data_8BUM # _model_server_result.job_id Qfqi734zLdQrKQgl7ZOFHQ _model_server_result.datetime_utc '2024-11-29 23:55:46' _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 8bum # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","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 . . . DA 5 -111.277 55.563 -47.691 1 127.2 ? C1 T6X 1101 E 1 HETATM 2 C C10 T6X . . . DA 5 -115.425 58.534 -48.828 1 125.78 ? C10 T6X 1101 E 1 HETATM 3 C C11 T6X . . . DA 5 -116.334 57.915 -49.89 1 107.72 ? C11 T6X 1101 E 1 HETATM 4 C C12 T6X . . . DA 5 -115.692 60.023 -48.586 1 131.15 ? C12 T6X 1101 E 1 HETATM 5 C C13 T6X . . . DA 5 -117.097 60.323 -48.081 1 120.96 ? C13 T6X 1101 E 1 HETATM 6 C C14 T6X . . . DA 5 -110.086 55.681 -46.768 1 129.23 ? C14 T6X 1101 E 1 HETATM 7 C C15 T6X . . . DA 5 -110.473 56.256 -45.435 1 125.51 ? C15 T6X 1101 E 1 HETATM 8 C C16 T6X . . . DA 5 -109.481 56.011 -44.314 1 130.78 ? C16 T6X 1101 E 1 HETATM 9 C C17 T6X . . . DA 5 -108.237 56.888 -44.457 1 133.59 ? C17 T6X 1101 E 1 HETATM 10 C C18 T6X . . . DA 5 -108.066 58.004 -43.453 1 135.46 ? C18 T6X 1101 E 1 HETATM 11 C C19 T6X . . . DA 5 -107.449 57.779 -42.259 1 133.66 ? C19 T6X 1101 E 1 HETATM 12 C C2 T6X . . . DA 5 -113.571 54.926 -47.139 1 109.86 ? C2 T6X 1101 E 1 HETATM 13 C C20 T6X . . . DA 5 -107.282 58.792 -41.3 1 123.24 ? C20 T6X 1101 E 1 HETATM 14 C C21 T6X . . . DA 5 -107.739 60.041 -41.544 1 123.13 ? C21 T6X 1101 E 1 HETATM 15 C C22 T6X . . . DA 5 -108.39 60.346 -42.76 1 124.36 ? C22 T6X 1101 E 1 HETATM 16 C C23 T6X . . . DA 5 -108.56 59.322 -43.733 1 127.47 ? C23 T6X 1101 E 1 HETATM 17 C C24 T6X . . . DA 5 -108.884 61.646 -43.025 1 124.3 ? C24 T6X 1101 E 1 HETATM 18 C C25 T6X . . . DA 5 -109.505 61.935 -44.197 1 111.46 ? C25 T6X 1101 E 1 HETATM 19 C C26 T6X . . . DA 5 -109.676 60.939 -45.164 1 116.96 ? C26 T6X 1101 E 1 HETATM 20 C C27 T6X . . . DA 5 -109.221 59.673 -44.938 1 127.68 ? C27 T6X 1101 E 1 HETATM 21 C C3 T6X . . . DA 5 -115.265 56.529 -47.34 1 128.49 ? C3 T6X 1101 E 1 HETATM 22 C C4 T6X . . . DA 5 -115.863 54.432 -46.839 1 112.45 ? C4 T6X 1101 E 1 HETATM 23 C C5 T6X . . . DA 5 -114.561 53.971 -46.86 1 108.87 ? C5 T6X 1101 E 1 HETATM 24 C C6 T6X . . . DA 5 -115.769 52.295 -46.397 1 117.51 ? C6 T6X 1101 E 1 HETATM 25 C C7 T6X . . . DA 5 -118.094 53.226 -46.394 1 115.45 ? C7 T6X 1101 E 1 HETATM 26 C C8 T6X . . . DA 5 -118.82 53.277 -47.735 1 114.53 ? C8 T6X 1101 E 1 HETATM 27 C C9 T6X . . . DA 5 -118.637 54.242 -45.403 1 121.62 ? C9 T6X 1101 E 1 HETATM 28 N N1 T6X . . . DA 5 -112.265 54.606 -47.235 1 118.55 ? N1 T6X 1101 E 1 HETATM 29 N N2 T6X . . . DA 5 -113.958 56.189 -47.414 1 119.44 ? N2 T6X 1101 E 1 HETATM 30 N N3 T6X . . . DA 5 -116.276 55.686 -47.061 1 127.78 ? N3 T6X 1101 E 1 HETATM 31 N N4 T6X . . . DA 5 -114.507 52.615 -46.575 1 114.01 ? N4 T6X 1101 E 1 HETATM 32 N N5 T6X . . . DA 5 -116.641 53.34 -46.533 1 113.12 ? N5 T6X 1101 E 1 HETATM 33 N N6 T6X . . . DA 5 -115.591 57.812 -47.563 1 130.96 ? N6 T6X 1101 E 1 HETATM 34 O O1 T6X . . . DA 5 -116.034 58.487 -51.137 1 134.91 ? O1 T6X 1101 E 1 HETATM 35 H H2 T6X . . . DA 5 -111.705 56.44 -47.774 0 152.81 ? H2 T6X 1101 E 1 HETATM 36 H H1 T6X . . . DA 5 -110.967 55.294 -48.58 0 152.81 ? H1 T6X 1101 E 1 HETATM 37 H H13 T6X . . . DA 5 -114.482 58.432 -49.145 0 151.11 ? H13 T6X 1101 E 1 HETATM 38 H H15 T6X . . . DA 5 -116.195 56.945 -49.922 0 129.43 ? H15 T6X 1101 E 1 HETATM 39 H H14 T6X . . . DA 5 -117.273 58.081 -49.66 0 129.43 ? H14 T6X 1101 E 1 HETATM 40 H H18 T6X . . . DA 5 -115.546 60.509 -49.425 0 157.55 ? H18 T6X 1101 E 1 HETATM 41 H H17 T6X . . . DA 5 -115.042 60.357 -47.931 0 157.55 ? H17 T6X 1101 E 1 HETATM 42 H H21 T6X . . . DA 5 -117.747 60.059 -48.754 0 145.32 ? H21 T6X 1101 E 1 HETATM 43 H H20 T6X . . . DA 5 -117.182 61.276 -47.905 0 145.32 ? H20 T6X 1101 E 1 HETATM 44 H H19 T6X . . . DA 5 -117.26 59.826 -47.261 0 145.32 ? H19 T6X 1101 E 1 HETATM 45 H H23 T6X . . . DA 5 -109.41 56.255 -47.187 0 155.25 ? H23 T6X 1101 E 1 HETATM 46 H H22 T6X . . . DA 5 -109.69 54.793 -46.638 0 155.25 ? H22 T6X 1101 E 1 HETATM 47 H H24 T6X . . . DA 5 -111.338 55.877 -45.171 0 150.78 ? H24 T6X 1101 E 1 HETATM 48 H H25 T6X . . . DA 5 -110.591 57.225 -45.535 0 150.78 ? H25 T6X 1101 E 1 HETATM 49 H H26 T6X . . . DA 5 -109.216 55.067 -44.318 0 157.1 ? H26 T6X 1101 E 1 HETATM 50 H H27 T6X . . . DA 5 -109.913 56.196 -43.454 0 157.1 ? H27 T6X 1101 E 1 HETATM 51 H H28 T6X . . . DA 5 -108.248 57.292 -45.361 0 160.47 ? H28 T6X 1101 E 1 HETATM 52 H H29 T6X . . . DA 5 -107.44 56.303 -44.4 0 160.47 ? H29 T6X 1101 E 1 HETATM 53 H H30 T6X . . . DA 5 -107.123 56.913 -42.072 0 160.56 ? H30 T6X 1101 E 1 HETATM 54 H H31 T6X . . . DA 5 -106.847 58.6 -40.479 0 148.06 ? H31 T6X 1101 E 1 HETATM 55 H H32 T6X . . . DA 5 -107.622 60.718 -40.896 0 147.93 ? H32 T6X 1101 E 1 HETATM 56 H H33 T6X . . . DA 5 -108.778 62.322 -42.375 0 149.33 ? H33 T6X 1101 E 1 HETATM 57 H H34 T6X . . . DA 5 -109.823 62.808 -44.359 0 133.92 ? H34 T6X 1101 E 1 HETATM 58 H H35 T6X . . . DA 5 -110.108 61.144 -45.977 0 140.52 ? H35 T6X 1101 E 1 HETATM 59 H H36 T6X . . . DA 5 -109.348 59.013 -45.599 0 153.38 ? H36 T6X 1101 E 1 HETATM 60 H H4 T6X . . . DA 5 -116.059 51.416 -46.19 0 141.18 ? H4 T6X 1101 E 1 HETATM 61 H H5 T6X . . . DA 5 -118.285 52.324 -46.023 0 138.7 ? H5 T6X 1101 E 1 HETATM 62 H H7 T6X . . . DA 5 -119.767 53.096 -47.599 0 137.6 ? H7 T6X 1101 E 1 HETATM 63 H H6 T6X . . . DA 5 -118.445 52.608 -48.333 0 137.6 ? H6 T6X 1101 E 1 HETATM 64 H H8 T6X . . . DA 5 -118.713 54.161 -48.128 0 137.6 ? H8 T6X 1101 E 1 HETATM 65 H H11 T6X . . . DA 5 -119.591 54.098 -45.28 0 146.12 ? H11 T6X 1101 E 1 HETATM 66 H H10 T6X . . . DA 5 -118.486 55.141 -45.744 0 146.12 ? H10 T6X 1101 E 1 HETATM 67 H H9 T6X . . . DA 5 -118.181 54.138 -44.549 0 146.12 ? H9 T6X 1101 E 1 HETATM 68 H H3 T6X . . . DA 5 -112.001 53.796 -47.016 0 142.43 ? H3 T6X 1101 E 1 HETATM 69 H H12 T6X . . . DA 5 -115.937 58.263 -46.891 0 157.32 ? H12 T6X 1101 E 1 HETATM 70 H H16 T6X . . . DA 5 -116.474 58.077 -51.733 0 162.06 ? H16 T6X 1101 E 1 # _model_server_stats.io_time_ms 130 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 92 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 70 #