data_6TD3
#
_model_server_result.job_id            BM7WkfCSau3mOq0VNXhLzA 
_model_server_result.datetime_utc      '2024-11-26 20:14:36' 
_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          6td3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1101}' 
#
_entry.id    6TD3 
#
_exptl.entry_id    6TD3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              431.533 
_entity.id                          4 
_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    3 
_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         120 
_cell.entry_id            6TD3 
_cell.length_a            250.749 
_cell.length_b            250.749 
_cell.length_c            217.92 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6TD3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 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
PISA trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
PISA trimeric 3 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,J 1 1 
D,E,F,K 2 1 
G,H,I,L 3 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
? 4 J N N 
? 4 K N N 
? 4 L 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 B C TYR 184 B TYR 892 1_555 B N TPO 185 B TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? 
covale ? covale2 B C TPO 185 B TPO 893 1_555 B N ASN 186 B ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? 
covale ? covale3 E C TYR 184 E TYR 892 1_555 E N TPO 185 E TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? 
covale ? covale4 E C TPO 185 E TPO 893 1_555 E N ASN 186 E ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? 
covale ? covale5 H C TYR 184 H TYR 892 1_555 H N TPO 185 H TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? 
covale ? covale6 H C TPO 185 H TPO 893 1_555 H N ASN 186 H ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
#
_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 275 n n 
N3 C2 RC8 doub 276 n y 
C2 N1 RC8 sing 277 n y 
N3 C4 RC8 sing 278 n y 
N9 C4 RC8 sing 279 n y 
C4 C5 RC8 doub 280 n y 
C5 C6 RC8 sing 281 n y 
C5 N7 RC8 sing 282 n y 
N1 C6 RC8 doub 283 n y 
C6 N6 RC8 sing 284 n n 
N9 C8 RC8 sing 285 n y 
C8 N7 RC8 doub 286 n y 
C8 H8 RC8 sing 287 n n 
C10 C9 RC8 sing 288 n n 
C9 N9 RC8 sing 289 n n 
C9 C11 RC8 sing 290 n n 
C9 H9 RC8 sing 291 n n 
C10 H10 RC8 sing 292 n n 
C10 H10A RC8 sing 293 n n 
C10 H10B RC8 sing 294 n n 
C13 C12 RC8 sing 295 n n 
C12 C15 RC8 sing 296 n n 
C12 N2 RC8 sing 297 n n 
C12 H12 RC8 sing 298 n n 
C14 C13 RC8 sing 299 n n 
C14 H14 RC8 sing 300 n n 
C14 H14A RC8 sing 301 n n 
C14 H14B RC8 sing 302 n n 
C15 O1 RC8 sing 303 n n 
O1 HO1 RC8 sing 304 n n 
C15 H15 RC8 sing 305 n n 
C15 H15A RC8 sing 306 n n 
C13 H13 RC8 sing 307 n n 
C13 H13A RC8 sing 308 n n 
N2 HN2 RC8 sing 309 n n 
C11 H11 RC8 sing 310 n n 
C11 H11A RC8 sing 311 n n 
C11 H11B RC8 sing 312 n n 
CA' N6 RC8 sing 313 n n 
N6 HN6 RC8 sing 314 n n 
CA' C1' RC8 sing 315 n n 
CA' HA' RC8 sing 316 n n 
CA' "HA'A" RC8 sing 317 n n 
C6' C1' RC8 doub 318 n y 
C1' C2' RC8 sing 319 n y 
C6' C5' RC8 sing 320 n y 
C6' H6' RC8 sing 321 n n 
C5' C4' RC8 doub 322 n y 
C5' H5' RC8 sing 323 n n 
C4' C3' RC8 sing 324 n y 
C4' C1B RC8 sing 325 n y 
C2' C3' RC8 doub 326 n y 
C3' H3' RC8 sing 327 n n 
C2' H2' RC8 sing 328 n n 
C2B C1B RC8 doub 329 n y 
C1B N1B RC8 sing 330 n y 
N1B C5B RC8 doub 331 n y 
C4B C5B RC8 sing 332 n y 
C5B H5B RC8 sing 333 n n 
C3B C4B RC8 doub 334 n y 
C4B H4B RC8 sing 335 n n 
C2B C3B RC8 sing 336 n y 
C3B H3B RC8 sing 337 n n 
C2B H2B RC8 sing 338 n n 
#
_atom_sites.entry_id                     6TD3 
_atom_sites.fract_transf_matrix[1][1]    0.003988 
_atom_sites.fract_transf_matrix[1][2]    0.002303 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004605 
_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]    0.004589 
_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
J 4 RC8 B 1 1101 1101 RC8 RC8 . 
K 4 RC8 E 1 1101 1101 RC8 RC8 . 
L 4 RC8 H 1 1101 1101 RC8 RC8 . 
#
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 . . . K 4 -114.851 56.482 -48.492 1 31.34 ? C2 RC8 1101 E 1 
HETATM 2 C C4 RC8 . . . K 4 -115.686 54.616 -47.284 1 27.68 ? C4 RC8 1101 E 1 
HETATM 3 C C5 RC8 . . . K 4 -114.448 54.38 -46.817 1 27.66 ? C5 RC8 1101 E 1 
HETATM 4 C C6 RC8 . . . K 4 -113.419 55.24 -47.208 1 29.89 ? C6 RC8 1101 E 1 
HETATM 5 C C8 RC8 . . . K 4 -115.8 52.879 -45.986 1 22.71 ? C8 RC8 1101 E 1 
HETATM 6 C C9 RC8 . . . K 4 -117.968 53.505 -47 1 21.87 ? C9 RC8 1101 E 1 
HETATM 7 C C10 RC8 . . . K 4 -118.441 54.108 -48.35 1 25.7 ? C10 RC8 1101 E 1 
HETATM 8 C C12 RC8 . . . K 4 -116.347 58.467 -48.905 1 34.33 ? C12 RC8 1101 E 1 
HETATM 9 C C14 RC8 . . . K 4 -118.27 57.594 -50.477 1 33.08 ? C14 RC8 1101 E 1 
HETATM 10 O O1 RC8 . . . K 4 -114.088 59.348 -49.234 1 36.01 ? O1 RC8 1101 E 1 
HETATM 11 C C15 RC8 . . . K 4 -115.467 59.602 -49.451 1 36.19 ? C15 RC8 1101 E 1 
HETATM 12 C C13 RC8 . . . K 4 -117.839 58.566 -49.332 1 34.24 ? C13 RC8 1101 E 1 
HETATM 13 N N2 RC8 . . . K 4 -115.798 57.201 -49.353 1 32.7 ? N2 RC8 1101 E 1 
HETATM 14 N N1 RC8 . . . K 4 -113.625 56.251 -48.017 1 31.34 ? N1 RC8 1101 E 1 
HETATM 15 N N9 RC8 . . . K 4 -116.517 53.675 -46.785 1 23.93 ? N9 RC8 1101 E 1 
HETATM 16 C C11 RC8 . . . K 4 -118.689 54.249 -45.864 1 22.66 ? C11 RC8 1101 E 1 
HETATM 17 N N7 RC8 . . . K 4 -114.523 53.297 -46.015 1 24.62 ? N7 RC8 1101 E 1 
HETATM 18 N N3 RC8 . . . K 4 -115.884 55.664 -48.127 1 29.84 ? N3 RC8 1101 E 1 
HETATM 19 N N6 RC8 . . . K 4 -112.187 54.747 -46.61 1 30 ? N6 RC8 1101 E 1 
HETATM 20 C CA' RC8 . . . K 4 -110.965 55.218 -47.281 1 31.57 ? CA' RC8 1101 E 1 
HETATM 21 C C1' RC8 . . . K 4 -110.492 56.457 -46.495 1 33.49 ? C1' RC8 1101 E 1 
HETATM 22 C C6' RC8 . . . K 4 -110.188 56.242 -45.162 1 33.6 ? C6' RC8 1101 E 1 
HETATM 23 C C5' RC8 . . . K 4 -109.79 57.29 -44.365 1 35.88 ? C5' RC8 1101 E 1 
HETATM 24 C C4' RC8 . . . K 4 -109.664 58.564 -44.908 1 37.87 ? C4' RC8 1101 E 1 
HETATM 25 C C3' RC8 . . . K 4 -110.034 58.788 -46.241 1 37.37 ? C3' RC8 1101 E 1 
HETATM 26 C C2' RC8 . . . K 4 -110.433 57.729 -47.048 1 35.27 ? C2' RC8 1101 E 1 
HETATM 27 C C1B RC8 . . . K 4 -109.244 59.622 -44.069 1 40.68 ? C1B RC8 1101 E 1 
HETATM 28 N N1B RC8 . . . K 4 -109.706 60.879 -44.301 1 42.69 ? N1B RC8 1101 E 1 
HETATM 29 C C5B RC8 . . . K 4 -109.341 61.898 -43.493 1 45.7 ? C5B RC8 1101 E 1 
HETATM 30 C C4B RC8 . . . K 4 -108.497 61.651 -42.417 1 46.93 ? C4B RC8 1101 E 1 
HETATM 31 C C3B RC8 . . . K 4 -108.022 60.398 -42.178 1 44.78 ? C3B RC8 1101 E 1 
HETATM 32 C C2B RC8 . . . K 4 -108.394 59.377 -42.982 1 41.58 ? C2B RC8 1101 E 1 
HETATM 33 H H8 RC8 . . . K 4 -116.122 52.145 -45.515 0 21.72 ? H8 RC8 1101 E 1 
HETATM 34 H H9 RC8 . . . K 4 -118.197 52.563 -46.972 0 20.92 ? H9 RC8 1101 E 1 
HETATM 35 H H10 RC8 . . . K 4 -119.378 53.902 -48.485 0 28.24 ? H10 RC8 1101 E 1 
HETATM 36 H H10A RC8 . . . K 4 -117.918 53.742 -49.077 0 28.68 ? H10A RC8 1101 E 1 
HETATM 37 H H10B RC8 . . . K 4 -118.333 55.072 -48.324 0 29.86 ? H10B RC8 1101 E 1 
HETATM 38 H H12 RC8 . . . K 4 -116.305 58.493 -47.936 0 45.51 ? H12 RC8 1101 E 1 
HETATM 39 H H14 RC8 . . . K 4 -119.17 57.822 -50.758 0 43.52 ? H14 RC8 1101 E 1 
HETATM 40 H H14A RC8 . . . K 4 -118.251 56.678 -50.161 0 41.61 ? H14A RC8 1101 E 1 
HETATM 41 H H14B RC8 . . . K 4 -117.662 57.695 -51.228 0 43.57 ? H14B RC8 1101 E 1 
HETATM 42 H HO1 RC8 . . . K 4 -113.624 59.982 -49.565 0 50.02 ? HO1 RC8 1101 E 1 
HETATM 43 H H15 RC8 . . . K 4 -115.704 60.427 -48.997 0 50.87 ? H15 RC8 1101 E 1 
HETATM 44 H H15A RC8 . . . K 4 -115.635 59.704 -50.4 0 49.82 ? H15A RC8 1101 E 1 
HETATM 45 H H13 RC8 . . . K 4 -118.022 59.478 -49.611 0 46.95 ? H13 RC8 1101 E 1 
HETATM 46 H H13A RC8 . . . K 4 -118.386 58.374 -48.554 0 44.73 ? H13A RC8 1101 E 1 
HETATM 47 H HN2 RC8 . . . K 4 -115.942 56.917 -50.153 0 41.71 ? HN2 RC8 1101 E 1 
HETATM 48 H H11 RC8 . . . K 4 -118.731 53.68 -45.083 0 22.05 ? H11 RC8 1101 E 1 
HETATM 49 H H11A RC8 . . . K 4 -119.591 54.475 -46.147 0 23.65 ? H11A RC8 1101 E 1 
HETATM 50 H H11B RC8 . . . K 4 -118.207 55.06 -45.648 0 24.9 ? H11B RC8 1101 E 1 
HETATM 51 H HN6 RC8 . . . K 4 -112.159 54.246 -45.914 0 35.17 ? HN6 RC8 1101 E 1 
HETATM 52 H HA' RC8 . . . K 4 -111.141 55.455 -48.205 0 39.76 ? HA' RC8 1101 E 1 
HETATM 53 H "HA'A" RC8 . . . K 4 -110.282 54.529 -47.243 0 39.18 ? "HA'A" RC8 1101 E 1 
HETATM 54 H H6' RC8 . . . K 4 -110.261 55.389 -44.803 0 42.75 ? H6' RC8 1101 E 1 
HETATM 55 H H5' RC8 . . . K 4 -109.579 57.122 -43.476 0 49.36 ? H5' RC8 1101 E 1 
HETATM 56 H H3' RC8 . . . K 4 -109.946 59.633 -46.617 0 53.37 ? H3' RC8 1101 E 1 
HETATM 57 H H2' RC8 . . . K 4 -110.639 57.865 -47.944 0 47.46 ? H2' RC8 1101 E 1 
HETATM 58 H H5B RC8 . . . K 4 -109.648 62.76 -43.656 0 71.95 ? H5B RC8 1101 E 1 
HETATM 59 H H4B RC8 . . . K 4 -108.237 62.356 -41.867 0 75.67 ? H4B RC8 1101 E 1 
HETATM 60 H H3B RC8 . . . K 4 -107.458 60.244 -41.456 0 69.53 ? H3B RC8 1101 E 1 
HETATM 61 H H2B RC8 . . . K 4 -108.075 58.521 -42.806 0 60.35 ? H2B RC8 1101 E 1 
#
_model_server_stats.io_time_ms              132 
_model_server_stats.parse_time_ms           48 
_model_server_stats.create_model_time_ms    456 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           61 
#