data_8GDK # _model_server_result.job_id RNBI433tEy5agIxihH560g _model_server_result.datetime_utc '2024-10-19 21:20:39' _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 8gdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":514}' # _entry.id 8GDK # _exptl.entry_id 8GDK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 440.939 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,5R)-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)-1-[(3R,5S)-3,4,5-trimethylpiperazine-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 8GDK _cell.length_a 61.418 _cell.length_b 65.997 _cell.length_c 90.826 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GDK _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,T _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 O _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale8 A ND2 ASN 225 A ASN 355 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale9 A ND2 ASN 255 A ASN 386 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale10 A ND2 ASN 261 A ASN 392 1_555 L C1 NAG . A NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale11 A ND2 ASN 274 A ASN 411 1_555 N C1 NAG . A NAG 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale12 A ND2 ASN 311 A ASN 448 1_555 K C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale13 A ND2 ASN 324 A ASN 461 1_555 M C1 NAG . A NAG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _chem_comp.formula 'C21 H30 Cl F N4 O3' _chem_comp.formula_weight 440.939 _chem_comp.id Z7N _chem_comp.mon_nstd_flag . _chem_comp.name (3S,5R)-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)-1-[(3R,5S)-3,4,5-trimethylpiperazine-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 C18 Z7N sing 439 n n C20 C18 Z7N doub 440 n y C20 C21 Z7N sing 441 n y C18 C16 Z7N sing 442 n y F17 C16 Z7N sing 443 n n C21 C14 Z7N doub 444 n y C16 C15 Z7N doub 445 n y C14 C15 Z7N sing 446 n y C14 N13 Z7N sing 447 n n N13 C11 Z7N sing 448 n n C11 O12 Z7N doub 449 n n C11 C10 Z7N sing 450 n n C22 C10 Z7N sing 451 n n C22 C23 Z7N sing 452 n n C10 C09 Z7N sing 453 n n C23 C24 Z7N sing 454 n n C23 C26 Z7N sing 455 n n C24 O25 Z7N sing 456 n n C09 N08 Z7N sing 457 n n C26 N08 Z7N sing 458 n n N08 C07 Z7N sing 459 n n C07 N06 Z7N sing 460 n n C07 O27 Z7N doub 461 n n C28 N06 Z7N sing 462 n n C28 C29 Z7N sing 463 n n N06 C05 Z7N sing 464 n n C05 C03 Z7N sing 465 n n C30 C29 Z7N sing 466 n n C29 N02 Z7N sing 467 n n C04 C03 Z7N sing 468 n n C03 N02 Z7N sing 469 n n N02 C01 Z7N sing 470 n n C10 H1 Z7N sing 471 n n C20 H2 Z7N sing 472 n n C21 H3 Z7N sing 473 n n C22 H4 Z7N sing 474 n n C22 H5 Z7N sing 475 n n C23 H6 Z7N sing 476 n n C24 H7 Z7N sing 477 n n C24 H8 Z7N sing 478 n n C26 H9 Z7N sing 479 n n C26 H10 Z7N sing 480 n n C28 H11 Z7N sing 481 n n C28 H12 Z7N sing 482 n n C30 H13 Z7N sing 483 n n C30 H14 Z7N sing 484 n n C30 H15 Z7N sing 485 n n C01 H16 Z7N sing 486 n n C01 H17 Z7N sing 487 n n C01 H18 Z7N sing 488 n n C03 H19 Z7N sing 489 n n C04 H20 Z7N sing 490 n n C04 H21 Z7N sing 491 n n C04 H22 Z7N sing 492 n n C05 H23 Z7N sing 493 n n C05 H24 Z7N sing 494 n n C09 H25 Z7N sing 495 n n C09 H26 Z7N sing 496 n n C15 H27 Z7N sing 497 n n C29 H28 Z7N sing 498 n n N13 H30 Z7N sing 499 n n O25 H31 Z7N sing 500 n n # _atom_sites.entry_id 8GDK _atom_sites.fract_transf_matrix[1][1] 0.016282 _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] 0.015152 _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] 0.01101 _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 2 NAG A 1 513 514 NAG NAG . O 3 Z7N A 1 514 1 Z7N MW8 . P 4 EPE A 1 515 1 EPE EPE . Q 5 CL A 1 516 1 CL CL . R 5 CL A 1 517 2 CL CL . S 5 CL A 1 518 3 CL CL . T 6 HOH A 1 601 2 HOH HOH . T 6 HOH A 2 602 3 HOH HOH . T 6 HOH A 3 603 4 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 Z7N . . . O 3 -1.889 17.655 -13.609 1 63.54 ? C10 Z7N 514 A 1 HETATM 2 O O12 Z7N . . . O 3 -4.145 17.021 -14.224 1 67.38 ? O12 Z7N 514 A 1 HETATM 3 C C16 Z7N . . . O 3 -5.582 16.713 -18.349 1 54.58 ? C16 Z7N 514 A 1 HETATM 4 C C20 Z7N . . . O 3 -3.488 16.333 -19.522 1 53.4 ? C20 Z7N 514 A 1 HETATM 5 C C21 Z7N . . . O 3 -2.792 16.633 -18.354 1 55.72 ? C21 Z7N 514 A 1 HETATM 6 C C22 Z7N . . . O 3 -1.57 19.09 -13.792 1 64.99 ? C22 Z7N 514 A 1 HETATM 7 C C23 Z7N . . . O 3 -0.225 19.362 -13.211 1 62.3 ? C23 Z7N 514 A 1 HETATM 8 C C24 Z7N . . . O 3 0.006 20.919 -13.183 1 75.08 ? C24 Z7N 514 A 1 HETATM 9 C C26 Z7N . . . O 3 -0.1 18.832 -11.791 1 69.8 ? C26 Z7N 514 A 1 HETATM 10 C C28 Z7N . . . O 3 -1.424 14.294 -10.803 1 76.53 ? C28 Z7N 514 A 1 HETATM 11 C C30 Z7N . . . O 3 -3.516 13.633 -9.476 1 78.68 ? C30 Z7N 514 A 1 HETATM 12 C C11 Z7N . . . O 3 -3.054 17.274 -14.598 1 59.33 ? C11 Z7N 514 A 1 HETATM 13 C C01 Z7N . . . O 3 -1.661 13.038 -7.485 1 78.18 ? C01 Z7N 514 A 1 HETATM 14 C C03 Z7N . . . O 3 0.112 13.213 -8.725 1 72.41 ? C03 Z7N 514 A 1 HETATM 15 C C04 Z7N . . . O 3 0.74 11.763 -8.802 1 75.49 ? C04 Z7N 514 A 1 HETATM 16 C C05 Z7N . . . O 3 0.7 14.049 -9.892 1 81.03 ? C05 Z7N 514 A 1 HETATM 17 C C07 Z7N . . . O 3 0.195 16.385 -10.869 1 67.21 ? C07 Z7N 514 A 1 HETATM 18 C C09 Z7N . . . O 3 -2.072 17.349 -12.115 1 67.66 ? C09 Z7N 514 A 1 HETATM 19 C C14 Z7N . . . O 3 -3.474 16.969 -17.182 1 54.49 ? C14 Z7N 514 A 1 HETATM 20 C C15 Z7N . . . O 3 -4.881 17.013 -17.18 1 53.94 ? C15 Z7N 514 A 1 HETATM 21 C C18 Z7N . . . O 3 -4.888 16.372 -19.522 1 52.19 ? C18 Z7N 514 A 1 HETATM 22 C C29 Z7N . . . O 3 -2.004 14.056 -9.385 1 76.6 ? C29 Z7N 514 A 1 HETATM 23 F F17 Z7N . . . O 3 -6.954 16.751 -18.355 1 56.46 ? F17 Z7N 514 A 1 HETATM 24 N N02 Z7N . . . O 3 -1.289 13.073 -8.69 1 76.44 ? N02 Z7N 514 A 1 HETATM 25 N N06 Z7N . . . O 3 -0.194 14.947 -10.559 1 74.17 ? N06 Z7N 514 A 1 HETATM 26 N N08 Z7N . . . O 3 -0.663 17.444 -11.557 1 73.68 ? N08 Z7N 514 A 1 HETATM 27 N N13 Z7N . . . O 3 -2.662 17.274 -16.003 1 55.16 ? N13 Z7N 514 A 1 HETATM 28 O O25 Z7N . . . O 3 0.166 21.323 -11.842 1 81.48 ? O25 Z7N 514 A 1 HETATM 29 O O27 Z7N . . . O 3 1.284 16.713 -10.543 1 72 ? O27 Z7N 514 A 1 HETATM 30 CL CL1 Z7N . . . O 3 -5.783 15.987 -21.029 1 61.19 ? CL1 Z7N 514 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #