data_8BUM # _model_server_result.job_id hLQaGMw9b0oOOMtkJfpB-A _model_server_result.datetime_utc '2024-11-05 04:18:12' _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 8bum # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"SA","auth_seq_id":1101}' # _entry.id 8BUM # _exptl.entry_id 8BUM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 460.614 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-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 8BUM _cell.length_a 249.635 _cell.length_b 249.635 _cell.length_c 218.865 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BUM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _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 ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 ? trimeric 3 author_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,K,L,M,N,O,P,Q,R,S,T,U 1 1 D,E,F,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA 2 1 G,H,I,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA 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 ? 5 Q N N ? 5 DA N N ? 5 SA 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 disulf ? disulf1 A SG CYS 22 A CYS 18 1_555 A SG CYS 317 A CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 B C TYR 184 B TYR 892 1_555 B N TPO 185 B TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale2 B C TPO 185 B TPO 893 1_555 B N ASN 186 B ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 E C TYR 184 E TYR 892 1_555 E N TPO 185 E TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 E C TPO 185 E TPO 893 1_555 E N ASN 186 E ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 H C TYR 184 H TYR 892 1_555 H N TPO 185 H TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 H C TPO 185 H TPO 893 1_555 H N ASN 186 H ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C27 H36 N6 O' _chem_comp.formula_weight 460.614 _chem_comp.id T6X _chem_comp.mon_nstd_flag . _chem_comp.name (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-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 O1 C11 T6X sing 292 n n C11 C10 T6X sing 293 n n C12 C10 T6X sing 294 n n C12 C13 T6X sing 295 n n C10 N6 T6X sing 296 n n N6 C3 T6X sing 297 n n C8 C7 T6X sing 298 n n C1 N1 T6X sing 299 n n C1 C14 T6X sing 300 n n C3 N2 T6X sing 301 n y C3 N3 T6X doub 302 n y N2 C2 T6X doub 303 n y N3 C4 T6X sing 304 n y N1 C2 T6X sing 305 n n C2 C5 T6X sing 306 n y C4 C5 T6X doub 307 n y C4 N5 T6X sing 308 n y C5 N4 T6X sing 309 n y C14 C15 T6X sing 310 n n N5 C7 T6X sing 311 n n N5 C6 T6X sing 312 n y N4 C6 T6X doub 313 n y C7 C9 T6X sing 314 n n C26 C27 T6X doub 315 n y C26 C25 T6X sing 316 n y C15 C16 T6X sing 317 n n C27 C23 T6X sing 318 n y C25 C24 T6X doub 319 n y C17 C16 T6X sing 320 n n C17 C18 T6X sing 321 n n C23 C18 T6X sing 322 n y C23 C22 T6X doub 323 n y C18 C19 T6X doub 324 n y C24 C22 T6X sing 325 n y C22 C21 T6X sing 326 n y C19 C20 T6X sing 327 n y C21 C20 T6X doub 328 n y C1 H2 T6X sing 329 n n C1 H1 T6X sing 330 n n C10 H13 T6X sing 331 n n C11 H15 T6X sing 332 n n C11 H14 T6X sing 333 n n C12 H18 T6X sing 334 n n C12 H17 T6X sing 335 n n C13 H21 T6X sing 336 n n C13 H20 T6X sing 337 n n C13 H19 T6X sing 338 n n C14 H23 T6X sing 339 n n C14 H22 T6X sing 340 n n C15 H24 T6X sing 341 n n C15 H25 T6X sing 342 n n C16 H26 T6X sing 343 n n C16 H27 T6X sing 344 n n C17 H28 T6X sing 345 n n C17 H29 T6X sing 346 n n C19 H30 T6X sing 347 n n C20 H31 T6X sing 348 n n C21 H32 T6X sing 349 n n C24 H33 T6X sing 350 n n C25 H34 T6X sing 351 n n C26 H35 T6X sing 352 n n C27 H36 T6X sing 353 n n C6 H4 T6X sing 354 n n C7 H5 T6X sing 355 n n C8 H7 T6X sing 356 n n C8 H6 T6X sing 357 n n C8 H8 T6X sing 358 n n C9 H11 T6X sing 359 n n C9 H10 T6X sing 360 n n C9 H9 T6X sing 361 n n N1 H3 T6X sing 362 n n N6 H12 T6X sing 363 n n O1 H16 T6X sing 364 n n # _atom_sites.entry_id 8BUM _atom_sites.fract_transf_matrix[1][1] 0.004006 _atom_sites.fract_transf_matrix[1][2] 0.002313 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004626 _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] 0.004569 _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 SO4 A 1 1201 3 SO4 SO4 . K 4 SO4 A 1 1202 5 SO4 SO4 . L 4 SO4 A 1 1203 6 SO4 SO4 . M 4 SO4 A 1 1204 10 SO4 SO4 . N 4 SO4 A 1 1205 11 SO4 SO4 . O 4 SO4 A 1 1206 27 SO4 SO4 . P 4 SO4 A 1 1207 35 SO4 SO4 . Q 5 T6X B 1 1101 1101 T6X D15 . R 4 SO4 C 1 301 4 SO4 SO4 . S 4 SO4 C 1 302 16 SO4 SO4 . T 4 SO4 C 1 303 22 SO4 SO4 . U 4 SO4 C 1 304 30 SO4 SO4 . V 4 SO4 D 1 1201 2 SO4 SO4 . W 4 SO4 D 1 1202 7 SO4 SO4 . X 4 SO4 D 1 1203 9 SO4 SO4 . Y 4 SO4 D 1 1204 20 SO4 SO4 . Z 4 SO4 D 1 1205 25 SO4 SO4 . AA 4 SO4 D 1 1206 29 SO4 SO4 . BA 4 SO4 D 1 1207 34 SO4 SO4 . CA 4 SO4 D 1 1208 36 SO4 SO4 . DA 5 T6X E 1 1101 1101 T6X D15 . EA 4 SO4 E 1 1102 40 SO4 SO4 . FA 4 SO4 E 1 1103 41 SO4 SO4 . GA 4 SO4 F 1 301 17 SO4 SO4 . HA 4 SO4 F 1 302 21 SO4 SO4 . IA 4 SO4 F 1 303 26 SO4 SO4 . JA 4 SO4 F 1 304 31 SO4 SO4 . KA 4 SO4 F 1 305 37 SO4 SO4 . LA 4 SO4 G 1 1201 1 SO4 SO4 . MA 4 SO4 G 1 1202 8 SO4 SO4 . NA 4 SO4 G 1 1203 13 SO4 SO4 . OA 4 SO4 G 1 1204 14 SO4 SO4 . PA 4 SO4 G 1 1205 15 SO4 SO4 . QA 4 SO4 G 1 1206 19 SO4 SO4 . RA 4 SO4 G 1 1207 28 SO4 SO4 . SA 5 T6X H 1 1101 1101 T6X D15 . TA 4 SO4 H 1 1102 33 SO4 SO4 . UA 4 SO4 H 1 1103 38 SO4 SO4 . VA 4 SO4 H 1 1104 39 SO4 SO4 . WA 4 SO4 I 1 301 12 SO4 SO4 . XA 4 SO4 I 1 302 18 SO4 SO4 . YA 4 SO4 I 1 303 32 SO4 SO4 . # 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 C1 T6X . . . SA 5 -133.102 13.289 8.486 1 122.04 ? C1 T6X 1101 H 1 HETATM 2 C C10 T6X . . . SA 5 -133.619 9.982 13.428 1 124.36 ? C10 T6X 1101 H 1 HETATM 3 C C11 T6X . . . SA 5 -133.018 8.574 13.392 1 127.73 ? C11 T6X 1101 H 1 HETATM 4 C C12 T6X . . . SA 5 -134.022 10.39 14.844 1 120.34 ? C12 T6X 1101 H 1 HETATM 5 C C13 T6X . . . SA 5 -134.564 11.801 15.067 1 113.63 ? C13 T6X 1101 H 1 HETATM 6 C C14 T6X . . . SA 5 -133.145 14.083 7.191 1 128.99 ? C14 T6X 1101 H 1 HETATM 7 C C15 T6X . . . SA 5 -134.202 15.169 7.172 1 130.73 ? C15 T6X 1101 H 1 HETATM 8 C C16 T6X . . . SA 5 -133.754 16.623 7.122 1 125.29 ? C16 T6X 1101 H 1 HETATM 9 C C17 T6X . . . SA 5 -132.906 17.017 8.327 1 124.51 ? C17 T6X 1101 H 1 HETATM 10 C C18 T6X . . . SA 5 -133.333 18.244 9.098 1 127.38 ? C18 T6X 1101 H 1 HETATM 11 C C19 T6X . . . SA 5 -132.8 19.471 8.841 1 121.9 ? C19 T6X 1101 H 1 HETATM 12 C C2 T6X . . . SA 5 -131.792 11.456 9.477 1 111.75 ? C2 T6X 1101 H 1 HETATM 13 C C20 T6X . . . SA 5 -133.185 20.618 9.564 1 115.67 ? C20 T6X 1101 H 1 HETATM 14 C C21 T6X . . . SA 5 -134.113 20.522 10.548 1 113.16 ? C21 T6X 1101 H 1 HETATM 15 C C22 T6X . . . SA 5 -134.706 19.279 10.862 1 114.94 ? C22 T6X 1101 H 1 HETATM 16 C C23 T6X . . . SA 5 -134.315 18.124 10.132 1 124.84 ? C23 T6X 1101 H 1 HETATM 17 C C24 T6X . . . SA 5 -135.679 19.156 11.883 1 127.86 ? C24 T6X 1101 H 1 HETATM 18 C C25 T6X . . . SA 5 -136.244 17.957 12.173 1 130.92 ? C25 T6X 1101 H 1 HETATM 19 C C26 T6X . . . SA 5 -135.869 16.815 11.464 1 132.67 ? C26 T6X 1101 H 1 HETATM 20 C C27 T6X . . . SA 5 -134.935 16.896 10.476 1 135.99 ? C27 T6X 1101 H 1 HETATM 21 C C3 T6X . . . SA 5 -132.019 10.833 11.713 1 122.94 ? C3 T6X 1101 H 1 HETATM 22 C C4 T6X . . . SA 5 -130.249 10.05 10.606 1 118.25 ? C4 T6X 1101 H 1 HETATM 23 C C5 T6X . . . SA 5 -130.602 10.701 9.442 1 109 ? C5 T6X 1101 H 1 HETATM 24 C C6 T6X . . . SA 5 -128.796 9.658 9.031 1 107.68 ? C6 T6X 1101 H 1 HETATM 25 C C7 T6X . . . SA 5 -128.271 8.51 11.219 1 115.92 ? C7 T6X 1101 H 1 HETATM 26 C C8 T6X . . . SA 5 -128.97 7.199 11.535 1 129.64 ? C8 T6X 1101 H 1 HETATM 27 C C9 T6X . . . SA 5 -127.798 9.28 12.437 1 123.59 ? C9 T6X 1101 H 1 HETATM 28 N N1 T6X . . . SA 5 -132.176 12.174 8.407 1 117.38 ? N1 T6X 1101 H 1 HETATM 29 N N2 T6X . . . SA 5 -132.473 11.541 10.643 1 115.33 ? N2 T6X 1101 H 1 HETATM 30 N N3 T6X . . . SA 5 -130.905 10.091 11.763 1 126.22 ? N3 T6X 1101 H 1 HETATM 31 N N4 T6X . . . SA 5 -129.671 10.449 8.446 1 105.46 ? N4 T6X 1101 H 1 HETATM 32 N N5 T6X . . . SA 5 -129.076 9.366 10.338 1 109.21 ? N5 T6X 1101 H 1 HETATM 33 N N6 T6X . . . SA 5 -132.662 10.939 12.881 1 123.71 ? N6 T6X 1101 H 1 HETATM 34 O O1 T6X . . . SA 5 -132.917 8.093 12.082 1 114.96 ? O1 T6X 1101 H 1 HETATM 35 H H2 T6X . . . SA 5 -133.997 12.947 8.689 0 146.61 ? H2 T6X 1101 H 1 HETATM 36 H H1 T6X . . . SA 5 -132.831 13.877 9.221 0 146.61 ? H1 T6X 1101 H 1 HETATM 37 H H13 T6X . . . SA 5 -134.433 10.003 12.846 0 149.4 ? H13 T6X 1101 H 1 HETATM 38 H H15 T6X . . . SA 5 -132.127 8.595 13.803 0 153.44 ? H15 T6X 1101 H 1 HETATM 39 H H14 T6X . . . SA 5 -133.582 7.971 13.92 0 153.44 ? H14 T6X 1101 H 1 HETATM 40 H H18 T6X . . . SA 5 -133.234 10.28 15.418 0 144.58 ? H18 T6X 1101 H 1 HETATM 41 H H17 T6X . . . SA 5 -134.706 9.757 15.15 0 144.58 ? H17 T6X 1101 H 1 HETATM 42 H H21 T6X . . . SA 5 -133.903 12.453 14.776 0 136.52 ? H21 T6X 1101 H 1 HETATM 43 H H20 T6X . . . SA 5 -135.383 11.919 14.554 0 136.52 ? H20 T6X 1101 H 1 HETATM 44 H H19 T6X . . . SA 5 -134.753 11.931 16.012 0 136.52 ? H19 T6X 1101 H 1 HETATM 45 H H23 T6X . . . SA 5 -132.265 14.494 7.048 0 154.96 ? H23 T6X 1101 H 1 HETATM 46 H H22 T6X . . . SA 5 -133.313 13.463 6.45 0 154.96 ? H22 T6X 1101 H 1 HETATM 47 H H24 T6X . . . SA 5 -134.755 15.06 7.974 0 157.04 ? H24 T6X 1101 H 1 HETATM 48 H H25 T6X . . . SA 5 -134.775 15.012 6.391 0 157.04 ? H25 T6X 1101 H 1 HETATM 49 H H26 T6X . . . SA 5 -134.545 17.2 7.083 0 150.51 ? H26 T6X 1101 H 1 HETATM 50 H H27 T6X . . . SA 5 -133.237 16.77 6.303 0 150.51 ? H27 T6X 1101 H 1 HETATM 51 H H28 T6X . . . SA 5 -131.978 17.164 8.015 0 149.58 ? H28 T6X 1101 H 1 HETATM 52 H H29 T6X . . . SA 5 -132.893 16.253 8.957 0 149.58 ? H29 T6X 1101 H 1 HETATM 53 H H30 T6X . . . SA 5 -132.154 19.554 8.158 0 146.45 ? H30 T6X 1101 H 1 HETATM 54 H H31 T6X . . . SA 5 -132.794 21.458 9.363 0 138.98 ? H31 T6X 1101 H 1 HETATM 55 H H32 T6X . . . SA 5 -134.367 21.293 11.029 0 135.96 ? H32 T6X 1101 H 1 HETATM 56 H H33 T6X . . . SA 5 -135.938 19.922 12.369 0 153.6 ? H33 T6X 1101 H 1 HETATM 57 H H34 T6X . . . SA 5 -136.892 17.895 12.856 0 157.28 ? H34 T6X 1101 H 1 HETATM 58 H H35 T6X . . . SA 5 -136.264 15.983 11.67 0 159.37 ? H35 T6X 1101 H 1 HETATM 59 H H36 T6X . . . SA 5 -134.693 16.115 10.006 0 163.35 ? H36 T6X 1101 H 1 HETATM 60 H H4 T6X . . . SA 5 -128.031 9.315 8.589 0 129.38 ? H4 T6X 1101 H 1 HETATM 61 H H5 T6X . . . SA 5 -127.445 8.237 10.738 0 139.27 ? H5 T6X 1101 H 1 HETATM 62 H H7 T6X . . . SA 5 -129.26 6.778 10.707 0 155.74 ? H7 T6X 1101 H 1 HETATM 63 H H6 T6X . . . SA 5 -129.744 7.371 12.099 0 155.74 ? H6 T6X 1101 H 1 HETATM 64 H H8 T6X . . . SA 5 -128.354 6.607 12.001 0 155.74 ? H8 T6X 1101 H 1 HETATM 65 H H11 T6X . . . SA 5 -127.328 8.677 13.039 0 148.48 ? H11 T6X 1101 H 1 HETATM 66 H H10 T6X . . . SA 5 -127.197 9.992 12.156 0 148.48 ? H10 T6X 1101 H 1 HETATM 67 H H9 T6X . . . SA 5 -128.564 9.665 12.896 0 148.48 ? H9 T6X 1101 H 1 HETATM 68 H H3 T6X . . . SA 5 -131.852 11.96 7.617 0 141.02 ? H3 T6X 1101 H 1 HETATM 69 H H12 T6X . . . SA 5 -132.494 11.653 13.368 0 148.62 ? H12 T6X 1101 H 1 HETATM 70 H H16 T6X . . . SA 5 -133.69 8.084 11.739 0 138.12 ? H16 T6X 1101 H 1 # _model_server_stats.io_time_ms 126 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 77 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 70 #