RC8 . . . F 3 31.684 -19.156 37.849 1 59.6 ? C6' RC8 299 C 1 HETATM 23 C C5' RC8 . . . F 3 30.66 -19.749 38.586 1 59.81 ? C5' RC8 299 C 1 HETATM 24 C C4' RC8 . . . F 3 29.499 -20.174 37.939 1 60.24 ? C4' RC8 299 C 1 HETATM 25 C C3' RC8 . . . F 3 29.357 -19.985 36.563 1 60.06 ? C3' RC8 299 C 1 HETATM 26 C C2' RC8 . . . F 3 30.378 -19.39 35.825 1 59.37 ? C2' RC8 299 C 1 HETATM 27 C C1B RC8 . . . F 3 28.389 -20.781 38.722 1 60.6 ? C1B RC8 299 C 1 HETATM 28 N N1B RC8 . . . F 3 28.459 -20.787 40.071 1 62.54 ? N1B RC8 299 C 1 HETATM 29 C C5B RC8 . . . F 3 27.471 -21.304 40.831 1 62.93 ? C5B RC8 299 C 1 HETATM 30 C C4B RC8 . . . F 3 26.326 -21.834 40.229 1 62.23 ? C4B RC8 299 C 1 HETATM 31 C C3B RC8 . . . F 3 26.219 -21.826 38.838 1 62.14 ? C3B RC8 299 C 1 HETATM 32 C C2B RC8 . . . F 3 27.258 -21.288 38.076 1 61.69 ? C2B RC8 299 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #