data_8GD0 # _model_server_result.job_id zPNzgYmD7L4M3SAtIqHJwQ _model_server_result.datetime_utc '2025-01-10 16:36:18' _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 8gd0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":513}' # _entry.id 8GD0 # _exptl.entry_id 8GD0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 382.86 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S)-N-(4-chloro-3-fluorophenyl)-1-(4-methylpiperazine-1-carbonyl)piperidine-3-carboxamide _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 8GD0 _cell.length_a 63.577 _cell.length_b 66.275 _cell.length_c 91.388 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GD0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id N _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 13 A CYS 54 1_555 A SG CYS 33 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale8 A ND2 ASN 225 A ASN 355 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale9 A ND2 ASN 255 A ASN 386 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale10 A ND2 ASN 261 A ASN 392 1_555 L C1 NAG . A NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale11 A ND2 ASN 311 A ASN 448 1_555 K C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale12 A ND2 ASN 324 A ASN 461 1_555 M C1 NAG . A NAG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C18 H24 Cl F N4 O2' _chem_comp.formula_weight 382.86 _chem_comp.id Z3F _chem_comp.mon_nstd_flag . _chem_comp.name (3S)-N-(4-chloro-3-fluorophenyl)-1-(4-methylpiperazine-1-carbonyl)piperidine-3-carboxamide _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 CL1 C17 Z3F sing 439 n n C19 C17 Z3F doub 440 n y C19 C20 Z3F sing 441 n y C17 C15 Z3F sing 442 n y C20 C13 Z3F doub 443 n y C15 F16 Z3F sing 444 n n C15 C14 Z3F doub 445 n y C13 C14 Z3F sing 446 n y C13 N12 Z3F sing 447 n n N12 C10 Z3F sing 448 n n C10 O11 Z3F doub 449 n n C10 C09 Z3F sing 450 n n C21 C09 Z3F sing 451 n n C21 C22 Z3F sing 452 n n C09 C08 Z3F sing 453 n n C22 C23 Z3F sing 454 n n C08 N07 Z3F sing 455 n n C23 N07 Z3F sing 456 n n N07 C06 Z3F sing 457 n n C25 N05 Z3F sing 458 n n C25 C26 Z3F sing 459 n n C06 N05 Z3F sing 460 n n C06 O24 Z3F doub 461 n n N05 C04 Z3F sing 462 n n C04 C03 Z3F sing 463 n n C26 N02 Z3F sing 464 n n N02 C03 Z3F sing 465 n n N02 C01 Z3F sing 466 n n C01 H1 Z3F sing 467 n n C01 H2 Z3F sing 468 n n C01 H3 Z3F sing 469 n n C03 H4 Z3F sing 470 n n C03 H5 Z3F sing 471 n n C04 H6 Z3F sing 472 n n C04 H7 Z3F sing 473 n n C08 H8 Z3F sing 474 n n C08 H9 Z3F sing 475 n n C09 H10 Z3F sing 476 n n C14 H11 Z3F sing 477 n n C19 H12 Z3F sing 478 n n C20 H13 Z3F sing 479 n n C21 H14 Z3F sing 480 n n C21 H15 Z3F sing 481 n n C22 H16 Z3F sing 482 n n C22 H17 Z3F sing 483 n n C23 H18 Z3F sing 484 n n C23 H19 Z3F sing 485 n n C25 H20 Z3F sing 486 n n C25 H21 Z3F sing 487 n n C26 H22 Z3F sing 488 n n C26 H23 Z3F sing 489 n n N12 H25 Z3F sing 490 n n # _atom_sites.entry_id 8GD0 _atom_sites.fract_transf_matrix[1][1] 0.015729 _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] 0.015089 _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] 0.010942 _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 NAG A 1 501 502 NAG NAG . C 2 NAG A 1 502 503 NAG NAG . D 2 NAG A 1 503 504 NAG NAG . E 2 NAG A 1 504 505 NAG NAG . F 2 NAG A 1 505 506 NAG NAG . G 2 NAG A 1 506 507 NAG NAG . H 2 NAG A 1 507 508 NAG NAG . I 2 NAG A 1 508 509 NAG NAG . J 2 NAG A 1 509 510 NAG NAG . K 2 NAG A 1 510 511 NAG NAG . L 2 NAG A 1 511 512 NAG NAG . M 2 NAG A 1 512 513 NAG NAG . N 3 Z3F A 1 513 1 Z3F MW5 . O 4 EPE A 1 514 1 EPE EPE . P 5 CL A 1 515 1 CL CL . Q 5 CL A 1 516 2 CL CL . R 5 CL A 1 517 3 CL CL . S 6 HOH A 1 601 30 HOH HOH . S 6 HOH A 2 602 21 HOH HOH . S 6 HOH A 3 603 6 HOH HOH . S 6 HOH A 4 604 7 HOH HOH . S 6 HOH A 5 605 2 HOH HOH . S 6 HOH A 6 606 37 HOH HOH . S 6 HOH A 7 607 33 HOH HOH . S 6 HOH A 8 608 3 HOH HOH . S 6 HOH A 9 609 1 HOH HOH . S 6 HOH A 10 610 18 HOH HOH . S 6 HOH A 11 611 8 HOH HOH . S 6 HOH A 12 612 24 HOH HOH . S 6 HOH A 13 613 19 HOH HOH . S 6 HOH A 14 614 26 HOH HOH . S 6 HOH A 15 615 31 HOH HOH . S 6 HOH A 16 616 20 HOH HOH . S 6 HOH A 17 617 28 HOH HOH . S 6 HOH A 18 618 22 HOH HOH . S 6 HOH A 19 619 14 HOH HOH . S 6 HOH A 20 620 27 HOH HOH . S 6 HOH A 21 621 12 HOH HOH . S 6 HOH A 22 622 9 HOH HOH . S 6 HOH A 23 623 16 HOH HOH . S 6 HOH A 24 624 23 HOH HOH . S 6 HOH A 25 625 10 HOH HOH . S 6 HOH A 26 626 4 HOH HOH . S 6 HOH A 27 627 38 HOH HOH . S 6 HOH A 28 628 36 HOH HOH . S 6 HOH A 29 629 15 HOH HOH . S 6 HOH A 30 630 32 HOH HOH . S 6 HOH A 31 631 13 HOH HOH . S 6 HOH A 32 632 11 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 C C10 Z3F . . . N 3 -3.341 17.656 -14.981 1 39.87 ? C10 Z3F 513 A 1 HETATM 2 C C01 Z3F . . . N 3 -1.526 13.178 -8.412 1 66.79 ? C01 Z3F 513 A 1 HETATM 3 C C03 Z3F . . . N 3 0.223 13.943 -9.423 1 59.02 ? C03 Z3F 513 A 1 HETATM 4 C C04 Z3F . . . N 3 0.708 14.586 -10.719 1 55.44 ? C04 Z3F 513 A 1 HETATM 5 C C06 Z3F . . . N 3 -0.123 16.778 -11.371 1 48.35 ? C06 Z3F 513 A 1 HETATM 6 C C08 Z3F . . . N 3 -2.487 17.681 -12.45 1 41.69 ? C08 Z3F 513 A 1 HETATM 7 C C09 Z3F . . . N 3 -2.209 17.999 -13.941 1 44.87 ? C09 Z3F 513 A 1 HETATM 8 C C13 Z3F . . . N 3 -3.634 17.193 -17.552 1 37.83 ? C13 Z3F 513 A 1 HETATM 9 C C14 Z3F . . . N 3 -4.998 17.237 -17.532 1 35.31 ? C14 Z3F 513 A 1 HETATM 10 C C15 Z3F . . . N 3 -5.717 16.948 -18.702 1 37.93 ? C15 Z3F 513 A 1 HETATM 11 C C17 Z3F . . . N 3 -5.055 16.628 -19.866 1 38.59 ? C17 Z3F 513 A 1 HETATM 12 C C19 Z3F . . . N 3 -3.678 16.588 -19.892 1 36.22 ? C19 Z3F 513 A 1 HETATM 13 C C20 Z3F . . . N 3 -2.959 16.873 -18.732 1 38.1 ? C20 Z3F 513 A 1 HETATM 14 C C21 Z3F . . . N 3 -1.884 19.423 -14.132 1 43.3 ? C21 Z3F 513 A 1 HETATM 15 C C22 Z3F . . . N 3 -0.66 19.807 -13.381 1 40.72 ? C22 Z3F 513 A 1 HETATM 16 C C23 Z3F . . . N 3 -0.688 19.263 -11.95 1 44.19 ? C23 Z3F 513 A 1 HETATM 17 C C25 Z3F . . . N 3 -1.465 14.694 -11.566 1 53.3 ? C25 Z3F 513 A 1 HETATM 18 C C26 Z3F . . . N 3 -2.026 14.254 -10.201 1 56.61 ? C26 Z3F 513 A 1 HETATM 19 F F16 Z3F . . . N 3 -7.053 16.983 -18.696 1 39.55 ? F16 Z3F 513 A 1 HETATM 20 N N02 Z3F . . . N 3 -1.124 13.396 -9.493 1 68.13 ? N02 Z3F 513 A 1 HETATM 21 N N05 Z3F . . . N 3 -0.318 15.299 -11.249 1 55.3 ? N05 Z3F 513 A 1 HETATM 22 N N07 Z3F . . . N 3 -1.095 17.823 -11.875 1 49.23 ? N07 Z3F 513 A 1 HETATM 23 N N12 Z3F . . . N 3 -2.857 17.493 -16.361 1 38.22 ? N12 Z3F 513 A 1 HETATM 24 O O11 Z3F . . . N 3 -4.452 17.578 -14.671 1 42.89 ? O11 Z3F 513 A 1 HETATM 25 O O24 Z3F . . . N 3 0.935 17.181 -11.022 1 51.59 ? O24 Z3F 513 A 1 HETATM 26 CL CL1 Z3F . . . N 3 -6.023 16.268 -21.347 1 41.42 ? CL1 Z3F 513 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 26 #