data_3VYE # _model_server_result.job_id 9CN3YOEHe5DI2X4ZAu6CrQ _model_server_result.datetime_utc '2025-03-13 17:17:45' _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 3vye # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 3VYE # _exptl.entry_id 3VYE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 435.003 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-N-(3-methylbutyl)piperidine-3-carboxamide _entity.pdbx_number_of_molecules 2 _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 3VYE _cell.length_a 141.442 _cell.length_b 141.442 _cell.length_c 141.442 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VYE _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA hexameric 6 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 1 A,B,C,D,E,F,G,H 3 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' 6_577 z+1/2,-x+5/2,-y+2 0 0 1 -1 0 0 0 -1 0 70.721 353.605 282.884 3 'crystal symmetry operation' 12_774 -y+5/2,-z+2,x-1/2 0 -1 0 0 0 -1 1 0 0 353.605 282.884 -70.721 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 51 A CYS 51 1_555 A SG CYS 58 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf2 A SG CYS 217 A CYS 217 1_555 A SG CYS 221 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 259 A CYS 259 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 B SG CYS 51 B CYS 51 1_555 B SG CYS 58 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 B SG CYS 217 B CYS 217 1_555 B SG CYS 221 B CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 B SG CYS 259 B CYS 259 1_555 B SG CYS 296 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 75 A ASN 75 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale2 B ND2 ASN 75 B ASN 75 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? # _chem_comp.formula 'C23 H35 Cl N4 O2' _chem_comp.formula_weight 435.003 _chem_comp.id VYE _chem_comp.mon_nstd_flag . _chem_comp.name (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-N-(3-methylbutyl)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 C19 C20 VYE doub 406 n y C19 C18 VYE sing 407 n y C20 C21 VYE sing 408 n y C18 C17 VYE doub 409 n y C21 C16 VYE doub 410 n y C17 C16 VYE sing 411 n y C17 CL1 VYE sing 412 n n C16 N10 VYE sing 413 n n C11 N10 VYE sing 414 n n C11 C12 VYE sing 415 n n N10 C9 VYE sing 416 n n C14 C12 VYE sing 417 n n C12 C15 VYE sing 418 n n C12 N7 VYE sing 419 n n C9 O13 VYE doub 420 n n C9 C8 VYE sing 421 n n N7 C8 VYE sing 422 n n N7 C5 VYE sing 423 n n C4 C5 VYE sing 424 n n C4 N3 VYE sing 425 n n C5 C6 VYE sing 426 n n N3 C2 VYE sing 427 n n C6 C1 VYE sing 428 n n C2 C1 VYE sing 429 n n C1 C23 VYE sing 430 n n C23 O24 VYE doub 431 n n C23 N25 VYE sing 432 n n N25 C26 VYE sing 433 n n C26 C27 VYE sing 434 n n C29 C28 VYE sing 435 n n C30 C28 VYE sing 436 n n C27 C28 VYE sing 437 n n C1 H1 VYE sing 438 n n C2 H2 VYE sing 439 n n C2 H3 VYE sing 440 n n N3 H4 VYE sing 441 n n C4 H6 VYE sing 442 n n C4 H7 VYE sing 443 n n C5 H8 VYE sing 444 n n C6 H9 VYE sing 445 n n C6 H10 VYE sing 446 n n C8 H12 VYE sing 447 n n C8 H13 VYE sing 448 n n C11 H14 VYE sing 449 n n C11 H15 VYE sing 450 n n C14 H16 VYE sing 451 n n C14 H17 VYE sing 452 n n C14 H18 VYE sing 453 n n C15 H19 VYE sing 454 n n C15 H20 VYE sing 455 n n C15 H21 VYE sing 456 n n C18 H22 VYE sing 457 n n C19 H23 VYE sing 458 n n C20 H24 VYE sing 459 n n C21 H25 VYE sing 460 n n N25 H26 VYE sing 461 n n C26 H27 VYE sing 462 n n C26 H28 VYE sing 463 n n C27 H29 VYE sing 464 n n C27 H30 VYE sing 465 n n C28 H31 VYE sing 466 n n C29 H32 VYE sing 467 n n C29 H33 VYE sing 468 n n C29 H34 VYE sing 469 n n C30 H35 VYE sing 470 n n C30 H36 VYE sing 471 n n C30 H37 VYE sing 472 n n # _atom_sites.entry_id 3VYE _atom_sites.fract_transf_matrix[1][1] 0.00707 _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] 0.00707 _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] 0.00707 _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 C 2 NAG A 1 401 401 NAG NAG . D 3 VYE A 1 402 7 VYE UNL . E 2 NAG B 1 401 401 NAG NAG . F 3 VYE B 1 402 8 VYE UNL . G 4 HOH A 1 501 1 HOH HOH . G 4 HOH A 2 502 2 HOH HOH . G 4 HOH A 3 503 4 HOH HOH . G 4 HOH A 4 504 5 HOH HOH . G 4 HOH A 5 505 6 HOH HOH . G 4 HOH A 6 506 7 HOH HOH . G 4 HOH A 7 507 8 HOH HOH . G 4 HOH A 8 508 9 HOH HOH . G 4 HOH A 9 509 10 HOH HOH . G 4 HOH A 10 510 11 HOH HOH . G 4 HOH A 11 511 13 HOH HOH . G 4 HOH A 12 512 14 HOH HOH . G 4 HOH A 13 513 15 HOH HOH . G 4 HOH A 14 514 16 HOH HOH . G 4 HOH A 15 515 21 HOH HOH . G 4 HOH A 16 516 22 HOH HOH . G 4 HOH A 17 517 24 HOH HOH . G 4 HOH A 18 518 25 HOH HOH . G 4 HOH A 19 519 26 HOH HOH . G 4 HOH A 20 520 27 HOH HOH . G 4 HOH A 21 521 28 HOH HOH . G 4 HOH A 22 522 32 HOH HOH . G 4 HOH A 23 523 33 HOH HOH . G 4 HOH A 24 524 34 HOH HOH . G 4 HOH A 25 525 35 HOH HOH . G 4 HOH A 26 526 39 HOH HOH . G 4 HOH A 27 527 40 HOH HOH . G 4 HOH A 28 528 41 HOH HOH . G 4 HOH A 29 529 43 HOH HOH . G 4 HOH A 30 530 45 HOH HOH . G 4 HOH A 31 531 47 HOH HOH . G 4 HOH A 32 532 52 HOH HOH . G 4 HOH A 33 533 54 HOH HOH . G 4 HOH A 34 534 55 HOH HOH . G 4 HOH A 35 535 57 HOH HOH . G 4 HOH A 36 536 58 HOH HOH . G 4 HOH A 37 537 60 HOH HOH . G 4 HOH A 38 538 61 HOH HOH . G 4 HOH A 39 539 62 HOH HOH . G 4 HOH A 40 540 67 HOH HOH . G 4 HOH A 41 541 68 HOH HOH . G 4 HOH A 42 542 69 HOH HOH . G 4 HOH A 43 543 70 HOH HOH . G 4 HOH A 44 544 71 HOH HOH . G 4 HOH A 45 545 72 HOH HOH . G 4 HOH A 46 546 76 HOH HOH . G 4 HOH A 47 547 77 HOH HOH . G 4 HOH A 48 548 79 HOH HOH . G 4 HOH A 49 549 80 HOH HOH . G 4 HOH A 50 550 82 HOH HOH . G 4 HOH A 51 551 83 HOH HOH . G 4 HOH A 52 552 84 HOH HOH . G 4 HOH A 53 553 85 HOH HOH . H 4 HOH B 1 501 3 HOH HOH . H 4 HOH B 2 502 12 HOH HOH . H 4 HOH B 3 503 17 HOH HOH . H 4 HOH B 4 504 18 HOH HOH . H 4 HOH B 5 505 19 HOH HOH . H 4 HOH B 6 506 20 HOH HOH . H 4 HOH B 7 507 23 HOH HOH . H 4 HOH B 8 508 29 HOH HOH . H 4 HOH B 9 509 30 HOH HOH . H 4 HOH B 10 510 31 HOH HOH . H 4 HOH B 11 511 36 HOH HOH . H 4 HOH B 12 512 37 HOH HOH . H 4 HOH B 13 513 38 HOH HOH . H 4 HOH B 14 514 42 HOH HOH . H 4 HOH B 15 515 44 HOH HOH . H 4 HOH B 16 516 46 HOH HOH . H 4 HOH B 17 517 48 HOH HOH . H 4 HOH B 18 518 49 HOH HOH . H 4 HOH B 19 519 51 HOH HOH . H 4 HOH B 20 520 53 HOH HOH . H 4 HOH B 21 521 56 HOH HOH . H 4 HOH B 22 522 59 HOH HOH . H 4 HOH B 23 523 63 HOH HOH . H 4 HOH B 24 524 64 HOH HOH . H 4 HOH B 25 525 65 HOH HOH . H 4 HOH B 26 526 66 HOH HOH . H 4 HOH B 27 527 73 HOH HOH . H 4 HOH B 28 528 74 HOH HOH . H 4 HOH B 29 529 75 HOH HOH . H 4 HOH B 30 530 78 HOH HOH . H 4 HOH B 31 531 86 HOH HOH . H 4 HOH B 32 532 87 HOH HOH . H 4 HOH B 33 533 88 HOH HOH . H 4 HOH B 34 534 89 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 C1 VYE . . . D 3 179.793 202.15 100.721 1 35.33 ? C1 VYE 402 A 1 HETATM 2 C C2 VYE . . . D 3 179.424 203.616 100.517 1 30.43 ? C2 VYE 402 A 1 HETATM 3 N N3 VYE . . . D 3 179.51 204.02 99.122 1 32.42 ? N3 VYE 402 A 1 HETATM 4 C C4 VYE . . . D 3 178.623 203.216 98.283 1 33.27 ? C4 VYE 402 A 1 HETATM 5 C C5 VYE . . . D 3 178.956 201.729 98.362 1 35.37 ? C5 VYE 402 A 1 HETATM 6 C C6 VYE . . . D 3 178.991 201.209 99.801 1 34.85 ? C6 VYE 402 A 1 HETATM 7 N N7 VYE . . . D 3 178.108 200.935 97.474 1 37.09 ? N7 VYE 402 A 1 HETATM 8 C C8 VYE . . . D 3 176.792 200.594 97.952 1 38.71 ? C8 VYE 402 A 1 HETATM 9 C C9 VYE . . . D 3 175.85 200.006 96.883 1 40.79 ? C9 VYE 402 A 1 HETATM 10 N N10 VYE . . . D 3 176.417 199.635 95.674 1 41.33 ? N10 VYE 402 A 1 HETATM 11 C C11 VYE . . . D 3 177.86 199.785 95.391 1 38.99 ? C11 VYE 402 A 1 HETATM 12 C C12 VYE . . . D 3 178.746 199.975 96.602 1 39.61 ? C12 VYE 402 A 1 HETATM 13 O O13 VYE . . . D 3 174.66 199.885 97.119 1 43.06 ? O13 VYE 402 A 1 HETATM 14 C C14 VYE . . . D 3 180.118 200.5 96.15 1 39.78 ? C14 VYE 402 A 1 HETATM 15 C C15 VYE . . . D 3 178.931 198.641 97.34 1 37.22 ? C15 VYE 402 A 1 HETATM 16 C C16 VYE . . . D 3 175.603 199.109 94.686 1 42.79 ? C16 VYE 402 A 1 HETATM 17 C C17 VYE . . . D 3 175.304 197.763 94.585 1 43.35 ? C17 VYE 402 A 1 HETATM 18 C C18 VYE . . . D 3 174.487 197.252 93.592 1 42.93 ? C18 VYE 402 A 1 HETATM 19 C C19 VYE . . . D 3 173.95 198.135 92.661 1 44.09 ? C19 VYE 402 A 1 HETATM 20 C C20 VYE . . . D 3 174.238 199.497 92.74 1 43.61 ? C20 VYE 402 A 1 HETATM 21 C C21 VYE . . . D 3 175.067 199.986 93.754 1 43.51 ? C21 VYE 402 A 1 HETATM 22 CL CL1 VYE . . . D 3 175.962 196.673 95.735 1 52.66 ? CL1 VYE 402 A 1 HETATM 23 C C23 VYE . . . D 3 179.645 201.751 102.197 1 36.21 ? C23 VYE 402 A 1 HETATM 24 O O24 VYE . . . D 3 178.706 201.065 102.592 1 38.14 ? O24 VYE 402 A 1 HETATM 25 N N25 VYE . . . D 3 180.635 202.223 102.977 1 35.84 ? N25 VYE 402 A 1 HETATM 26 C C26 VYE . . . D 3 180.6 201.903 104.397 1 33.53 ? C26 VYE 402 A 1 HETATM 27 C C27 VYE . . . D 3 181.038 200.452 104.606 1 32.46 ? C27 VYE 402 A 1 HETATM 28 C C28 VYE . . . D 3 182.519 200.3 104.962 1 33.9 ? C28 VYE 402 A 1 HETATM 29 C C29 VYE . . . D 3 183.097 198.957 104.515 1 32.42 ? C29 VYE 402 A 1 HETATM 30 C C30 VYE . . . D 3 183.389 201.487 104.534 1 33.48 ? C30 VYE 402 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #