data_2GBI # _model_server_result.job_id M9X8POQxhtB6JcfsZ8Vcvw _model_server_result.datetime_utc '2025-01-10 20:18:07' _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 2gbi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":901}' # _entry.id 2GBI # _exptl.entry_id 2GBI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 393.442 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]-1,3-DIMETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-7H-PURIN-7-YL}METHYL)BENZONITRILE _entity.pdbx_number_of_molecules 1 _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 2GBI _cell.length_a 208.547 _cell.length_b 208.547 _cell.length_c 208.547 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GBI _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # 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 hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1 A,B,C 2 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_454 -z-1/2,-x,y-1/2 0 0 -1 -1 0 0 0 1 0 -104.2735 0 -104.2735 3 'crystal symmetry operation' 10_554 -y,z+1/2,-x-1/2 0 -1 0 0 0 1 -1 0 0 0 104.2735 -104.2735 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 289 A CYS 326 1_555 A SG CYS 300 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 346 A CYS 383 1_555 A SG CYS 358 A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 408 A CYS 445 1_555 A SG CYS 411 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf4 A SG CYS 418 A CYS 455 1_555 A SG CYS 436 A CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 A SG CYS 613 A CYS 650 1_555 A SG CYS 726 A CYS 763 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 B SG CYS 289 B CYS 326 1_555 B SG CYS 300 B CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 346 B CYS 383 1_555 B SG CYS 358 B CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 B SG CYS 408 B CYS 445 1_555 B SG CYS 411 B CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 B SG CYS 418 B CYS 455 1_555 B SG CYS 436 B CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf10 B SG CYS 613 B CYS 650 1_555 B SG CYS 726 B CYS 763 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _chem_comp.formula 'C20 H23 N7 O2' _chem_comp.formula_weight 393.442 _chem_comp.id XIH _chem_comp.mon_nstd_flag . _chem_comp.name 2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]-1,3-DIMETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-7H-PURIN-7-YL}METHYL)BENZONITRILE _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 C5 C6 XIH doub 374 n y C5 C3 XIH sing 375 n y C5 N16 XIH sing 376 n y C6 N7 XIH sing 377 n y C6 N26 XIH sing 378 n y C8 N7 XIH doub 379 n y C8 N9 XIH sing 380 n n C8 N16 XIH sing 381 n y C10 N9 XIH sing 382 n n C10 C11 XIH sing 383 n n C10 H101 XIH sing 384 n n C10 H102 XIH sing 385 n n C13 C15 XIH sing 386 n n C13 C12 XIH sing 387 n n C13 N14 XIH sing 388 n n C13 H13 XIH sing 389 n n C15 N9 XIH sing 390 n n C15 H151 XIH sing 391 n n C15 H152 XIH sing 392 n n C17 N16 XIH sing 393 n n C17 C18 XIH sing 394 n n C17 H171 XIH sing 395 n n C17 H172 XIH sing 396 n n C20 C21 XIH doub 397 n y C20 C19 XIH sing 398 n y C20 H20 XIH sing 399 n n C21 C22 XIH sing 400 n y C21 H21 XIH sing 401 n n C22 C23 XIH doub 402 n y C22 H22 XIH sing 403 n n C24 C23 XIH sing 404 n n C24 N25 XIH trip 405 n n C28 N XIH sing 406 n y C28 N26 XIH sing 407 n y C28 O29 XIH doub 408 n n C N XIH sing 409 n n C H1 XIH sing 410 n n C H2 XIH sing 411 n n C H3 XIH sing 412 n n N C3 XIH sing 413 n y C3 O XIH doub 414 n n C11 C12 XIH sing 415 n n C11 H111 XIH sing 416 n n C11 H112 XIH sing 417 n n C12 H121 XIH sing 418 n n C12 H122 XIH sing 419 n n N14 H141 XIH sing 420 n n N14 H142 XIH sing 421 n n C18 C19 XIH doub 422 n y C18 C23 XIH sing 423 n y C19 H19 XIH sing 424 n n N26 C27 XIH sing 425 n n C27 H271 XIH sing 426 n n C27 H272 XIH sing 427 n n C27 H273 XIH sing 428 n n # _atom_sites.entry_id 2GBI _atom_sites.fract_transf_matrix[1][1] 0.004795 _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] 0.004795 _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] 0.004795 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id XIH _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 901 _pdbx_nonpoly_scheme.auth_seq_num 901 _pdbx_nonpoly_scheme.pdb_mon_id XIH _pdbx_nonpoly_scheme.auth_mon_id XIH _pdbx_nonpoly_scheme.pdb_ins_code . # 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 C5 XIH . . . C 2 17.13 40.577 -80.062 1 48.57 ? C5 XIH 901 A 1 HETATM 2 C C6 XIH . . . C 2 17.211 40.161 -78.782 1 48.57 ? C6 XIH 901 A 1 HETATM 3 C C8 XIH . . . C 2 15.177 39.509 -79.495 1 48.57 ? C8 XIH 901 A 1 HETATM 4 C C10 XIH . . . C 2 12.968 38.927 -78.302 1 48.57 ? C10 XIH 901 A 1 HETATM 5 C C13 XIH . . . C 2 12.919 36.866 -80.465 1 48.57 ? C13 XIH 901 A 1 HETATM 6 C C15 XIH . . . C 2 13.273 38.312 -80.708 1 48.57 ? C15 XIH 901 A 1 HETATM 7 C C17 XIH . . . C 2 15.359 40.448 -81.909 1 48.57 ? C17 XIH 901 A 1 HETATM 8 C C20 XIH . . . C 2 15.701 39.237 -85.479 1 48.57 ? C20 XIH 901 A 1 HETATM 9 C C21 XIH . . . C 2 16.187 37.929 -85.366 1 48.57 ? C21 XIH 901 A 1 HETATM 10 C C22 XIH . . . C 2 16.434 37.342 -84.107 1 48.57 ? C22 XIH 901 A 1 HETATM 11 C C24 XIH . . . C 2 16.482 37.337 -81.74 1 48.57 ? C24 XIH 901 A 1 HETATM 12 C C28 XIH . . . C 2 19.539 41.127 -78.557 1 48.57 ? C28 XIH 901 A 1 HETATM 13 C C XIH . . . C 2 20.548 42.276 -80.528 1 48.57 ? C XIH 901 A 1 HETATM 14 N N XIH . . . C 2 19.408 41.538 -79.882 1 48.57 ? N XIH 901 A 1 HETATM 15 C C3 XIH . . . C 2 18.296 41.318 -80.664 1 48.57 ? C3 XIH 901 A 1 HETATM 16 O O XIH . . . C 2 18.206 41.698 -81.864 1 48.57 ? O XIH 901 A 1 HETATM 17 N N7 XIH . . . C 2 15.968 39.468 -78.416 1 48.57 ? N7 XIH 901 A 1 HETATM 18 N N9 XIH . . . C 2 13.826 38.948 -79.521 1 48.57 ? N9 XIH 901 A 1 HETATM 19 C C11 XIH . . . C 2 12.451 37.481 -78.021 1 48.57 ? C11 XIH 901 A 1 HETATM 20 C C12 XIH . . . C 2 11.897 36.799 -79.295 1 48.57 ? C12 XIH 901 A 1 HETATM 21 N N14 XIH . . . C 2 12.435 36.235 -81.705 1 48.57 ? N14 XIH 901 A 1 HETATM 22 N N16 XIH . . . C 2 15.797 40.157 -80.553 1 48.57 ? N16 XIH 901 A 1 HETATM 23 C C18 XIH . . . C 2 15.696 39.435 -83.006 1 48.57 ? C18 XIH 901 A 1 HETATM 24 C C19 XIH . . . C 2 15.465 39.97 -84.308 1 48.57 ? C19 XIH 901 A 1 HETATM 25 C C23 XIH . . . C 2 16.195 38.069 -82.935 1 48.57 ? C23 XIH 901 A 1 HETATM 26 N N25 XIH . . . C 2 16.616 36.742 -80.775 1 48.57 ? N25 XIH 901 A 1 HETATM 27 N N26 XIH . . . C 2 18.443 40.437 -78.003 1 48.57 ? N26 XIH 901 A 1 HETATM 28 C C27 XIH . . . C 2 18.494 39.964 -76.604 1 48.57 ? C27 XIH 901 A 1 HETATM 29 O O29 XIH . . . C 2 20.569 41.333 -77.868 1 48.57 ? O29 XIH 901 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 29 #