data_8GDJ # _model_server_result.job_id PwU544JcBI_mZtbxeEXj-g _model_server_result.datetime_utc '2024-10-19 21:38:08' _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 8gdj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":513}' # _entry.id 8GDJ # _exptl.entry_id 8GDJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 412.886 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,5R)-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)-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 8GDJ _cell.length_a 62.18 _cell.length_b 66.115 _cell.length_c 91.173 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GDJ _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 A ND2 ASN 225 A ASN 355 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale9 A ND2 ASN 255 A ASN 386 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale10 A ND2 ASN 261 A ASN 392 1_555 L C1 NAG . A NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale11 A ND2 ASN 311 A ASN 448 1_555 K C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale12 A ND2 ASN 324 A ASN 461 1_555 M C1 NAG . A NAG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _chem_comp.formula 'C19 H26 Cl F N4 O3' _chem_comp.formula_weight 412.886 _chem_comp.id Z6F _chem_comp.mon_nstd_flag . _chem_comp.name (3S,5R)-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)-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 Z6F sing 439 n n C17 C19 Z6F doub 440 n y C17 C15 Z6F sing 441 n y C19 C20 Z6F sing 442 n y F16 C15 Z6F sing 443 n n C15 C14 Z6F doub 444 n y C20 C13 Z6F doub 445 n y C14 C13 Z6F sing 446 n y C13 N12 Z6F sing 447 n n N12 C10 Z6F sing 448 n n C10 O11 Z6F doub 449 n n C10 C09 Z6F sing 450 n n C21 C09 Z6F sing 451 n n C21 C22 Z6F sing 452 n n C09 C08 Z6F sing 453 n n C22 C23 Z6F sing 454 n n C22 C25 Z6F sing 455 n n C23 O24 Z6F sing 456 n n C08 N07 Z6F sing 457 n n C25 N07 Z6F sing 458 n n N07 C06 Z6F sing 459 n n C27 N05 Z6F sing 460 n n C27 C28 Z6F sing 461 n n C06 N05 Z6F sing 462 n n C06 O26 Z6F doub 463 n n N05 C04 Z6F sing 464 n n C04 C03 Z6F sing 465 n n C28 N02 Z6F sing 466 n n C03 N02 Z6F sing 467 n n N02 C01 Z6F sing 468 n n C01 H1 Z6F sing 469 n n C01 H2 Z6F sing 470 n n C01 H3 Z6F sing 471 n n C03 H4 Z6F sing 472 n n C03 H5 Z6F sing 473 n n C04 H6 Z6F sing 474 n n C04 H7 Z6F sing 475 n n C08 H8 Z6F sing 476 n n C08 H9 Z6F sing 477 n n C09 H10 Z6F sing 478 n n C14 H11 Z6F sing 479 n n C19 H12 Z6F sing 480 n n C20 H13 Z6F sing 481 n n C21 H14 Z6F sing 482 n n C21 H15 Z6F sing 483 n n C22 H16 Z6F sing 484 n n C23 H17 Z6F sing 485 n n C23 H18 Z6F sing 486 n n C25 H19 Z6F sing 487 n n C25 H20 Z6F sing 488 n n C27 H21 Z6F sing 489 n n C27 H22 Z6F sing 490 n n C28 H23 Z6F sing 491 n n C28 H24 Z6F sing 492 n n N12 H26 Z6F sing 493 n n O24 H27 Z6F sing 494 n n # _atom_sites.entry_id 8GDJ _atom_sites.fract_transf_matrix[1][1] 0.016082 _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] 0.015125 _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] 0.010968 _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 Z6F A 1 513 1 Z6F MW7 . O 4 EPE A 1 514 1 EPE EPE . P 5 HOH A 1 601 22 HOH HOH . P 5 HOH A 2 602 33 HOH HOH . P 5 HOH A 3 603 25 HOH HOH . P 5 HOH A 4 604 1 HOH HOH . P 5 HOH A 5 605 2 HOH HOH . P 5 HOH A 6 606 6 HOH HOH . P 5 HOH A 7 607 26 HOH HOH . P 5 HOH A 8 608 4 HOH HOH . P 5 HOH A 9 609 37 HOH HOH . P 5 HOH A 10 610 10 HOH HOH . P 5 HOH A 11 611 31 HOH HOH . P 5 HOH A 12 612 17 HOH HOH . P 5 HOH A 13 613 19 HOH HOH . P 5 HOH A 14 614 18 HOH HOH . P 5 HOH A 15 615 8 HOH HOH . P 5 HOH A 16 616 9 HOH HOH . P 5 HOH A 17 617 3 HOH HOH . P 5 HOH A 18 618 7 HOH HOH . P 5 HOH A 19 619 34 HOH HOH . P 5 HOH A 20 620 30 HOH HOH . P 5 HOH A 21 621 5 HOH HOH . P 5 HOH A 22 622 36 HOH HOH . P 5 HOH A 23 623 14 HOH HOH . P 5 HOH A 24 624 13 HOH HOH . P 5 HOH A 25 625 21 HOH HOH . P 5 HOH A 26 626 20 HOH HOH . P 5 HOH A 27 627 32 HOH HOH . P 5 HOH A 28 628 24 HOH HOH . P 5 HOH A 29 629 15 HOH HOH . P 5 HOH A 30 630 28 HOH HOH . P 5 HOH A 31 631 12 HOH HOH . P 5 HOH A 32 632 27 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 C01 Z6F . . . N 3 -1.71 13.316 -7.777 1 67.07 ? C01 Z6F 513 A 1 HETATM 2 C C03 Z6F . . . N 3 0.082 13.662 -8.991 1 66.36 ? C03 Z6F 513 A 1 HETATM 3 C C04 Z6F . . . N 3 0.596 14.072 -10.374 1 58.08 ? C04 Z6F 513 A 1 HETATM 4 C C06 Z6F . . . N 3 0.039 16.44 -11.15 1 60.03 ? C06 Z6F 513 A 1 HETATM 5 C C08 Z6F . . . N 3 -2.27 17.393 -12.197 1 54.04 ? C08 Z6F 513 A 1 HETATM 6 C C09 Z6F . . . N 3 -2.094 17.787 -13.688 1 50.43 ? C09 Z6F 513 A 1 HETATM 7 O O11 Z6F . . . N 3 -4.365 17.317 -14.364 1 47.05 ? O11 Z6F 513 A 1 HETATM 8 C C10 Z6F . . . N 3 -3.235 17.449 -14.695 1 48.02 ? C10 Z6F 513 A 1 HETATM 9 C C13 Z6F . . . N 3 -3.556 17.055 -17.253 1 45.61 ? C13 Z6F 513 A 1 HETATM 10 C C14 Z6F . . . N 3 -4.943 17.125 -17.263 1 39.32 ? C14 Z6F 513 A 1 HETATM 11 C C15 Z6F . . . N 3 -5.62 16.855 -18.449 1 41.51 ? C15 Z6F 513 A 1 HETATM 12 C C17 Z6F . . . N 3 -4.917 16.527 -19.596 1 43.4 ? C17 Z6F 513 A 1 HETATM 13 C C19 Z6F . . . N 3 -3.531 16.462 -19.588 1 43.15 ? C19 Z6F 513 A 1 HETATM 14 C C20 Z6F . . . N 3 -2.853 16.731 -18.412 1 44.43 ? C20 Z6F 513 A 1 HETATM 15 C C21 Z6F . . . N 3 -1.839 19.229 -13.784 1 49.9 ? C21 Z6F 513 A 1 HETATM 16 C C22 Z6F . . . N 3 -0.466 19.423 -13.274 1 55.17 ? C22 Z6F 513 A 1 HETATM 17 C C23 Z6F . . . N 3 -0.136 20.931 -13.248 1 56.04 ? C23 Z6F 513 A 1 HETATM 18 C C25 Z6F . . . N 3 -0.33 18.87 -11.845 1 58.37 ? C25 Z6F 513 A 1 HETATM 19 C C27 Z6F . . . N 3 -1.513 14.351 -11.163 1 60.66 ? C27 Z6F 513 A 1 HETATM 20 C C28 Z6F . . . N 3 -2.11 14.128 -9.771 1 66.02 ? C28 Z6F 513 A 1 HETATM 21 F F16 Z6F . . . N 3 -6.985 16.9 -18.521 1 40.14 ? F16 Z6F 513 A 1 HETATM 22 N N02 Z6F . . . N 3 -1.283 13.335 -8.962 1 77 ? N02 Z6F 513 A 1 HETATM 23 N N05 Z6F . . . N 3 -0.292 15.017 -10.943 1 61.28 ? N05 Z6F 513 A 1 HETATM 24 N N07 Z6F . . . N 3 -0.852 17.477 -11.689 1 61.58 ? N07 Z6F 513 A 1 HETATM 25 N N12 Z6F . . . N 3 -2.77 17.341 -16.066 1 43.27 ? N12 Z6F 513 A 1 HETATM 26 O O24 Z6F . . . N 3 0.213 21.25 -11.935 1 62.73 ? O24 Z6F 513 A 1 HETATM 27 O O26 Z6F . . . N 3 1.13 16.805 -10.856 1 59.65 ? O26 Z6F 513 A 1 HETATM 28 CL CL1 Z6F . . . N 3 -5.835 16.187 -21.086 1 56.36 ? CL1 Z6F 513 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #