data_4ZSD # _model_server_result.job_id j6iVffkgAHWbXk2yD4vTyA _model_server_result.datetime_utc '2024-11-14 23:32:20' _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 4zsd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4ZSD # _exptl.entry_id 4ZSD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 472.666 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-(4-aminobenzyl)-3-[(2S)-4-(methylsulfanyl)-1-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-1-oxobutan-2-yl]urea _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 4ZSD _cell.length_a 57.943 _cell.length_b 57.943 _cell.length_c 88.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZSD _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C24 H32 N4 O2 S2' _chem_comp.formula_weight 472.666 _chem_comp.id 7I6 _chem_comp.mon_nstd_flag . _chem_comp.name 1-(4-aminobenzyl)-3-[(2S)-4-(methylsulfanyl)-1-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-1-oxobutan-2-yl]urea _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 CAB SAW 7I6 sing 1 n n SAW CBB 7I6 sing 2 n n CAH CBB 7I6 doub 3 n y CAH CAF 7I6 sing 4 n y CBB CBC 7I6 sing 5 n y CAF CAG 7I6 doub 6 n y SD CG 7I6 sing 7 n n SD CE 7I6 sing 8 n n CBC CBE 7I6 sing 9 n n CBC CAI 7I6 doub 10 n y CBE CAQ 7I6 sing 11 n n CBE NBF 7I6 sing 12 n n OAD CAX 7I6 doub 13 n n CAQ CAN 7I6 sing 14 n n CAG CAI 7I6 sing 15 n y CG CB 7I6 sing 16 n n CAX N 7I6 sing 17 n n CAX NAT 7I6 sing 18 n n CA CB 7I6 sing 19 n n CA N 7I6 sing 20 n n CA C 7I6 sing 21 n n NAT CAP 7I6 sing 22 n n CAP CBA 7I6 sing 23 n n NBF C 7I6 sing 24 n n NBF CAS 7I6 sing 25 n n CAN CAS 7I6 sing 26 n n C O 7I6 doub 27 n n CBA CAM 7I6 doub 28 n y CBA CAL 7I6 sing 29 n y CAM CAK 7I6 sing 30 n y CAL CAJ 7I6 doub 31 n y CAK CAZ 7I6 doub 32 n y CAJ CAZ 7I6 sing 33 n y CAZ NAC 7I6 sing 34 n n CAB H1 7I6 sing 35 n n CAB H2 7I6 sing 36 n n CAB H3 7I6 sing 37 n n CAH H4 7I6 sing 38 n n CAF H5 7I6 sing 39 n n CAG H6 7I6 sing 40 n n CAI H7 7I6 sing 41 n n CBE H8 7I6 sing 42 n n CAQ H9 7I6 sing 43 n n CAQ H10 7I6 sing 44 n n CAN H11 7I6 sing 45 n n CAN H12 7I6 sing 46 n n CAS H13 7I6 sing 47 n n CAS H14 7I6 sing 48 n n CA H15 7I6 sing 49 n n CB H16 7I6 sing 50 n n CB H17 7I6 sing 51 n n CG H18 7I6 sing 52 n n CG H19 7I6 sing 53 n n CE H20 7I6 sing 54 n n CE H21 7I6 sing 55 n n CE H22 7I6 sing 56 n n N H23 7I6 sing 57 n n NAT H24 7I6 sing 58 n n CAP H25 7I6 sing 59 n n CAP H26 7I6 sing 60 n n CAL H27 7I6 sing 61 n n CAJ H28 7I6 sing 62 n n NAC H29 7I6 sing 63 n n NAC H30 7I6 sing 64 n n CAK H31 7I6 sing 65 n n CAM H32 7I6 sing 66 n n # _atom_sites.entry_id 4ZSD _atom_sites.fract_transf_matrix[1][1] 0.017258 _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] 0.017258 _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] 0.011291 _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 7I6 A 1 301 1 7I6 7I6 . C 3 HOH A 1 401 30 HOH HOH . C 3 HOH A 2 402 125 HOH HOH . C 3 HOH A 3 403 124 HOH HOH . C 3 HOH A 4 404 50 HOH HOH . C 3 HOH A 5 405 17 HOH HOH . C 3 HOH A 6 406 12 HOH HOH . C 3 HOH A 7 407 45 HOH HOH . C 3 HOH A 8 408 4 HOH HOH . C 3 HOH A 9 409 32 HOH HOH . C 3 HOH A 10 410 60 HOH HOH . C 3 HOH A 11 411 7 HOH HOH . C 3 HOH A 12 412 72 HOH HOH . C 3 HOH A 13 413 67 HOH HOH . C 3 HOH A 14 414 40 HOH HOH . C 3 HOH A 15 415 36 HOH HOH . C 3 HOH A 16 416 10 HOH HOH . C 3 HOH A 17 417 75 HOH HOH . C 3 HOH A 18 418 5 HOH HOH . C 3 HOH A 19 419 53 HOH HOH . C 3 HOH A 20 420 69 HOH HOH . C 3 HOH A 21 421 46 HOH HOH . C 3 HOH A 22 422 101 HOH HOH . C 3 HOH A 23 423 128 HOH HOH . C 3 HOH A 24 424 23 HOH HOH . C 3 HOH A 25 425 13 HOH HOH . C 3 HOH A 26 426 2 HOH HOH . C 3 HOH A 27 427 31 HOH HOH . C 3 HOH A 28 428 35 HOH HOH . C 3 HOH A 29 429 24 HOH HOH . C 3 HOH A 30 430 83 HOH HOH . C 3 HOH A 31 431 19 HOH HOH . C 3 HOH A 32 432 20 HOH HOH . C 3 HOH A 33 433 15 HOH HOH . C 3 HOH A 34 434 49 HOH HOH . C 3 HOH A 35 435 63 HOH HOH . C 3 HOH A 36 436 16 HOH HOH . C 3 HOH A 37 437 11 HOH HOH . C 3 HOH A 38 438 37 HOH HOH . C 3 HOH A 39 439 87 HOH HOH . C 3 HOH A 40 440 39 HOH HOH . C 3 HOH A 41 441 29 HOH HOH . C 3 HOH A 42 442 105 HOH HOH . C 3 HOH A 43 443 43 HOH HOH . C 3 HOH A 44 444 82 HOH HOH . C 3 HOH A 45 445 6 HOH HOH . C 3 HOH A 46 446 3 HOH HOH . C 3 HOH A 47 447 85 HOH HOH . C 3 HOH A 48 448 91 HOH HOH . C 3 HOH A 49 449 79 HOH HOH . C 3 HOH A 50 450 34 HOH HOH . C 3 HOH A 51 451 100 HOH HOH . C 3 HOH A 52 452 97 HOH HOH . C 3 HOH A 53 453 99 HOH HOH . C 3 HOH A 54 454 122 HOH HOH . C 3 HOH A 55 455 112 HOH HOH . C 3 HOH A 56 456 56 HOH HOH . C 3 HOH A 57 457 77 HOH HOH . C 3 HOH A 58 458 70 HOH HOH . C 3 HOH A 59 459 44 HOH HOH . C 3 HOH A 60 460 66 HOH HOH . C 3 HOH A 61 461 8 HOH HOH . C 3 HOH A 62 462 58 HOH HOH . C 3 HOH A 63 463 1 HOH HOH . C 3 HOH A 64 464 106 HOH HOH . C 3 HOH A 65 465 118 HOH HOH . C 3 HOH A 66 466 103 HOH HOH . C 3 HOH A 67 467 22 HOH HOH . C 3 HOH A 68 468 28 HOH HOH . C 3 HOH A 69 469 25 HOH HOH . C 3 HOH A 70 470 114 HOH HOH . C 3 HOH A 71 471 96 HOH HOH . C 3 HOH A 72 472 27 HOH HOH . C 3 HOH A 73 473 42 HOH HOH . C 3 HOH A 74 474 33 HOH HOH . C 3 HOH A 75 475 14 HOH HOH . C 3 HOH A 76 476 84 HOH HOH . C 3 HOH A 77 477 108 HOH HOH . C 3 HOH A 78 478 9 HOH HOH . C 3 HOH A 79 479 81 HOH HOH . C 3 HOH A 80 480 78 HOH HOH . C 3 HOH A 81 481 130 HOH HOH . C 3 HOH A 82 482 26 HOH HOH . C 3 HOH A 83 483 18 HOH HOH . C 3 HOH A 84 484 129 HOH HOH . C 3 HOH A 85 485 109 HOH HOH . C 3 HOH A 86 486 65 HOH HOH . C 3 HOH A 87 487 119 HOH HOH . C 3 HOH A 88 488 51 HOH HOH . C 3 HOH A 89 489 38 HOH HOH . C 3 HOH A 90 490 126 HOH HOH . C 3 HOH A 91 491 127 HOH HOH . C 3 HOH A 92 492 102 HOH HOH . C 3 HOH A 93 493 64 HOH HOH . C 3 HOH A 94 494 76 HOH HOH . C 3 HOH A 95 495 41 HOH HOH . C 3 HOH A 96 496 121 HOH HOH . C 3 HOH A 97 497 48 HOH HOH . C 3 HOH A 98 498 113 HOH HOH . C 3 HOH A 99 499 94 HOH HOH . C 3 HOH A 100 500 47 HOH HOH . C 3 HOH A 101 501 93 HOH HOH . C 3 HOH A 102 502 59 HOH HOH . C 3 HOH A 103 503 62 HOH HOH . C 3 HOH A 104 504 95 HOH HOH . C 3 HOH A 105 505 71 HOH HOH . C 3 HOH A 106 506 98 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 CAB 7I6 . . . B 2 6.341 35.537 79.167 0.7 22.74 ? CAB 7I6 301 A 1 HETATM 2 S SAW 7I6 . . . B 2 7.14 35.861 80.732 0.7 21.93 ? SAW 7I6 301 A 1 HETATM 3 C CBB 7I6 . . . B 2 5.834 35.656 82.003 0.7 21.62 ? CBB 7I6 301 A 1 HETATM 4 C CAH 7I6 . . . B 2 4.488 35.499 81.646 0.7 21.9 ? CAH 7I6 301 A 1 HETATM 5 C CAF 7I6 . . . B 2 3.509 35.357 82.626 0.7 21.87 ? CAF 7I6 301 A 1 HETATM 6 C CAG 7I6 . . . B 2 3.861 35.37 83.972 0.7 21.68 ? CAG 7I6 301 A 1 HETATM 7 C CAI 7I6 . . . B 2 5.195 35.527 84.337 0.7 21.23 ? CAI 7I6 301 A 1 HETATM 8 C CBC 7I6 . . . B 2 6.199 35.668 83.361 0.7 20.18 ? CBC 7I6 301 A 1 HETATM 9 C CBE 7I6 . . . B 2 7.571 35.846 83.712 0.7 19.14 ? CBE 7I6 301 A 1 HETATM 10 C CAQ 7I6 . . . B 2 7.918 37.336 83.776 0.7 18.59 ? CAQ 7I6 301 A 1 HETATM 11 C CAN 7I6 . . . B 2 7.528 37.739 85.137 0.7 18.64 ? CAN 7I6 301 A 1 HETATM 12 C CAS 7I6 . . . B 2 8.171 36.654 85.926 0.7 18.39 ? CAS 7I6 301 A 1 HETATM 13 N NBF 7I6 . . . B 2 7.981 35.403 85.072 0.7 18.33 ? NBF 7I6 301 A 1 HETATM 14 C C 7I6 . . . B 2 8.278 34.17 85.54 0.7 17.25 ? C 7I6 301 A 1 HETATM 15 O O 7I6 . . . B 2 8.633 33.994 86.687 0.7 13.29 ? O 7I6 301 A 1 HETATM 16 C CA 7I6 . . . B 2 8.142 32.938 84.622 0.7 19.08 ? CA 7I6 301 A 1 HETATM 17 C CB 7I6 . . . B 2 6.817 32.247 84.929 0.7 21.08 ? CB 7I6 301 A 1 HETATM 18 C CG 7I6 . . . B 2 6.759 30.996 84.052 0.7 24.22 ? CG 7I6 301 A 1 HETATM 19 S SD 7I6 . . . B 2 6.189 31.43 82.366 0.4 29.38 ? SD 7I6 301 A 1 HETATM 20 C CE 7I6 . . . B 2 4.434 31.578 82.614 0.4 27.02 ? CE 7I6 301 A 1 HETATM 21 N N 7I6 . . . B 2 9.294 32.001 84.846 0.7 17.87 ? N 7I6 301 A 1 HETATM 22 C CAX 7I6 . . . B 2 10.525 32.177 84.29 0.7 18.23 ? CAX 7I6 301 A 1 HETATM 23 O OAD 7I6 . . . B 2 10.732 33.167 83.596 0.7 19 ? OAD 7I6 301 A 1 HETATM 24 N NAT 7I6 . . . B 2 11.57 31.316 84.515 0.7 19.6 ? NAT 7I6 301 A 1 HETATM 25 C CAP 7I6 . . . B 2 11.521 30.044 85.223 0.7 19.11 ? CAP 7I6 301 A 1 HETATM 26 C CBA 7I6 . . . B 2 12.159 30.032 86.489 0.7 18.31 ? CBA 7I6 301 A 1 HETATM 27 C CAL 7I6 . . . B 2 11.973 31.061 87.416 0.7 17.73 ? CAL 7I6 301 A 1 HETATM 28 C CAJ 7I6 . . . B 2 12.578 31 88.673 0.7 16.93 ? CAJ 7I6 301 A 1 HETATM 29 C CAZ 7I6 . . . B 2 13.358 29.913 89.048 0.7 17.55 ? CAZ 7I6 301 A 1 HETATM 30 N NAC 7I6 . . . B 2 13.908 29.88 90.257 0.7 18.01 ? NAC 7I6 301 A 1 HETATM 31 C CAK 7I6 . . . B 2 13.541 28.869 88.138 0.7 17.84 ? CAK 7I6 301 A 1 HETATM 32 C CAM 7I6 . . . B 2 12.943 28.925 86.875 0.7 18.84 ? CAM 7I6 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #