data_8DL9 # _model_server_result.job_id U1NuwZWTlbu8BmOCDai2GQ _model_server_result.datetime_utc '2024-10-19 12:23:54' _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 8dl9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8DL9 # _exptl.entry_id 8DL9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 268.354 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-{4-[(naphthalen-1-yl)methyl]piperazin-1-yl}ethan-1-one _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 101.18 _cell.angle_gamma 90 _cell.entry_id 8DL9 _cell.length_a 45.215 _cell.length_b 54.547 _cell.length_c 113.946 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DL9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 145 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 145 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C _struct_conn.ptnr2_label_comp_id T4V _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id T4V _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 1.824 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C17 H20 N2 O' _chem_comp.formula_weight 268.354 _chem_comp.id T4V _chem_comp.mon_nstd_flag . _chem_comp.name 1-{4-[(naphthalen-1-yl)methyl]piperazin-1-yl}ethan-1-one _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 C1 C T4V sing 290 n n O C1 T4V doub 291 n n C1 N T4V sing 292 n n N C2 T4V sing 293 n n C3 C2 T4V sing 294 n n N1 C3 T4V sing 295 n n N1 C4 T4V sing 296 n n C4 C5 T4V sing 297 n n C5 C6 T4V sing 298 n y C7 C6 T4V doub 299 n y C8 C7 T4V sing 300 n y C9 C8 T4V doub 301 n y C10 C9 T4V sing 302 n y C11 C10 T4V doub 303 n y C12 C11 T4V sing 304 n y C13 C12 T4V doub 305 n y C14 C13 T4V sing 306 n y C5 C14 T4V doub 307 n y C14 C9 T4V sing 308 n y C15 N1 T4V sing 309 n n C16 C15 T4V sing 310 n n N C16 T4V sing 311 n n C4 H6 T4V sing 312 n n C4 H7 T4V sing 313 n n C6 H8 T4V sing 314 n n C7 H9 T4V sing 315 n n C8 H10 T4V sing 316 n n C10 H11 T4V sing 317 n n C13 H14 T4V sing 318 n n C15 H16 T4V sing 319 n n C15 H15 T4V sing 320 n n C H T4V sing 321 n n C H20 T4V sing 322 n n C H1 T4V sing 323 n n C11 H12 T4V sing 324 n n C12 H13 T4V sing 325 n n C16 H18 T4V sing 326 n n C16 H17 T4V sing 327 n n C2 H3 T4V sing 328 n n C2 H2 T4V sing 329 n n C3 H5 T4V sing 330 n n C3 H4 T4V sing 331 n n # _atom_sites.entry_id 8DL9 _atom_sites.fract_transf_matrix[1][1] 0.022117 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00437 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018333 _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] 0.008946 _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 B 2 T4V A 1 401 401 T4V Z22 . C 3 HOH A 1 501 35 HOH HOH . C 3 HOH A 2 502 21 HOH HOH . C 3 HOH A 3 503 79 HOH HOH . C 3 HOH A 4 504 4 HOH HOH . C 3 HOH A 5 505 85 HOH HOH . C 3 HOH A 6 506 12 HOH HOH . C 3 HOH A 7 507 30 HOH HOH . C 3 HOH A 8 508 80 HOH HOH . C 3 HOH A 9 509 51 HOH HOH . C 3 HOH A 10 510 14 HOH HOH . C 3 HOH A 11 511 63 HOH HOH . C 3 HOH A 12 512 22 HOH HOH . C 3 HOH A 13 513 84 HOH HOH . C 3 HOH A 14 514 53 HOH HOH . C 3 HOH A 15 515 60 HOH HOH . C 3 HOH A 16 516 34 HOH HOH . C 3 HOH A 17 517 43 HOH HOH . C 3 HOH A 18 518 37 HOH HOH . C 3 HOH A 19 519 26 HOH HOH . C 3 HOH A 20 520 2 HOH HOH . C 3 HOH A 21 521 18 HOH HOH . C 3 HOH A 22 522 64 HOH HOH . C 3 HOH A 23 523 33 HOH HOH . C 3 HOH A 24 524 19 HOH HOH . C 3 HOH A 25 525 1 HOH HOH . C 3 HOH A 26 526 68 HOH HOH . C 3 HOH A 27 527 9 HOH HOH . C 3 HOH A 28 528 72 HOH HOH . C 3 HOH A 29 529 8 HOH HOH . C 3 HOH A 30 530 32 HOH HOH . C 3 HOH A 31 531 49 HOH HOH . C 3 HOH A 32 532 38 HOH HOH . C 3 HOH A 33 533 61 HOH HOH . C 3 HOH A 34 534 31 HOH HOH . C 3 HOH A 35 535 24 HOH HOH . C 3 HOH A 36 536 5 HOH HOH . C 3 HOH A 37 537 77 HOH HOH . C 3 HOH A 38 538 47 HOH HOH . C 3 HOH A 39 539 3 HOH HOH . C 3 HOH A 40 540 23 HOH HOH . C 3 HOH A 41 541 11 HOH HOH . C 3 HOH A 42 542 7 HOH HOH . C 3 HOH A 43 543 42 HOH HOH . C 3 HOH A 44 544 15 HOH HOH . C 3 HOH A 45 545 39 HOH HOH . C 3 HOH A 46 546 6 HOH HOH . C 3 HOH A 47 547 29 HOH HOH . C 3 HOH A 48 548 13 HOH HOH . C 3 HOH A 49 549 50 HOH HOH . C 3 HOH A 50 550 73 HOH HOH . C 3 HOH A 51 551 25 HOH HOH . C 3 HOH A 52 552 55 HOH HOH . C 3 HOH A 53 553 10 HOH HOH . C 3 HOH A 54 554 40 HOH HOH . C 3 HOH A 55 555 54 HOH HOH . C 3 HOH A 56 556 62 HOH HOH . C 3 HOH A 57 557 65 HOH HOH . C 3 HOH A 58 558 20 HOH HOH . C 3 HOH A 59 559 27 HOH HOH . C 3 HOH A 60 560 45 HOH HOH . C 3 HOH A 61 561 46 HOH HOH . C 3 HOH A 62 562 59 HOH HOH . C 3 HOH A 63 563 41 HOH HOH . C 3 HOH A 64 564 44 HOH HOH . C 3 HOH A 65 565 58 HOH HOH . C 3 HOH A 66 566 36 HOH HOH . C 3 HOH A 67 567 57 HOH HOH . C 3 HOH A 68 568 17 HOH HOH . C 3 HOH A 69 569 16 HOH HOH . C 3 HOH A 70 570 69 HOH HOH . C 3 HOH A 71 571 70 HOH HOH . C 3 HOH A 72 572 75 HOH HOH . C 3 HOH A 73 573 67 HOH HOH . C 3 HOH A 74 574 56 HOH HOH . C 3 HOH A 75 575 48 HOH HOH . C 3 HOH A 76 576 78 HOH HOH . C 3 HOH A 77 577 81 HOH HOH . C 3 HOH A 78 578 71 HOH HOH . C 3 HOH A 79 579 66 HOH HOH . C 3 HOH A 80 580 82 HOH HOH . C 3 HOH A 81 581 52 HOH HOH . C 3 HOH A 82 582 74 HOH HOH . C 3 HOH A 83 583 76 HOH HOH . C 3 HOH A 84 584 28 HOH HOH . # 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 N N1 T4V . . . B 2 -21.273 -2.311 13.439 1 43.94 ? N1 T4V 401 A 1 HETATM 2 C C4 T4V . . . B 2 -21.317 -2.596 14.893 1 47.3 ? C4 T4V 401 A 1 HETATM 3 C C5 T4V . . . B 2 -20.698 -1.623 15.898 1 59.23 ? C5 T4V 401 A 1 HETATM 4 C C6 T4V . . . B 2 -19.576 -1.935 16.651 1 54.83 ? C6 T4V 401 A 1 HETATM 5 C C7 T4V . . . B 2 -18.99 -1.047 17.593 1 45.03 ? C7 T4V 401 A 1 HETATM 6 C C8 T4V . . . B 2 -19.549 0.187 17.797 1 49.08 ? C8 T4V 401 A 1 HETATM 7 C C10 T4V . . . B 2 -21.296 1.836 17.246 1 55.76 ? C10 T4V 401 A 1 HETATM 8 C C13 T4V . . . B 2 -22.455 0.061 15.386 1 55.6 ? C13 T4V 401 A 1 HETATM 9 C C15 T4V . . . B 2 -21.248 -3.51 12.58 1 44.91 ? C15 T4V 401 A 1 HETATM 10 N N T4V . . . B 2 -19.077 -2.767 11.529 1 42.75 ? N T4V 401 A 1 HETATM 11 C C T4V . . . B 2 -16.683 -2.506 11.144 1 24.56 ? C T4V 401 A 1 HETATM 12 O O T4V . . . B 2 -17.991 -4.209 10.109 1 32.54 ? O T4V 401 A 1 HETATM 13 C C1 T4V . . . B 2 -17.982 -3.228 10.868 1 35.5 ? C1 T4V 401 A 1 HETATM 14 C C11 T4V . . . B 2 -22.407 2.193 16.521 1 59.88 ? C11 T4V 401 A 1 HETATM 15 C C12 T4V . . . B 2 -22.998 1.302 15.596 1 56.44 ? C12 T4V 401 A 1 HETATM 16 C C14 T4V . . . B 2 -21.297 -0.342 16.104 1 56.82 ? C14 T4V 401 A 1 HETATM 17 C C16 T4V . . . B 2 -20.367 -3.438 11.335 1 40.4 ? C16 T4V 401 A 1 HETATM 18 C C2 T4V . . . B 2 -19.061 -1.625 12.456 1 42.84 ? C2 T4V 401 A 1 HETATM 19 C C3 T4V . . . B 2 -20.437 -1.202 12.957 1 47.4 ? C3 T4V 401 A 1 HETATM 20 C C9 T4V . . . B 2 -20.705 0.565 17.057 1 49.66 ? C9 T4V 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #