data_8DNI # _model_server_result.job_id 3f1HmPDJfsVLeZgwNE9xMQ _model_server_result.datetime_utc '2025-06-16 12:51:40' _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 8dni # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 8DNI # _exptl.entry_id 8DNI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 470.569 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4P)-4-(5-methyl-1H-indazol-4-yl)-6-(2-propanoyl-2,6-diazaspiro[3.4]octan-6-yl)-2-(pyrrolidin-1-yl)pyrimidine-5-carbonitrile _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 120 _cell.entry_id 8DNI _cell.length_a 41.202 _cell.length_b 41.202 _cell.length_c 348.5 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DNI _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 4 _struct_asym.id D _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 covale ? covale1 A SG CYS 26 A CYS 12 1_555 D C25 U4L . A U4L 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.813 ? metalc ? metalc1 A OG SER 31 A SER 17 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc2 B MG MG . A MG 301 1_555 C O1B GDP . A GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc3 B MG MG . A MG 301 1_555 E O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc4 B MG MG . A MG 301 1_555 E O HOH . A HOH 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc5 B MG MG . A MG 301 1_555 E O HOH . A HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc6 B MG MG . A MG 301 1_555 E O HOH . A HOH 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? # _chem_comp.formula 'C26 H30 N8 O' _chem_comp.formula_weight 470.569 _chem_comp.id U4L _chem_comp.mon_nstd_flag . _chem_comp.name (4P)-4-(5-methyl-1H-indazol-4-yl)-6-(2-propanoyl-2,6-diazaspiro[3.4]octan-6-yl)-2-(pyrrolidin-1-yl)pyrimidine-5-carbonitrile _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 O1 C23 U4L doub 375 n n C23 C24 U4L sing 376 n n C23 N7 U4L sing 377 n n C24 C25 U4L sing 378 n n N7 C18 U4L sing 379 n n N7 C17 U4L sing 380 n n C18 C14 U4L sing 381 n n C15 C14 U4L sing 382 n n C15 C16 U4L sing 383 n n C17 C14 U4L sing 384 n n C14 C13 U4L sing 385 n n C16 N4 U4L sing 386 n n N8 C26 U4L trip 387 n n C26 C3 U4L sing 388 n n C13 N4 U4L sing 389 n n N4 C4 U4L sing 390 n n C4 C3 U4L doub 391 n y C4 N1 U4L sing 392 n y C3 C2 U4L sing 393 n y C11 C6 U4L sing 394 n n C6 C7 U4L doub 395 n y C6 C5 U4L sing 396 n y N1 C1 U4L doub 397 n y C7 C8 U4L sing 398 n y C2 C5 U4L sing 399 n n C2 N2 U4L doub 400 n y C5 C10 U4L doub 401 n y C8 C9 U4L doub 402 n y C10 C9 U4L sing 403 n y C10 C12 U4L sing 404 n y C9 N5 U4L sing 405 n y C12 N6 U4L doub 406 n y N5 N6 U4L sing 407 n y C1 N2 U4L sing 408 n y C1 N3 U4L sing 409 n n C19 N3 U4L sing 410 n n C19 C20 U4L sing 411 n n N3 C22 U4L sing 412 n n C20 C21 U4L sing 413 n n C22 C21 U4L sing 414 n n C11 H1 U4L sing 415 n n C11 H2 U4L sing 416 n n C11 H3 U4L sing 417 n n C7 H4 U4L sing 418 n n C8 H5 U4L sing 419 n n N5 H6 U4L sing 420 n n C12 H7 U4L sing 421 n n C19 H8 U4L sing 422 n n C19 H9 U4L sing 423 n n C20 H10 U4L sing 424 n n C20 H11 U4L sing 425 n n C21 H12 U4L sing 426 n n C21 H13 U4L sing 427 n n C22 H14 U4L sing 428 n n C22 H15 U4L sing 429 n n C13 H16 U4L sing 430 n n C13 H17 U4L sing 431 n n C16 H18 U4L sing 432 n n C16 H19 U4L sing 433 n n C15 H20 U4L sing 434 n n C15 H21 U4L sing 435 n n C18 H22 U4L sing 436 n n C18 H23 U4L sing 437 n n C17 H24 U4L sing 438 n n C17 H25 U4L sing 439 n n C24 H26 U4L sing 440 n n C24 H27 U4L sing 441 n n C25 H28 U4L sing 442 n n C25 H29 U4L sing 443 n n C25 H30 U4L sing 444 n n # _atom_sites.entry_id 8DNI _atom_sites.fract_transf_matrix[1][1] 0.024271 _atom_sites.fract_transf_matrix[1][2] 0.014013 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028025 _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] 0.002869 _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 MG A 1 301 301 MG MG . C 3 GDP A 1 302 501 GDP GDP . D 4 U4L A 1 303 701 U4L UNL . E 5 HOH A 1 401 102 HOH HOH . E 5 HOH A 2 402 144 HOH HOH . E 5 HOH A 3 403 111 HOH HOH . E 5 HOH A 4 404 59 HOH HOH . E 5 HOH A 5 405 8 HOH HOH . E 5 HOH A 6 406 120 HOH HOH . E 5 HOH A 7 407 403 HOH HOH . E 5 HOH A 8 408 22 HOH HOH . E 5 HOH A 9 409 74 HOH HOH . E 5 HOH A 10 410 14 HOH HOH . E 5 HOH A 11 411 146 HOH HOH . E 5 HOH A 12 412 140 HOH HOH . E 5 HOH A 13 413 36 HOH HOH . E 5 HOH A 14 414 39 HOH HOH . E 5 HOH A 15 415 145 HOH HOH . E 5 HOH A 16 416 95 HOH HOH . E 5 HOH A 17 417 85 HOH HOH . E 5 HOH A 18 418 58 HOH HOH . E 5 HOH A 19 419 53 HOH HOH . E 5 HOH A 20 420 103 HOH HOH . E 5 HOH A 21 421 401 HOH HOH . E 5 HOH A 22 422 109 HOH HOH . E 5 HOH A 23 423 44 HOH HOH . E 5 HOH A 24 424 402 HOH HOH . E 5 HOH A 25 425 94 HOH HOH . E 5 HOH A 26 426 86 HOH HOH . E 5 HOH A 27 427 404 HOH HOH . E 5 HOH A 28 428 83 HOH HOH . E 5 HOH A 29 429 23 HOH HOH . E 5 HOH A 30 430 54 HOH HOH . E 5 HOH A 31 431 33 HOH HOH . E 5 HOH A 32 432 42 HOH HOH . E 5 HOH A 33 433 12 HOH HOH . E 5 HOH A 34 434 106 HOH HOH . E 5 HOH A 35 435 55 HOH HOH . E 5 HOH A 36 436 127 HOH HOH . E 5 HOH A 37 437 26 HOH HOH . E 5 HOH A 38 438 21 HOH HOH . E 5 HOH A 39 439 20 HOH HOH . E 5 HOH A 40 440 25 HOH HOH . E 5 HOH A 41 441 125 HOH HOH . E 5 HOH A 42 442 56 HOH HOH . E 5 HOH A 43 443 24 HOH HOH . E 5 HOH A 44 444 98 HOH HOH . E 5 HOH A 45 445 69 HOH HOH . E 5 HOH A 46 446 45 HOH HOH . E 5 HOH A 47 447 5 HOH HOH . E 5 HOH A 48 448 3 HOH HOH . E 5 HOH A 49 449 15 HOH HOH . E 5 HOH A 50 450 110 HOH HOH . E 5 HOH A 51 451 138 HOH HOH . E 5 HOH A 52 452 52 HOH HOH . E 5 HOH A 53 453 141 HOH HOH . E 5 HOH A 54 454 38 HOH HOH . E 5 HOH A 55 455 46 HOH HOH . E 5 HOH A 56 456 1 HOH HOH . E 5 HOH A 57 457 73 HOH HOH . E 5 HOH A 58 458 117 HOH HOH . E 5 HOH A 59 459 7 HOH HOH . E 5 HOH A 60 460 43 HOH HOH . E 5 HOH A 61 461 28 HOH HOH . E 5 HOH A 62 462 93 HOH HOH . E 5 HOH A 63 463 134 HOH HOH . E 5 HOH A 64 464 11 HOH HOH . E 5 HOH A 65 465 47 HOH HOH . E 5 HOH A 66 466 64 HOH HOH . E 5 HOH A 67 467 147 HOH HOH . E 5 HOH A 68 468 34 HOH HOH . E 5 HOH A 69 469 35 HOH HOH . E 5 HOH A 70 470 121 HOH HOH . E 5 HOH A 71 471 76 HOH HOH . E 5 HOH A 72 472 48 HOH HOH . E 5 HOH A 73 473 32 HOH HOH . E 5 HOH A 74 474 68 HOH HOH . E 5 HOH A 75 475 57 HOH HOH . E 5 HOH A 76 476 16 HOH HOH . E 5 HOH A 77 477 100 HOH HOH . E 5 HOH A 78 478 119 HOH HOH . E 5 HOH A 79 479 97 HOH HOH . E 5 HOH A 80 480 116 HOH HOH . E 5 HOH A 81 481 122 HOH HOH . E 5 HOH A 82 482 13 HOH HOH . E 5 HOH A 83 483 80 HOH HOH . E 5 HOH A 84 484 18 HOH HOH . E 5 HOH A 85 485 50 HOH HOH . E 5 HOH A 86 486 2 HOH HOH . E 5 HOH A 87 487 30 HOH HOH . E 5 HOH A 88 488 89 HOH HOH . E 5 HOH A 89 489 113 HOH HOH . E 5 HOH A 90 490 17 HOH HOH . E 5 HOH A 91 491 92 HOH HOH . E 5 HOH A 92 492 90 HOH HOH . E 5 HOH A 93 493 67 HOH HOH . E 5 HOH A 94 494 9 HOH HOH . E 5 HOH A 95 495 40 HOH HOH . E 5 HOH A 96 496 130 HOH HOH . E 5 HOH A 97 497 62 HOH HOH . E 5 HOH A 98 498 88 HOH HOH . E 5 HOH A 99 499 19 HOH HOH . E 5 HOH A 100 500 107 HOH HOH . E 5 HOH A 101 501 108 HOH HOH . E 5 HOH A 102 502 63 HOH HOH . E 5 HOH A 103 503 61 HOH HOH . E 5 HOH A 104 504 29 HOH HOH . E 5 HOH A 105 505 78 HOH HOH . E 5 HOH A 106 506 4 HOH HOH . E 5 HOH A 107 507 10 HOH HOH . E 5 HOH A 108 508 136 HOH HOH . E 5 HOH A 109 509 31 HOH HOH . E 5 HOH A 110 510 123 HOH HOH . E 5 HOH A 111 511 114 HOH HOH . E 5 HOH A 112 512 104 HOH HOH . E 5 HOH A 113 513 101 HOH HOH . E 5 HOH A 114 514 129 HOH HOH . E 5 HOH A 115 515 6 HOH HOH . E 5 HOH A 116 516 71 HOH HOH . E 5 HOH A 117 517 115 HOH HOH . E 5 HOH A 118 518 105 HOH HOH . E 5 HOH A 119 519 87 HOH HOH . E 5 HOH A 120 520 49 HOH HOH . E 5 HOH A 121 521 51 HOH HOH . E 5 HOH A 122 522 99 HOH HOH . E 5 HOH A 123 523 118 HOH HOH . E 5 HOH A 124 524 65 HOH HOH . E 5 HOH A 125 525 66 HOH HOH . E 5 HOH A 126 526 81 HOH HOH . E 5 HOH A 127 527 82 HOH HOH . E 5 HOH A 128 528 84 HOH HOH . E 5 HOH A 129 529 77 HOH HOH . E 5 HOH A 130 530 137 HOH HOH . E 5 HOH A 131 531 133 HOH HOH . E 5 HOH A 132 532 60 HOH HOH . E 5 HOH A 133 533 37 HOH HOH . E 5 HOH A 134 534 128 HOH HOH . E 5 HOH A 135 535 139 HOH HOH . E 5 HOH A 136 536 135 HOH HOH . E 5 HOH A 137 537 75 HOH HOH . E 5 HOH A 138 538 126 HOH HOH . E 5 HOH A 139 539 41 HOH HOH . E 5 HOH A 140 540 143 HOH HOH . E 5 HOH A 141 541 132 HOH HOH . E 5 HOH A 142 542 96 HOH HOH . E 5 HOH A 143 543 27 HOH HOH . E 5 HOH A 144 544 79 HOH HOH . E 5 HOH A 145 545 91 HOH HOH . E 5 HOH A 146 546 72 HOH HOH . E 5 HOH A 147 547 124 HOH HOH . E 5 HOH A 148 548 70 HOH HOH . E 5 HOH A 149 549 142 HOH HOH . E 5 HOH A 150 550 112 HOH HOH . E 5 HOH A 151 551 131 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 C11 U4L . . . D 4 -1.192 -16.493 22.482 1 9.86 ? C11 U4L 303 A 1 HETATM 2 C C6 U4L . . . D 4 -0.845 -17.916 22.917 1 9.86 ? C6 U4L 303 A 1 HETATM 3 C C7 U4L . . . D 4 0.493 -18.293 23.048 1 9.97 ? C7 U4L 303 A 1 HETATM 4 C C8 U4L . . . D 4 0.838 -19.585 23.444 1 10.07 ? C8 U4L 303 A 1 HETATM 5 C C9 U4L . . . D 4 -0.175 -20.506 23.704 1 10.02 ? C9 U4L 303 A 1 HETATM 6 N N5 U4L . . . D 4 -0.172 -21.78 24.094 1 10.15 ? N5 U4L 303 A 1 HETATM 7 N N6 U4L . . . D 4 -1.334 -22.196 24.201 1 10.2 ? N6 U4L 303 A 1 HETATM 8 C C12 U4L . . . D 4 -2.199 -21.221 23.893 1 10.13 ? C12 U4L 303 A 1 HETATM 9 C C10 U4L . . . D 4 -1.504 -20.133 23.572 1 10 ? C10 U4L 303 A 1 HETATM 10 C C5 U4L . . . D 4 -1.864 -18.834 23.174 1 9.9 ? C5 U4L 303 A 1 HETATM 11 C C2 U4L . . . D 4 -3.229 -18.512 23.071 1 9.86 ? C2 U4L 303 A 1 HETATM 12 C C3 U4L . . . D 4 -3.975 -18.758 21.909 1 9.82 ? C3 U4L 303 A 1 HETATM 13 C C26 U4L . . . D 4 -3.268 -19.326 20.802 1 10.14 ? C26 U4L 303 A 1 HETATM 14 N N8 U4L . . . D 4 -2.695 -19.774 19.925 1 10.61 ? N8 U4L 303 A 1 HETATM 15 N N2 U4L . . . D 4 -3.846 -17.982 24.145 1 9.9 ? N2 U4L 303 A 1 HETATM 16 C C1 U4L . . . D 4 -5.155 -17.673 24.117 1 9.95 ? C1 U4L 303 A 1 HETATM 17 N N3 U4L . . . D 4 -5.766 -17.114 25.166 1 10.18 ? N3 U4L 303 A 1 HETATM 18 C C19 U4L . . . D 4 -7.157 -16.636 25.127 1 10.4 ? C19 U4L 303 A 1 HETATM 19 C C20 U4L . . . D 4 -7.325 -15.695 26.321 1 10.51 ? C20 U4L 303 A 1 HETATM 20 C C21 U4L . . . D 4 -5.953 -15.637 27.006 1 10.58 ? C21 U4L 303 A 1 HETATM 21 C C22 U4L . . . D 4 -5.123 -16.797 26.449 1 10.42 ? C22 U4L 303 A 1 HETATM 22 N N1 U4L . . . D 4 -5.879 -17.896 23.004 1 9.76 ? N1 U4L 303 A 1 HETATM 23 C C4 U4L . . . D 4 -5.349 -18.432 21.893 1 9.68 ? C4 U4L 303 A 1 HETATM 24 N N4 U4L . . . D 4 -6.196 -18.627 20.859 1 9.51 ? N4 U4L 303 A 1 HETATM 25 C C13 U4L . . . D 4 -7.608 -18.17 20.855 1 9.36 ? C13 U4L 303 A 1 HETATM 26 C C16 U4L . . . D 4 -5.901 -19.438 19.665 1 9.42 ? C16 U4L 303 A 1 HETATM 27 C C15 U4L . . . D 4 -7.267 -19.978 19.215 1 9.27 ? C15 U4L 303 A 1 HETATM 28 C C14 U4L . . . D 4 -8.185 -18.794 19.568 1 9.2 ? C14 U4L 303 A 1 HETATM 29 C C18 U4L . . . D 4 -8.348 -17.764 18.453 1 9.09 ? C18 U4L 303 A 1 HETATM 30 C C17 U4L . . . D 4 -9.688 -19.082 19.485 1 9.07 ? C17 U4L 303 A 1 HETATM 31 N N7 U4L . . . D 4 -9.679 -18.354 18.193 1 8.95 ? N7 U4L 303 A 1 HETATM 32 C C23 U4L . . . D 4 -10.503 -18.257 17.157 1 8.89 ? C23 U4L 303 A 1 HETATM 33 O O1 U4L . . . D 4 -10.251 -17.533 16.195 1 8.63 ? O1 U4L 303 A 1 HETATM 34 C C24 U4L . . . D 4 -11.826 -19.032 17.17 1 8.81 ? C24 U4L 303 A 1 HETATM 35 C C25 U4L . . . D 4 -13.144 -18.273 17.309 1 8.64 ? C25 U4L 303 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 484 _model_server_stats.create_model_time_ms 95 _model_server_stats.query_time_ms 1708 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 35 #