data_5NYH # _model_server_result.job_id L3u5M--5_OkQfcDYuCXC7g _model_server_result.datetime_utc '2025-07-14 15:45:07' _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 5nyh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5NYH # _exptl.entry_id 5NYH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 449.502 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}-methyl-~{N}-(4-morpholin-4-ylphenyl)-6-oxidanyl-3-pyrrolidin-1-ylcarbonyl-2~{H}-indazole-5-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 5NYH _cell.length_a 69.979 _cell.length_b 88.54 _cell.length_c 97.091 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NYH _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 1,2 # 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' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 88.54 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 H27 N5 O4' _chem_comp.formula_weight 449.502 _chem_comp.id 9EK _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}-methyl-~{N}-(4-morpholin-4-ylphenyl)-6-oxidanyl-3-pyrrolidin-1-ylcarbonyl-2~{H}-indazole-5-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 C27 N2 9EK sing 1 n n O3 C1 9EK doub 2 n n N2 C1 9EK sing 3 n n N2 C21 9EK sing 4 n n C1 C4 9EK sing 5 n n C22 C21 9EK doub 6 n y C22 C25 9EK sing 7 n y C21 C26 9EK sing 8 n y C4 C5 9EK doub 9 n y C4 C7 9EK sing 10 n y O8 C7 9EK sing 11 n n C25 C23 9EK doub 12 n y C18 C17 9EK sing 13 n n C18 C19 9EK sing 14 n n C5 C10 9EK sing 15 n y C7 C6 9EK doub 16 n y C26 C24 9EK doub 17 n y C17 C16 9EK sing 18 n n C19 N15 9EK sing 19 n n C23 C24 9EK sing 20 n y C23 N28 9EK sing 21 n n C16 N15 9EK sing 22 n n N15 C14 9EK sing 23 n n C10 C9 9EK sing 24 n y C10 C11 9EK doub 25 n y C6 C9 9EK sing 26 n y C29 N28 9EK sing 27 n n C29 C30 9EK sing 28 n n N28 C33 9EK sing 29 n n C9 N13 9EK doub 30 n y C14 C11 9EK sing 31 n n C14 O20 9EK doub 32 n n C11 N12 9EK sing 33 n y C30 O31 9EK sing 34 n n C33 C32 9EK sing 35 n n N13 N12 9EK sing 36 n y O31 C32 9EK sing 37 n n C16 H1 9EK sing 38 n n C16 H2 9EK sing 39 n n C19 H3 9EK sing 40 n n C19 H4 9EK sing 41 n n C22 H5 9EK sing 42 n n C24 H6 9EK sing 43 n n C27 H7 9EK sing 44 n n C27 H8 9EK sing 45 n n C27 H9 9EK sing 46 n n C30 H10 9EK sing 47 n n C30 H11 9EK sing 48 n n C32 H12 9EK sing 49 n n C32 H13 9EK sing 50 n n C33 H14 9EK sing 51 n n C33 H15 9EK sing 52 n n C5 H16 9EK sing 53 n n C6 H17 9EK sing 54 n n O8 H18 9EK sing 55 n n N12 H19 9EK sing 56 n n C17 H20 9EK sing 57 n n C17 H21 9EK sing 58 n n C18 H22 9EK sing 59 n n C18 H23 9EK sing 60 n n C25 H24 9EK sing 61 n n C26 H25 9EK sing 62 n n C29 H26 9EK sing 63 n n C29 H27 9EK sing 64 n n # _atom_sites.entry_id 5NYH _atom_sites.fract_transf_matrix[1][1] 0.01429 _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] 0.011294 _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] 0.0103 _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 9EK A 1 301 1 9EK INH . C 3 HOH A 1 401 88 HOH HOH . C 3 HOH A 2 402 201 HOH HOH . C 3 HOH A 3 403 199 HOH HOH . C 3 HOH A 4 404 189 HOH HOH . C 3 HOH A 5 405 70 HOH HOH . C 3 HOH A 6 406 190 HOH HOH . C 3 HOH A 7 407 198 HOH HOH . C 3 HOH A 8 408 51 HOH HOH . C 3 HOH A 9 409 37 HOH HOH . C 3 HOH A 10 410 10 HOH HOH . C 3 HOH A 11 411 166 HOH HOH . C 3 HOH A 12 412 90 HOH HOH . C 3 HOH A 13 413 24 HOH HOH . C 3 HOH A 14 414 185 HOH HOH . C 3 HOH A 15 415 5 HOH HOH . C 3 HOH A 16 416 27 HOH HOH . C 3 HOH A 17 417 36 HOH HOH . C 3 HOH A 18 418 7 HOH HOH . C 3 HOH A 19 419 128 HOH HOH . C 3 HOH A 20 420 54 HOH HOH . C 3 HOH A 21 421 159 HOH HOH . C 3 HOH A 22 422 44 HOH HOH . C 3 HOH A 23 423 35 HOH HOH . C 3 HOH A 24 424 19 HOH HOH . C 3 HOH A 25 425 130 HOH HOH . C 3 HOH A 26 426 50 HOH HOH . C 3 HOH A 27 427 206 HOH HOH . C 3 HOH A 28 428 49 HOH HOH . C 3 HOH A 29 429 12 HOH HOH . C 3 HOH A 30 430 89 HOH HOH . C 3 HOH A 31 431 193 HOH HOH . C 3 HOH A 32 432 179 HOH HOH . C 3 HOH A 33 433 14 HOH HOH . C 3 HOH A 34 434 191 HOH HOH . C 3 HOH A 35 435 94 HOH HOH . C 3 HOH A 36 436 43 HOH HOH . C 3 HOH A 37 437 15 HOH HOH . C 3 HOH A 38 438 25 HOH HOH . C 3 HOH A 39 439 186 HOH HOH . C 3 HOH A 40 440 111 HOH HOH . C 3 HOH A 41 441 207 HOH HOH . C 3 HOH A 42 442 23 HOH HOH . C 3 HOH A 43 443 153 HOH HOH . C 3 HOH A 44 444 196 HOH HOH . C 3 HOH A 45 445 203 HOH HOH . C 3 HOH A 46 446 187 HOH HOH . C 3 HOH A 47 447 64 HOH HOH . C 3 HOH A 48 448 100 HOH HOH . C 3 HOH A 49 449 152 HOH HOH . C 3 HOH A 50 450 95 HOH HOH . C 3 HOH A 51 451 163 HOH HOH . C 3 HOH A 52 452 17 HOH HOH . C 3 HOH A 53 453 39 HOH HOH . C 3 HOH A 54 454 11 HOH HOH . C 3 HOH A 55 455 180 HOH HOH . C 3 HOH A 56 456 76 HOH HOH . C 3 HOH A 57 457 55 HOH HOH . C 3 HOH A 58 458 83 HOH HOH . C 3 HOH A 59 459 99 HOH HOH . C 3 HOH A 60 460 151 HOH HOH . C 3 HOH A 61 461 2 HOH HOH . C 3 HOH A 62 462 66 HOH HOH . C 3 HOH A 63 463 71 HOH HOH . C 3 HOH A 64 464 110 HOH HOH . C 3 HOH A 65 465 208 HOH HOH . C 3 HOH A 66 466 192 HOH HOH . C 3 HOH A 67 467 107 HOH HOH . C 3 HOH A 68 468 133 HOH HOH . C 3 HOH A 69 469 29 HOH HOH . C 3 HOH A 70 470 73 HOH HOH . C 3 HOH A 71 471 3 HOH HOH . C 3 HOH A 72 472 6 HOH HOH . C 3 HOH A 73 473 26 HOH HOH . C 3 HOH A 74 474 147 HOH HOH . C 3 HOH A 75 475 92 HOH HOH . C 3 HOH A 76 476 112 HOH HOH . C 3 HOH A 77 477 57 HOH HOH . C 3 HOH A 78 478 20 HOH HOH . C 3 HOH A 79 479 52 HOH HOH . C 3 HOH A 80 480 176 HOH HOH . C 3 HOH A 81 481 121 HOH HOH . C 3 HOH A 82 482 154 HOH HOH . C 3 HOH A 83 483 45 HOH HOH . C 3 HOH A 84 484 146 HOH HOH . C 3 HOH A 85 485 65 HOH HOH . C 3 HOH A 86 486 144 HOH HOH . C 3 HOH A 87 487 161 HOH HOH . C 3 HOH A 88 488 30 HOH HOH . C 3 HOH A 89 489 85 HOH HOH . C 3 HOH A 90 490 40 HOH HOH . C 3 HOH A 91 491 1 HOH HOH . C 3 HOH A 92 492 172 HOH HOH . C 3 HOH A 93 493 79 HOH HOH . C 3 HOH A 94 494 87 HOH HOH . C 3 HOH A 95 495 74 HOH HOH . C 3 HOH A 96 496 122 HOH HOH . C 3 HOH A 97 497 98 HOH HOH . C 3 HOH A 98 498 114 HOH HOH . C 3 HOH A 99 499 56 HOH HOH . C 3 HOH A 100 500 91 HOH HOH . C 3 HOH A 101 501 165 HOH HOH . C 3 HOH A 102 502 138 HOH HOH . C 3 HOH A 103 503 13 HOH HOH . C 3 HOH A 104 504 9 HOH HOH . C 3 HOH A 105 505 183 HOH HOH . C 3 HOH A 106 506 67 HOH HOH . C 3 HOH A 107 507 59 HOH HOH . C 3 HOH A 108 508 200 HOH HOH . C 3 HOH A 109 509 72 HOH HOH . C 3 HOH A 110 510 106 HOH HOH . C 3 HOH A 111 511 197 HOH HOH . C 3 HOH A 112 512 205 HOH HOH . C 3 HOH A 113 513 58 HOH HOH . C 3 HOH A 114 514 22 HOH HOH . C 3 HOH A 115 515 4 HOH HOH . C 3 HOH A 116 516 38 HOH HOH . C 3 HOH A 117 517 78 HOH HOH . C 3 HOH A 118 518 170 HOH HOH . C 3 HOH A 119 519 47 HOH HOH . C 3 HOH A 120 520 60 HOH HOH . C 3 HOH A 121 521 32 HOH HOH . C 3 HOH A 122 522 204 HOH HOH . C 3 HOH A 123 523 104 HOH HOH . C 3 HOH A 124 524 18 HOH HOH . C 3 HOH A 125 525 142 HOH HOH . C 3 HOH A 126 526 77 HOH HOH . C 3 HOH A 127 527 118 HOH HOH . C 3 HOH A 128 528 42 HOH HOH . C 3 HOH A 129 529 53 HOH HOH . C 3 HOH A 130 530 116 HOH HOH . C 3 HOH A 131 531 131 HOH HOH . C 3 HOH A 132 532 16 HOH HOH . C 3 HOH A 133 533 119 HOH HOH . C 3 HOH A 134 534 81 HOH HOH . C 3 HOH A 135 535 75 HOH HOH . C 3 HOH A 136 536 124 HOH HOH . C 3 HOH A 137 537 136 HOH HOH . C 3 HOH A 138 538 8 HOH HOH . C 3 HOH A 139 539 21 HOH HOH . C 3 HOH A 140 540 28 HOH HOH . C 3 HOH A 141 541 46 HOH HOH . C 3 HOH A 142 542 123 HOH HOH . C 3 HOH A 143 543 97 HOH HOH . C 3 HOH A 144 544 169 HOH HOH . C 3 HOH A 145 545 160 HOH HOH . C 3 HOH A 146 546 82 HOH HOH . C 3 HOH A 147 547 69 HOH HOH . C 3 HOH A 148 548 84 HOH HOH . C 3 HOH A 149 549 62 HOH HOH . C 3 HOH A 150 550 41 HOH HOH . C 3 HOH A 151 551 195 HOH HOH . C 3 HOH A 152 552 31 HOH HOH . C 3 HOH A 153 553 132 HOH HOH . C 3 HOH A 154 554 34 HOH HOH . C 3 HOH A 155 555 129 HOH HOH . C 3 HOH A 156 556 115 HOH HOH . C 3 HOH A 157 557 63 HOH HOH . C 3 HOH A 158 558 113 HOH HOH . C 3 HOH A 159 559 210 HOH HOH . C 3 HOH A 160 560 141 HOH HOH . C 3 HOH A 161 561 157 HOH HOH . C 3 HOH A 162 562 93 HOH HOH . C 3 HOH A 163 563 105 HOH HOH . C 3 HOH A 164 564 48 HOH HOH . C 3 HOH A 165 565 143 HOH HOH . C 3 HOH A 166 566 184 HOH HOH . C 3 HOH A 167 567 101 HOH HOH . C 3 HOH A 168 568 125 HOH HOH . C 3 HOH A 169 569 117 HOH HOH . C 3 HOH A 170 570 103 HOH HOH . C 3 HOH A 171 571 149 HOH HOH . C 3 HOH A 172 572 126 HOH HOH . C 3 HOH A 173 573 174 HOH HOH . C 3 HOH A 174 574 135 HOH HOH . C 3 HOH A 175 575 127 HOH HOH . C 3 HOH A 176 576 171 HOH HOH . C 3 HOH A 177 577 156 HOH HOH . C 3 HOH A 178 578 167 HOH HOH . C 3 HOH A 179 579 175 HOH HOH . C 3 HOH A 180 580 80 HOH HOH . C 3 HOH A 181 581 61 HOH HOH . C 3 HOH A 182 582 162 HOH HOH . C 3 HOH A 183 583 96 HOH HOH . C 3 HOH A 184 584 181 HOH HOH . C 3 HOH A 185 585 33 HOH HOH . C 3 HOH A 186 586 134 HOH HOH . C 3 HOH A 187 587 68 HOH HOH . C 3 HOH A 188 588 120 HOH HOH . C 3 HOH A 189 589 202 HOH HOH . C 3 HOH A 190 590 148 HOH HOH . C 3 HOH A 191 591 173 HOH HOH . C 3 HOH A 192 592 86 HOH HOH . C 3 HOH A 193 593 139 HOH HOH . C 3 HOH A 194 594 168 HOH HOH . C 3 HOH A 195 595 164 HOH HOH . C 3 HOH A 196 596 102 HOH HOH . C 3 HOH A 197 597 140 HOH HOH . C 3 HOH A 198 598 155 HOH HOH . C 3 HOH A 199 599 109 HOH HOH . C 3 HOH A 200 600 178 HOH HOH . C 3 HOH A 201 601 182 HOH HOH . C 3 HOH A 202 602 145 HOH HOH . C 3 HOH A 203 603 158 HOH HOH . C 3 HOH A 204 604 108 HOH HOH . C 3 HOH A 205 605 137 HOH HOH . C 3 HOH A 206 606 188 HOH HOH . C 3 HOH A 207 607 209 HOH HOH . C 3 HOH A 208 608 194 HOH HOH . C 3 HOH A 209 609 177 HOH HOH . C 3 HOH A 210 610 150 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 9EK . . . B 2 -0.162 33.711 21.793 1 25.15 ? C1 9EK 301 A 1 HETATM 2 C C7 9EK . . . B 2 -1.296 32.664 23.775 1 24.4 ? C7 9EK 301 A 1 HETATM 3 C C9 9EK . . . B 2 -0.05 31.807 25.615 1 22.51 ? C9 9EK 301 A 1 HETATM 4 C C10 9EK . . . B 2 1.158 32.135 24.981 1 24.37 ? C10 9EK 301 A 1 HETATM 5 C C11 9EK . . . B 2 2.213 31.77 25.908 1 24.42 ? C11 9EK 301 A 1 HETATM 6 C C14 9EK . . . B 2 3.672 32.049 25.696 1 25.06 ? C14 9EK 301 A 1 HETATM 7 C C16 9EK . . . B 2 5.819 31.403 24.635 1 28.84 ? C16 9EK 301 A 1 HETATM 8 C C19 9EK . . . B 2 3.889 29.985 24.345 1 27.65 ? C19 9EK 301 A 1 HETATM 9 C C21 9EK . . . B 2 1.217 35.57 22.679 1 24.15 ? C21 9EK 301 A 1 HETATM 10 C C22 9EK . . . B 2 2.566 35.792 22.52 1 24.45 ? C22 9EK 301 A 1 HETATM 11 C C24 9EK . . . B 2 1.283 36.785 24.747 1 26.2 ? C24 9EK 301 A 1 HETATM 12 C C27 9EK . . . B 2 0.396 35.585 20.368 1 23.75 ? C27 9EK 301 A 1 HETATM 13 C C30 9EK . . . B 2 5.369 38.971 26.205 1 37.03 ? C30 9EK 301 A 1 HETATM 14 C C32 9EK . . . B 2 3.711 38.649 27.79 1 38.82 ? C32 9EK 301 A 1 HETATM 15 C C33 9EK . . . B 2 2.703 38.208 26.759 1 36.97 ? C33 9EK 301 A 1 HETATM 16 N N2 9EK . . . B 2 0.469 34.906 21.652 1 24.32 ? N2 9EK 301 A 1 HETATM 17 O O3 9EK . . . B 2 -0.798 33.215 20.895 1 23.5 ? O3 9EK 301 A 1 HETATM 18 C C4 9EK . . . B 2 -0.099 33.02 23.124 1 25.65 ? C4 9EK 301 A 1 HETATM 19 C C5 9EK . . . B 2 1.123 32.736 23.73 1 24.6 ? C5 9EK 301 A 1 HETATM 20 C C6 9EK . . . B 2 -1.278 32.058 25.021 1 24.94 ? C6 9EK 301 A 1 HETATM 21 O O8 9EK . . . B 2 -2.484 32.9 23.181 1 22 ? O8 9EK 301 A 1 HETATM 22 N N12 9EK . . . B 2 1.623 31.252 26.993 1 26.13 ? N12 9EK 301 A 1 HETATM 23 N N13 9EK . . . B 2 0.284 31.284 26.816 1 24.5 ? N13 9EK 301 A 1 HETATM 24 N N15 9EK . . . B 2 4.401 31.215 24.944 1 26.7 ? N15 9EK 301 A 1 HETATM 25 C C17 9EK . . . B 2 6.242 30.061 24.1 1 29.8 ? C17 9EK 301 A 1 HETATM 26 C C18 9EK . . . B 2 5.047 29.469 23.532 1 27.05 ? C18 9EK 301 A 1 HETATM 27 O O20 9EK . . . B 2 4.138 33.02 26.243 1 25.69 ? O20 9EK 301 A 1 HETATM 28 C C23 9EK . . . B 2 2.644 37.015 24.593 1 25.36 ? C23 9EK 301 A 1 HETATM 29 C C25 9EK . . . B 2 3.271 36.51 23.463 1 26.86 ? C25 9EK 301 A 1 HETATM 30 C C26 9EK . . . B 2 0.579 36.067 23.799 1 25.33 ? C26 9EK 301 A 1 HETATM 31 N N28 9EK . . . B 2 3.38 37.694 25.562 1 31.62 ? N28 9EK 301 A 1 HETATM 32 C C29 9EK . . . B 2 4.465 38.545 25.063 1 35.16 ? C29 9EK 301 A 1 HETATM 33 O O31 9EK . . . B 2 4.63 39.563 27.254 1 36.99 ? O31 9EK 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #