data_3VYE # _model_server_result.job_id gCdYG41vslGIC1TYV39Efg _model_server_result.datetime_utc '2025-03-13 16:59:12' _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":"F","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 . . . F 3 159.578 236.201 71.438 1 50.37 ? C1 VYE 402 B 1 HETATM 2 C C2 VYE . . . F 3 159.921 235.312 70.233 1 48.62 ? C2 VYE 402 B 1 HETATM 3 N N3 VYE . . . F 3 160.367 233.964 70.593 1 48.52 ? N3 VYE 402 B 1 HETATM 4 C C4 VYE . . . F 3 159.373 233.293 71.427 1 50.93 ? C4 VYE 402 B 1 HETATM 5 C C5 VYE . . . F 3 159.144 234.06 72.731 1 53.41 ? C5 VYE 402 B 1 HETATM 6 C C6 VYE . . . F 3 158.699 235.492 72.48 1 51.64 ? C6 VYE 402 B 1 HETATM 7 N N7 VYE . . . F 3 158.325 233.332 73.698 1 54.22 ? N7 VYE 402 B 1 HETATM 8 C C8 VYE . . . F 3 156.894 233.503 73.676 1 56.08 ? C8 VYE 402 B 1 HETATM 9 C C9 VYE . . . F 3 156.231 232.186 74.05 1 59.54 ? C9 VYE 402 B 1 HETATM 10 N N10 VYE . . . F 3 156.822 231.532 75.099 1 60.31 ? N10 VYE 402 B 1 HETATM 11 C C11 VYE . . . F 3 158.002 232.093 75.796 1 56.47 ? C11 VYE 402 B 1 HETATM 12 C C12 VYE . . . F 3 158.916 233.046 74.992 1 54.12 ? C12 VYE 402 B 1 HETATM 13 O O13 VYE . . . F 3 155.249 231.767 73.446 1 60.46 ? O13 VYE 402 B 1 HETATM 14 C C14 VYE . . . F 3 160.285 232.393 74.79 1 53.27 ? C14 VYE 402 B 1 HETATM 15 C C15 VYE . . . F 3 159.083 234.348 75.76 1 51.82 ? C15 VYE 402 B 1 HETATM 16 C C16 VYE . . . F 3 156.304 230.322 75.517 1 64.03 ? C16 VYE 402 B 1 HETATM 17 C C17 VYE . . . F 3 155.585 230.181 76.691 1 67.01 ? C17 VYE 402 B 1 HETATM 18 C C18 VYE . . . F 3 155.066 228.961 77.096 1 67.27 ? C18 VYE 402 B 1 HETATM 19 C C19 VYE . . . F 3 155.286 227.846 76.299 1 68.09 ? C19 VYE 402 B 1 HETATM 20 C C20 VYE . . . F 3 156.007 227.965 75.109 1 68.29 ? C20 VYE 402 B 1 HETATM 21 C C21 VYE . . . F 3 156.521 229.205 74.72 1 65.98 ? C21 VYE 402 B 1 HETATM 22 CL CL1 VYE . . . F 3 155.315 231.574 77.683 1 72.09 ? CL1 VYE 402 B 1 HETATM 23 C C23 VYE . . . F 3 158.866 237.46 70.954 1 49.16 ? C23 VYE 402 B 1 HETATM 24 O O24 VYE . . . F 3 157.65 237.52 70.872 1 50.2 ? O24 VYE 402 B 1 HETATM 25 N N25 VYE . . . F 3 159.713 238.453 70.633 1 49.27 ? N25 VYE 402 B 1 HETATM 26 C C26 VYE . . . F 3 159.145 239.698 70.151 1 48.21 ? C26 VYE 402 B 1 HETATM 27 C C27 VYE . . . F 3 159.006 240.678 71.32 1 48.63 ? C27 VYE 402 B 1 HETATM 28 C C28 VYE . . . F 3 160.075 241.771 71.302 1 48.82 ? C28 VYE 402 B 1 HETATM 29 C C29 VYE . . . F 3 160.039 242.636 72.559 1 48.93 ? C29 VYE 402 B 1 HETATM 30 C C30 VYE . . . F 3 161.477 241.249 70.986 1 48.78 ? C30 VYE 402 B 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 30 #