data_1YYY # _model_server_result.job_id Qt5D7mbZ6Ccfj0JOyhHjkQ _model_server_result.datetime_utc '2024-10-12 16:30:58' _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 1yyy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 1YYY # _exptl.entry_id 1YYY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.618 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3S)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide _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 1YYY _cell.length_a 63.76 _cell.length_b 63.14 _cell.length_c 69.29 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YYY _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 _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 C _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 7 1 CYS 22 1_555 A SG CYS 137 1 CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? disulf ? disulf2 A SG CYS 25 1 CYS 42 1_555 A SG CYS 41 1 CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf3 A SG CYS 109 1 CYS 128 1_555 A SG CYS 210 1 CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf4 A SG CYS 116 1 CYS 136 1_555 A SG CYS 183 1 CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? disulf ? disulf5 A SG CYS 148 1 CYS 168 1_555 A SG CYS 162 1 CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 A SG CYS 173 1 CYS 191 1_555 A SG CYS 197 1 CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc1 A OE1 GLU 52 1 GLU 70 1_555 B CA CA . 1 CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc2 A O ASN 54 1 ASN 72 1_555 B CA CA . 1 CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc3 A O VAL 57 1 VAL 75 1_555 B CA CA . 1 CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc4 A OE2 GLU 62 1 GLU 80 1_555 B CA CA . 1 CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc5 D O HOH . 1 HOH 409 1_555 B CA CA . 1 CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc6 D O HOH . 1 HOH 574 1_555 B CA CA . 1 CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? # _chem_comp.formula 'C23 H34 N6 O5 S' _chem_comp.formula_weight 506.618 _chem_comp.id 0KV _chem_comp.mon_nstd_flag . _chem_comp.name 2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3S)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms CVS1695 # _atom_sites.entry_id 1YYY _atom_sites.fract_transf_matrix[1][1] 0.015684 _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] 0.015838 _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] 0.014432 _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 CA 1 1 701 701 CA CA . C 3 0KV 1 1 1 1 0KV 0IV . D 4 HOH 1 1 401 401 HOH HOH . D 4 HOH 1 2 402 402 HOH HOH . D 4 HOH 1 3 403 403 HOH HOH . D 4 HOH 1 4 404 404 HOH HOH . D 4 HOH 1 5 405 405 HOH HOH . D 4 HOH 1 6 406 406 HOH HOH . D 4 HOH 1 7 407 407 HOH HOH . D 4 HOH 1 8 408 408 HOH HOH . D 4 HOH 1 9 409 409 HOH HOH . D 4 HOH 1 10 410 410 HOH HOH . D 4 HOH 1 11 411 411 HOH HOH . D 4 HOH 1 12 412 412 HOH HOH . D 4 HOH 1 13 413 413 HOH HOH . D 4 HOH 1 14 414 414 HOH HOH . D 4 HOH 1 15 415 415 HOH HOH . D 4 HOH 1 16 416 416 HOH HOH . D 4 HOH 1 17 417 417 HOH HOH . D 4 HOH 1 18 418 418 HOH HOH . D 4 HOH 1 19 419 419 HOH HOH . D 4 HOH 1 20 420 420 HOH HOH . D 4 HOH 1 21 421 421 HOH HOH . D 4 HOH 1 22 422 422 HOH HOH . D 4 HOH 1 23 423 423 HOH HOH . D 4 HOH 1 24 424 424 HOH HOH . D 4 HOH 1 25 425 425 HOH HOH . D 4 HOH 1 26 426 426 HOH HOH . D 4 HOH 1 27 427 427 HOH HOH . D 4 HOH 1 28 428 428 HOH HOH . D 4 HOH 1 29 429 429 HOH HOH . D 4 HOH 1 30 430 430 HOH HOH . D 4 HOH 1 31 431 431 HOH HOH . D 4 HOH 1 32 432 432 HOH HOH . D 4 HOH 1 33 433 433 HOH HOH . D 4 HOH 1 34 434 434 HOH HOH . D 4 HOH 1 35 435 435 HOH HOH . D 4 HOH 1 36 436 436 HOH HOH . D 4 HOH 1 37 437 437 HOH HOH . D 4 HOH 1 38 438 438 HOH HOH . D 4 HOH 1 39 439 439 HOH HOH . D 4 HOH 1 40 440 440 HOH HOH . D 4 HOH 1 41 441 441 HOH HOH . D 4 HOH 1 42 442 442 HOH HOH . D 4 HOH 1 43 443 443 HOH HOH . D 4 HOH 1 44 444 444 HOH HOH . D 4 HOH 1 45 445 445 HOH HOH . D 4 HOH 1 46 446 446 HOH HOH . D 4 HOH 1 47 447 447 HOH HOH . D 4 HOH 1 48 448 448 HOH HOH . D 4 HOH 1 49 449 449 HOH HOH . D 4 HOH 1 50 451 451 HOH HOH . D 4 HOH 1 51 452 452 HOH HOH . D 4 HOH 1 52 453 453 HOH HOH . D 4 HOH 1 53 454 454 HOH HOH . D 4 HOH 1 54 455 455 HOH HOH . D 4 HOH 1 55 456 456 HOH HOH . D 4 HOH 1 56 457 457 HOH HOH . D 4 HOH 1 57 458 458 HOH HOH . D 4 HOH 1 58 460 460 HOH HOH . D 4 HOH 1 59 461 461 HOH HOH . D 4 HOH 1 60 462 462 HOH HOH . D 4 HOH 1 61 463 463 HOH HOH . D 4 HOH 1 62 464 464 HOH HOH . D 4 HOH 1 63 466 466 HOH HOH . D 4 HOH 1 64 467 467 HOH HOH . D 4 HOH 1 65 468 468 HOH HOH . D 4 HOH 1 66 469 469 HOH HOH . D 4 HOH 1 67 470 470 HOH HOH . D 4 HOH 1 68 471 471 HOH HOH . D 4 HOH 1 69 473 473 HOH HOH . D 4 HOH 1 70 474 474 HOH HOH . D 4 HOH 1 71 475 475 HOH HOH . D 4 HOH 1 72 476 476 HOH HOH . D 4 HOH 1 73 478 478 HOH HOH . D 4 HOH 1 74 481 481 HOH HOH . D 4 HOH 1 75 483 483 HOH HOH . D 4 HOH 1 76 486 486 HOH HOH . D 4 HOH 1 77 487 487 HOH HOH . D 4 HOH 1 78 490 490 HOH HOH . D 4 HOH 1 79 491 491 HOH HOH . D 4 HOH 1 80 493 493 HOH HOH . D 4 HOH 1 81 494 494 HOH HOH . D 4 HOH 1 82 496 496 HOH HOH . D 4 HOH 1 83 497 497 HOH HOH . D 4 HOH 1 84 498 498 HOH HOH . D 4 HOH 1 85 499 499 HOH HOH . D 4 HOH 1 86 500 500 HOH HOH . D 4 HOH 1 87 501 501 HOH HOH . D 4 HOH 1 88 502 502 HOH HOH . D 4 HOH 1 89 503 503 HOH HOH . D 4 HOH 1 90 504 504 HOH HOH . D 4 HOH 1 91 505 505 HOH HOH . D 4 HOH 1 92 506 506 HOH HOH . D 4 HOH 1 93 507 507 HOH HOH . D 4 HOH 1 94 508 508 HOH HOH . D 4 HOH 1 95 509 509 HOH HOH . D 4 HOH 1 96 510 510 HOH HOH . D 4 HOH 1 97 511 511 HOH HOH . D 4 HOH 1 98 512 512 HOH HOH . D 4 HOH 1 99 514 514 HOH HOH . D 4 HOH 1 100 515 515 HOH HOH . D 4 HOH 1 101 516 516 HOH HOH . D 4 HOH 1 102 517 517 HOH HOH . D 4 HOH 1 103 521 521 HOH HOH . D 4 HOH 1 104 522 522 HOH HOH . D 4 HOH 1 105 525 525 HOH HOH . D 4 HOH 1 106 526 526 HOH HOH . D 4 HOH 1 107 527 527 HOH HOH . D 4 HOH 1 108 528 528 HOH HOH . D 4 HOH 1 109 530 530 HOH HOH . D 4 HOH 1 110 532 532 HOH HOH . D 4 HOH 1 111 534 534 HOH HOH . D 4 HOH 1 112 535 535 HOH HOH . D 4 HOH 1 113 536 536 HOH HOH . D 4 HOH 1 114 539 539 HOH HOH . D 4 HOH 1 115 540 540 HOH HOH . D 4 HOH 1 116 541 541 HOH HOH . D 4 HOH 1 117 542 542 HOH HOH . D 4 HOH 1 118 547 547 HOH HOH . D 4 HOH 1 119 550 550 HOH HOH . D 4 HOH 1 120 553 553 HOH HOH . D 4 HOH 1 121 554 554 HOH HOH . D 4 HOH 1 122 555 555 HOH HOH . D 4 HOH 1 123 556 556 HOH HOH . D 4 HOH 1 124 558 558 HOH HOH . D 4 HOH 1 125 559 559 HOH HOH . D 4 HOH 1 126 561 561 HOH HOH . D 4 HOH 1 127 562 562 HOH HOH . D 4 HOH 1 128 567 567 HOH HOH . D 4 HOH 1 129 569 569 HOH HOH . D 4 HOH 1 130 570 570 HOH HOH . D 4 HOH 1 131 573 573 HOH HOH . D 4 HOH 1 132 574 574 HOH HOH . D 4 HOH 1 133 576 576 HOH HOH . D 4 HOH 1 134 577 577 HOH HOH . D 4 HOH 1 135 583 583 HOH HOH . D 4 HOH 1 136 584 584 HOH HOH . D 4 HOH 1 137 585 585 HOH HOH . D 4 HOH 1 138 587 587 HOH HOH . D 4 HOH 1 139 588 588 HOH HOH . D 4 HOH 1 140 589 589 HOH HOH . D 4 HOH 1 141 591 591 HOH HOH . D 4 HOH 1 142 592 592 HOH HOH . D 4 HOH 1 143 594 594 HOH HOH . D 4 HOH 1 144 595 595 HOH HOH . D 4 HOH 1 145 596 596 HOH HOH . D 4 HOH 1 146 598 598 HOH HOH . D 4 HOH 1 147 602 602 HOH HOH . D 4 HOH 1 148 603 603 HOH HOH . D 4 HOH 1 149 610 610 HOH HOH . D 4 HOH 1 150 612 612 HOH HOH . D 4 HOH 1 151 614 614 HOH HOH . D 4 HOH 1 152 617 617 HOH HOH . D 4 HOH 1 153 623 623 HOH HOH . D 4 HOH 1 154 626 626 HOH HOH . D 4 HOH 1 155 627 627 HOH HOH . D 4 HOH 1 156 634 634 HOH HOH . D 4 HOH 1 157 644 644 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 S S 0KV . . . C 3 24.117 5.695 29.969 1 54.72 ? S 0KV 1 1 1 HETATM 2 O O1S 0KV . . . C 3 23.224 6.185 28.923 1 52.77 ? O1S 0KV 1 1 1 HETATM 3 O O2S 0KV . . . C 3 23.372 4.965 30.993 1 54.1 ? O2S 0KV 1 1 1 HETATM 4 N N1 0KV . . . C 3 25.207 4.636 29.261 1 50.31 ? N1 0KV 1 1 1 HETATM 5 C C1 0KV . . . C 3 24.516 2.217 29.508 1 33.99 ? C1 0KV 1 1 1 HETATM 6 O O1 0KV . . . C 3 23.777 2.406 28.531 1 31.35 ? O1 0KV 1 1 1 HETATM 7 C CA1 0KV . . . C 3 25.608 3.334 29.673 1 42.73 ? CA1 0KV 1 1 1 HETATM 8 C CB1 0KV . . . C 3 26.163 3.397 31.071 1 39.28 ? CB1 0KV 1 1 1 HETATM 9 C CD1 0KV . . . C 3 25.227 1.082 31.616 1 30.81 ? CD1 0KV 1 1 1 HETATM 10 C CG1 0KV . . . C 3 26.384 2.051 31.714 1 39.38 ? CG1 0KV 1 1 1 HETATM 11 C C2 0KV . . . C 3 22.361 0.952 30.366 1 31.06 ? C2 0KV 1 1 1 HETATM 12 N N2 0KV . . . C 3 24.55 1.128 30.295 1 32.96 ? N2 0KV 1 1 1 HETATM 13 O O2 0KV . . . C 3 22.155 1.388 31.546 1 31.42 ? O2 0KV 1 1 1 HETATM 14 C CA2 0KV . . . C 3 23.556 0.065 29.941 1 30.92 ? CA2 0KV 1 1 1 HETATM 15 C C3 0KV . . . C 3 19.52 -0.646 31.047 1 29.54 ? C3 0KV 1 1 1 HETATM 16 N N3 0KV . . . C 3 21.421 0.237 29.593 1 28.8 ? N3 0KV 1 1 1 HETATM 17 O O3 0KV . . . C 3 18.096 -0.575 31.173 1 30.86 ? O3 0KV 1 1 1 HETATM 18 C C4 0KV . . . C 3 19.721 3.355 29.027 1 26.89 ? C4 0KV 1 1 1 HETATM 19 C C5 0KV . . . C 3 20.438 4.623 28.446 1 27.33 ? C5 0KV 1 1 1 HETATM 20 C C6 0KV . . . C 3 21.277 4.267 27.206 1 27.52 ? C6 0KV 1 1 1 HETATM 21 C CA3 0KV . . . C 3 20.027 0.437 30.099 1 29.14 ? CA3 0KV 1 1 1 HETATM 22 C CB3 0KV . . . C 3 19.123 0.878 28.904 1 28.32 ? CB3 0KV 1 1 1 HETATM 23 C CD3 0KV . . . C 3 20.102 2.022 26.753 1 27.16 ? CD3 0KV 1 1 1 HETATM 24 N NE3 0KV . . . C 3 20.48 3.389 26.255 1 26.58 ? NE3 0KV 1 1 1 HETATM 25 C CG3 0KV . . . C 3 19.966 2.022 28.283 1 27.56 ? CG3 0KV 1 1 1 HETATM 26 C CZ3 0KV . . . C 3 20.021 3.861 24.959 1 26.77 ? CZ3 0KV 1 1 1 HETATM 27 N NH1 0KV . . . C 3 20.221 5.119 24.63 1 25.8 ? NH1 0KV 1 1 1 HETATM 28 N NH2 0KV . . . C 3 19.428 2.997 24.184 1 25.3 ? NH2 0KV 1 1 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #