data_5NHF # _model_server_result.job_id wWDHQiaLtUTcJBdv-lOeKA _model_server_result.datetime_utc '2025-02-11 23:07:18' _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 5nhf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5NHF # _exptl.entry_id 5NHF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.477 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[2-(oxan-4-ylamino)pyrimidin-4-yl]-5-(phenylmethyl)-6,7-dihydro-1~{H}-pyrrolo[3,2-c]pyridin-4-one _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 109.31 _cell.angle_gamma 90 _cell.entry_id 5NHF _cell.length_a 49.019 _cell.length_b 70.047 _cell.length_c 60.363 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NHF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 covale ? covale1 A C THR 179 A THR 160 1_555 A N CME 180 A CME 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C CME 180 A CME 161 1_555 A N ASP 181 A ASP 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _chem_comp.formula 'C23 H25 N5 O2' _chem_comp.formula_weight 403.477 _chem_comp.id 8X5 _chem_comp.mon_nstd_flag . _chem_comp.name 2-[2-(oxan-4-ylamino)pyrimidin-4-yl]-5-(phenylmethyl)-6,7-dihydro-1~{H}-pyrrolo[3,2-c]pyridin-4-one _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 C C1 8X5 doub 1 n y C C5 8X5 sing 2 n y C1 C2 8X5 sing 3 n y C5 C4 8X5 doub 4 n y C2 C3 8X5 doub 5 n y C4 C3 8X5 sing 6 n y C3 C6 8X5 sing 7 n n O1 C22 8X5 doub 8 n n C6 N 8X5 sing 9 n n C22 N 8X5 sing 10 n n C22 C10 8X5 sing 11 n n N C7 8X5 sing 12 n n C11 C10 8X5 sing 13 n y C11 C12 8X5 doub 14 n y C10 C9 8X5 doub 15 n y C14 C15 8X5 doub 16 n y C14 C13 8X5 sing 17 n y C12 C13 8X5 sing 18 n n C12 N1 8X5 sing 19 n y C15 N2 8X5 sing 20 n y C9 C8 8X5 sing 21 n n C9 N1 8X5 sing 22 n y C13 N3 8X5 doub 23 n y C7 C8 8X5 sing 24 n n N2 C16 8X5 doub 25 n y N3 C16 8X5 sing 26 n y C16 N4 8X5 sing 27 n n N4 C17 8X5 sing 28 n n C17 C21 8X5 sing 29 n n C17 C18 8X5 sing 30 n n C21 C20 8X5 sing 31 n n C20 O 8X5 sing 32 n n C18 C19 8X5 sing 33 n n C19 O 8X5 sing 34 n n C1 H1 8X5 sing 35 n n C2 H2 8X5 sing 36 n n C7 H3 8X5 sing 37 n n C7 H4 8X5 sing 38 n n C8 H5 8X5 sing 39 n n C8 H6 8X5 sing 40 n n C11 H7 8X5 sing 41 n n C14 H8 8X5 sing 42 n n C15 H9 8X5 sing 43 n n C19 H10 8X5 sing 44 n n C19 H11 8X5 sing 45 n n C20 H12 8X5 sing 46 n n C20 H13 8X5 sing 47 n n C21 H14 8X5 sing 48 n n C21 H15 8X5 sing 49 n n C6 H16 8X5 sing 50 n n C6 H17 8X5 sing 51 n n C4 H18 8X5 sing 52 n n C5 H19 8X5 sing 53 n n C H20 8X5 sing 54 n n N1 H21 8X5 sing 55 n n N4 H22 8X5 sing 56 n n C17 H23 8X5 sing 57 n n C18 H24 8X5 sing 58 n n C18 H25 8X5 sing 59 n n # _atom_sites.entry_id 5NHF _atom_sites.fract_transf_matrix[1][1] 0.0204 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007148 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014276 _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] 0.017554 _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 SO4 A 1 401 1 SO4 SO4 . C 3 8X5 A 1 402 1 8X5 INH . D 4 HOH A 1 501 4 HOH HOH . D 4 HOH A 2 502 48 HOH HOH . D 4 HOH A 3 503 36 HOH HOH . D 4 HOH A 4 504 15 HOH HOH . D 4 HOH A 5 505 17 HOH HOH . D 4 HOH A 6 506 32 HOH HOH . D 4 HOH A 7 507 2 HOH HOH . D 4 HOH A 8 508 69 HOH HOH . D 4 HOH A 9 509 56 HOH HOH . D 4 HOH A 10 510 20 HOH HOH . D 4 HOH A 11 511 14 HOH HOH . D 4 HOH A 12 512 24 HOH HOH . D 4 HOH A 13 513 53 HOH HOH . D 4 HOH A 14 514 5 HOH HOH . D 4 HOH A 15 515 62 HOH HOH . D 4 HOH A 16 516 39 HOH HOH . D 4 HOH A 17 517 61 HOH HOH . D 4 HOH A 18 518 6 HOH HOH . D 4 HOH A 19 519 8 HOH HOH . D 4 HOH A 20 520 16 HOH HOH . D 4 HOH A 21 521 33 HOH HOH . D 4 HOH A 22 522 54 HOH HOH . D 4 HOH A 23 523 55 HOH HOH . D 4 HOH A 24 524 19 HOH HOH . D 4 HOH A 25 525 50 HOH HOH . D 4 HOH A 26 526 12 HOH HOH . D 4 HOH A 27 527 21 HOH HOH . D 4 HOH A 28 528 23 HOH HOH . D 4 HOH A 29 529 73 HOH HOH . D 4 HOH A 30 530 40 HOH HOH . D 4 HOH A 31 531 3 HOH HOH . D 4 HOH A 32 532 42 HOH HOH . D 4 HOH A 33 533 63 HOH HOH . D 4 HOH A 34 534 27 HOH HOH . D 4 HOH A 35 535 29 HOH HOH . D 4 HOH A 36 536 30 HOH HOH . D 4 HOH A 37 537 11 HOH HOH . D 4 HOH A 38 538 10 HOH HOH . D 4 HOH A 39 539 34 HOH HOH . D 4 HOH A 40 540 1 HOH HOH . D 4 HOH A 41 541 47 HOH HOH . D 4 HOH A 42 542 72 HOH HOH . D 4 HOH A 43 543 9 HOH HOH . D 4 HOH A 44 544 67 HOH HOH . D 4 HOH A 45 545 71 HOH HOH . D 4 HOH A 46 546 26 HOH HOH . D 4 HOH A 47 547 49 HOH HOH . D 4 HOH A 48 548 28 HOH HOH . D 4 HOH A 49 549 38 HOH HOH . D 4 HOH A 50 550 41 HOH HOH . D 4 HOH A 51 551 51 HOH HOH . D 4 HOH A 52 552 52 HOH HOH . D 4 HOH A 53 553 35 HOH HOH . D 4 HOH A 54 554 31 HOH HOH . D 4 HOH A 55 555 22 HOH HOH . D 4 HOH A 56 556 60 HOH HOH . D 4 HOH A 57 557 45 HOH HOH . D 4 HOH A 58 558 7 HOH HOH . D 4 HOH A 59 559 43 HOH HOH . D 4 HOH A 60 560 66 HOH HOH . D 4 HOH A 61 561 70 HOH HOH . D 4 HOH A 62 562 37 HOH HOH . D 4 HOH A 63 563 58 HOH HOH . D 4 HOH A 64 564 68 HOH HOH . D 4 HOH A 65 565 25 HOH HOH . D 4 HOH A 66 566 74 HOH HOH . D 4 HOH A 67 567 59 HOH HOH . D 4 HOH A 68 568 75 HOH HOH . D 4 HOH A 69 569 57 HOH HOH . D 4 HOH A 70 570 64 HOH HOH . D 4 HOH A 71 571 44 HOH HOH . D 4 HOH A 72 572 18 HOH HOH . D 4 HOH A 73 573 65 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 8X5 . . . C 3 -9.836 16.917 36.149 1 48.58 ? C1 8X5 402 A 1 HETATM 2 C C2 8X5 . . . C 3 -10.01 16.695 37.507 1 48.84 ? C2 8X5 402 A 1 HETATM 3 C C3 8X5 . . . C 3 -9 16.119 38.269 1 48.32 ? C3 8X5 402 A 1 HETATM 4 C C7 8X5 . . . C 3 -10.977 16.335 41.369 1 45.96 ? C7 8X5 402 A 1 HETATM 5 C C8 8X5 . . . C 3 -12.475 16.609 41.407 1 45.13 ? C8 8X5 402 A 1 HETATM 6 C C9 8X5 . . . C 3 -13.102 15.297 41.07 1 43.99 ? C9 8X5 402 A 1 HETATM 7 C C10 8X5 . . . C 3 -12.511 14.296 40.319 1 43.59 ? C10 8X5 402 A 1 HETATM 8 C C11 8X5 . . . C 3 -13.457 13.233 40.219 1 43.19 ? C11 8X5 402 A 1 HETATM 9 C C12 8X5 . . . C 3 -14.582 13.648 40.904 1 43.26 ? C12 8X5 402 A 1 HETATM 10 C C13 8X5 . . . C 3 -15.859 12.95 41.112 1 42.54 ? C13 8X5 402 A 1 HETATM 11 C C14 8X5 . . . C 3 -16.102 11.68 40.605 1 40.72 ? C14 8X5 402 A 1 HETATM 12 C C15 8X5 . . . C 3 -17.33 11.122 40.905 1 41.83 ? C15 8X5 402 A 1 HETATM 13 C C16 8X5 . . . C 3 -17.945 12.99 42.048 1 43.55 ? C16 8X5 402 A 1 HETATM 14 C C19 8X5 . . . C 3 -17.657 16.098 45.404 1 51.2 ? C19 8X5 402 A 1 HETATM 15 C C20 8X5 . . . C 3 -19.757 16.826 44.629 1 51.6 ? C20 8X5 402 A 1 HETATM 16 C C21 8X5 . . . C 3 -20.004 15.55 43.857 1 51.03 ? C21 8X5 402 A 1 HETATM 17 C C22 8X5 . . . C 3 -11.154 14.436 39.807 1 43.66 ? C22 8X5 402 A 1 HETATM 18 O O1 8X5 . . . C 3 -10.582 13.551 39.174 1 42.51 ? O1 8X5 402 A 1 HETATM 19 N N 8X5 . . . C 3 -10.571 15.612 40.153 1 46.11 ? N 8X5 402 A 1 HETATM 20 C C6 8X5 . . . C 3 -9.184 15.868 39.747 1 46.99 ? C6 8X5 402 A 1 HETATM 21 C C4 8X5 . . . C 3 -7.8 15.799 37.644 1 49.28 ? C4 8X5 402 A 1 HETATM 22 C C5 8X5 . . . C 3 -7.621 16.037 36.288 1 49.62 ? C5 8X5 402 A 1 HETATM 23 C C 8X5 . . . C 3 -8.64 16.591 35.541 1 49.29 ? C 8X5 402 A 1 HETATM 24 N N1 8X5 . . . C 3 -14.363 14.906 41.416 1 43.47 ? N1 8X5 402 A 1 HETATM 25 N N3 8X5 . . . C 3 -16.769 13.616 41.84 1 43.12 ? N3 8X5 402 A 1 HETATM 26 N N2 8X5 . . . C 3 -18.282 11.762 41.605 1 42.18 ? N2 8X5 402 A 1 HETATM 27 N N4 8X5 . . . C 3 -18.864 13.642 42.789 1 46.33 ? N4 8X5 402 A 1 HETATM 28 C C17 8X5 . . . C 3 -18.673 14.928 43.462 1 49.38 ? C17 8X5 402 A 1 HETATM 29 O O 8X5 . . . C 3 -18.947 16.585 45.788 1 51.57 ? O 8X5 402 A 1 HETATM 30 C C18 8X5 . . . C 3 -17.767 14.777 44.68 1 50.51 ? C18 8X5 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 30 #