data_6TD3
#
_model_server_result.job_id            E-CS0xjEPcIF6FzO2YTB1Q 
_model_server_result.datetime_utc      '2024-11-05 04:06:37' 
_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":"J","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 . . . J 4 -61.079 23.515 -5.651 1 43.08 ? C2 RC8 1101 B 1 
HETATM 2 C C4 RC8 . . . J 4 -62.406 23.898 -7.597 1 39.13 ? C4 RC8 1101 B 1 
HETATM 3 C C5 RC8 . . . J 4 -63.489 23.471 -6.922 1 38.86 ? C5 RC8 1101 B 1 
HETATM 4 C C6 RC8 . . . J 4 -63.321 23.079 -5.585 1 41.05 ? C6 RC8 1101 B 1 
HETATM 5 C C8 RC8 . . . J 4 -64.104 24.02 -8.949 1 36.09 ? C8 RC8 1101 B 1 
HETATM 6 C C9 RC8 . . . J 4 -61.965 24.735 -9.968 1 37.56 ? C9 RC8 1101 B 1 
HETATM 7 C C10 RC8 . . . J 4 -60.478 24.319 -9.842 1 40.02 ? C10 RC8 1101 B 1 
HETATM 8 C C12 RC8 . . . J 4 -59.064 24.954 -5.221 1 47.88 ? C12 RC8 1101 B 1 
HETATM 9 C C14 RC8 . . . J 4 -57.378 24.412 -7.166 1 47.45 ? C14 RC8 1101 B 1 
HETATM 10 O O1 RC8 . . . J 4 -59.552 23.966 -3.03 1 50.2 ? O1 RC8 1101 B 1 
HETATM 11 C C15 RC8 . . . J 4 -58.583 24.667 -3.788 1 50.72 ? C15 RC8 1101 B 1 
HETATM 12 C C13 RC8 . . . J 4 -57.944 25.471 -6.167 1 48.5 ? C13 RC8 1101 B 1 
HETATM 13 N N2 RC8 . . . J 4 -59.637 23.742 -5.771 1 45.13 ? N2 RC8 1101 B 1 
HETATM 14 N N1 RC8 . . . J 4 -62.155 23.103 -4.982 1 42.89 ? N1 RC8 1101 B 1 
HETATM 15 N N9 RC8 . . . J 4 -62.784 24.219 -8.857 1 37.3 ? N9 RC8 1101 B 1 
HETATM 16 C C11 RC8 . . . J 4 -62.036 26.266 -9.917 1 38.56 ? C11 RC8 1101 B 1 
HETATM 17 N N7 RC8 . . . J 4 -64.54 23.546 -7.77 1 36.99 ? N7 RC8 1101 B 1 
HETATM 18 N N3 RC8 . . . J 4 -61.201 23.916 -6.957 1 41.41 ? N3 RC8 1101 B 1 
HETATM 19 N N6 RC8 . . . J 4 -64.614 22.625 -5.104 1 41.45 ? N6 RC8 1101 B 1 
HETATM 20 C CA' RC8 . . . J 4 -64.533 21.747 -3.925 1 43.5 ? CA' RC8 1101 B 1 
HETATM 21 C C1' RC8 . . . J 4 -64.737 22.658 -2.702 1 47.02 ? C1' RC8 1101 B 1 
HETATM 22 C C6' RC8 . . . J 4 -65.939 23.341 -2.656 1 48.06 ? C6' RC8 1101 B 1 
HETATM 23 C C5' RC8 . . . J 4 -66.201 24.216 -1.629 1 51.94 ? C5' RC8 1101 B 1 
HETATM 24 C C4' RC8 . . . J 4 -65.266 24.388 -0.617 1 54.57 ? C4' RC8 1101 B 1 
HETATM 25 C C3' RC8 . . . J 4 -64.034 23.729 -0.693 1 53.24 ? C3' RC8 1101 B 1 
HETATM 26 C C2' RC8 . . . J 4 -63.766 22.852 -1.735 1 49.57 ? C2' RC8 1101 B 1 
HETATM 27 C C1B RC8 . . . J 4 -65.564 25.279 0.435 1 59.22 ? C1B RC8 1101 B 1 
HETATM 28 N N1B RC8 . . . J 4 -64.555 25.953 1.048 1 61.84 ? N1B RC8 1101 B 1 
HETATM 29 C C5B RC8 . . . J 4 -64.835 26.819 2.05 1 66.6 ? C5B RC8 1101 B 1 
HETATM 30 C C4B RC8 . . . J 4 -66.155 27.03 2.441 1 69.23 ? C4B RC8 1101 B 1 
HETATM 31 C C3B RC8 . . . J 4 -67.17 26.36 1.838 1 66.7 ? C3B RC8 1101 B 1 
HETATM 32 C C2B RC8 . . . J 4 -66.891 25.499 0.835 1 61.53 ? C2B RC8 1101 B 1 
HETATM 33 H H8 RC8 . . . J 4 -64.625 24.163 -9.704 0 47.78 ? H8 RC8 1101 B 1 
HETATM 34 H H9 RC8 . . . J 4 -62.323 24.413 -10.811 0 51.07 ? H9 RC8 1101 B 1 
HETATM 35 H H10 RC8 . . . J 4 -59.998 24.6 -10.636 0 58.51 ? H10 RC8 1101 B 1 
HETATM 36 H H10A RC8 . . . J 4 -60.408 23.357 -9.753 0 57.59 ? H10A RC8 1101 B 1 
HETATM 37 H H10B RC8 . . . J 4 -60.087 24.744 -9.062 0 59.72 ? H10B RC8 1101 B 1 
HETATM 38 H H12 RC8 . . . J 4 -59.761 25.629 -5.175 0 75.17 ? H12 RC8 1101 B 1 
HETATM 39 H H14 RC8 . . . J 4 -56.604 24.78 -7.617 0 76.41 ? H14 RC8 1101 B 1 
HETATM 40 H H14A RC8 . . . J 4 -58.052 24.183 -7.825 0 72.54 ? H14A RC8 1101 B 1 
HETATM 41 H H14B RC8 . . . J 4 -57.11 23.615 -6.679 0 75.38 ? H14B RC8 1101 B 1 
HETATM 42 H HO1 RC8 . . . J 4 -59.255 23.819 -2.249 0 81.63 ? HO1 RC8 1101 B 1 
HETATM 43 H H15 RC8 . . . J 4 -58.39 25.507 -3.348 0 83.33 ? H15 RC8 1101 B 1 
HETATM 44 H H15A RC8 . . . J 4 -57.771 24.135 -3.828 0 82.22 ? H15A RC8 1101 B 1 
HETATM 45 H H13 RC8 . . . J 4 -57.216 25.807 -5.621 0 79.44 ? H13 RC8 1101 B 1 
HETATM 46 H H13A RC8 . . . J 4 -58.308 26.207 -6.683 0 76.1 ? H13A RC8 1101 B 1 
HETATM 47 H HN2 RC8 . . . J 4 -59.134 23.116 -6.078 0 69.04 ? HN2 RC8 1101 B 1 
HETATM 48 H H11 RC8 . . . J 4 -62.845 26.562 -10.364 0 53.65 ? H11 RC8 1101 B 1 
HETATM 49 H H11A RC8 . . . J 4 -61.265 26.64 -10.368 0 56.07 ? H11A RC8 1101 B 1 
HETATM 50 H H11B RC8 . . . J 4 -62.052 26.563 -8.993 0 56.57 ? H11B RC8 1101 B 1 
HETATM 51 H HN6 RC8 . . . J 4 -65.362 22.855 -5.458 0 60.35 ? HN6 RC8 1101 B 1 
HETATM 52 H HA' RC8 . . . J 4 -63.675 21.296 -3.877 0 65.5 ? HA' RC8 1101 B 1 
HETATM 53 H "HA'A" RC8 . . . J 4 -65.244 21.088 -3.963 0 65.37 ? "HA'A" RC8 1101 B 1 
HETATM 54 H H6' RC8 . . . J 4 -66.571 23.221 -3.329 0 74.24 ? H6' RC8 1101 B 1 
HETATM 55 H H5' RC8 . . . J 4 -67.021 24.656 -1.61 0 85.37 ? H5' RC8 1101 B 1 
HETATM 56 H H3' RC8 . . . J 4 -63.407 23.827 -0.012 0 88.71 ? H3' RC8 1101 B 1 
HETATM 57 H H2' RC8 . . . J 4 -62.961 22.386 -1.768 0 78.38 ? H2' RC8 1101 B 1 
HETATM 58 H H5B RC8 . . . J 4 -64.148 27.279 2.474 0 117.84 ? H5B RC8 1101 B 1 
HETATM 59 H H4B RC8 . . . J 4 -66.344 27.624 3.131 0 125.73 ? H4B RC8 1101 B 1 
HETATM 60 H H3B RC8 . . . J 4 -68.049 26.507 2.099 0 119 ? H3B RC8 1101 B 1 
HETATM 61 H H2B RC8 . . . J 4 -67.594 25.047 0.431 0 104.18 ? H2B RC8 1101 B 1 
#
_model_server_stats.io_time_ms              135 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    98 
_model_server_stats.query_time_ms           341 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           61 
#