data_3H9F # _model_server_result.job_id ZhpRr9fX2vElmTXRg-o24A _model_server_result.datetime_utc '2025-02-18 05:51:29' _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 3h9f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":809}' # _entry.id 3H9F # _exptl.entry_id 3H9F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 466.576 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '9-cyclopentyl-2-(4-(4-hydroxypiperidin-1-yl)-2-methoxyphenylamino)-5-methyl-8,9-dihydro-5H-pyrimido[4,5-b][1,4]diazepin -6(7H)-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 90 _cell.angle_gamma 90 _cell.entry_id 3H9F _cell.length_a 70.69 _cell.length_b 110.75 _cell.length_c 115.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H9F _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 software_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1,2,3,4 A,B,C,D,E 2 1 # 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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 115.2 4 'crystal symmetry operation' 4_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 115.2 # _struct_asym.details ? _struct_asym.entity_id 3 _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 C ASP 179 A ASP 674 1_555 A N TPO 180 A TPO 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 A C TPO 180 A TPO 675 1_555 A N TPO 181 A TPO 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C TPO 181 A TPO 676 1_555 A N SEP 182 A SEP 677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? metalc ? metalc1 B MG MG . A MG 1 1_555 A O3P TPO 180 A TPO 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc2 B MG MG . A MG 1 1_555 A O1P SEP 182 A SEP 677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc3 C MG MG . A MG 2 1_555 A O2P TPO 180 A TPO 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? # _chem_comp.formula 'C25 H34 N6 O3' _chem_comp.formula_weight 466.576 _chem_comp.id 92M _chem_comp.mon_nstd_flag . _chem_comp.name '9-cyclopentyl-2-(4-(4-hydroxypiperidin-1-yl)-2-methoxyphenylamino)-5-methyl-8,9-dihydro-5H-pyrimido[4,5-b][1,4]diazepin -6(7H)-one' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '9-cyclopentyl-2-{[4-(4-hydroxypiperidin-1-yl)-2-methoxyphenyl]amino}-5-methyl-5,7,8,9-tetrahydro-6H-pyrimido[4,5-b][1,4 ]diazepin-6-one' # 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 C4 C5 92M doub 1 n y C4 N3 92M sing 2 n y C4 NAE 92M sing 3 n n C5 C6 92M sing 4 n y C5 NBG 92M sing 5 n n C6 N1 92M doub 6 n y N1 C2 92M sing 7 n y N3 C2 92M doub 8 n y CAT CAU 92M sing 9 n n CAT NAS 92M sing 10 n n CAU CAV 92M sing 11 n n CAV OAW 92M sing 12 n n CAV CAX 92M sing 13 n n CAX CAY 92M sing 14 n n CAY NAS 92M sing 15 n n NAS CAR 92M sing 16 n n CAR CAZ 92M doub 17 n y CAR CAQ 92M sing 18 n y CAZ CBA 92M sing 19 n y CBA OBB 92M sing 20 n n CBA CAO 92M doub 21 n y OBB CBC 92M sing 22 n n CAQ CAP 92M doub 23 n y CAP CAO 92M sing 24 n y CAO NAN 92M sing 25 n n NAN C2 92M sing 26 n n NBG CBH 92M sing 27 n n NBG CAB 92M sing 28 n n CAB OAA 92M doub 29 n n CAB CAC 92M sing 30 n n CAC CAD 92M sing 31 n n CAD NAE 92M sing 32 n n NAE CAF 92M sing 33 n n CAF CAG 92M sing 34 n n CAF CAJ 92M sing 35 n n CAG CAH 92M sing 36 n n CAH CAI 92M sing 37 n n CAI CAJ 92M sing 38 n n C6 H6 92M sing 39 n n CAT HAT 92M sing 40 n n CAT HATA 92M sing 41 n n CAU HAU 92M sing 42 n n CAU HAUA 92M sing 43 n n CAV HAV 92M sing 44 n n OAW HOAW 92M sing 45 n n CAX HAX 92M sing 46 n n CAX HAXA 92M sing 47 n n CAY HAY 92M sing 48 n n CAY HAYA 92M sing 49 n n CAZ HAZ 92M sing 50 n n CBC HBC 92M sing 51 n n CBC HBCA 92M sing 52 n n CBC HBCB 92M sing 53 n n CAQ HAQ 92M sing 54 n n CAP HAP 92M sing 55 n n NAN HNAN 92M sing 56 n n CBH HBH 92M sing 57 n n CBH HBHA 92M sing 58 n n CBH HBHB 92M sing 59 n n CAC HAC 92M sing 60 n n CAC HACA 92M sing 61 n n CAD HAD 92M sing 62 n n CAD HADA 92M sing 63 n n CAF HAF 92M sing 64 n n CAG HAG 92M sing 65 n n CAG HAGA 92M sing 66 n n CAH HAH 92M sing 67 n n CAH HAHA 92M sing 68 n n CAI HAI 92M sing 69 n n CAI HAIA 92M sing 70 n n CAJ HAJ 92M sing 71 n n CAJ HAJA 92M sing 72 n n # _atom_sites.entry_id 3H9F _atom_sites.fract_transf_matrix[1][1] 0.014146 _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] 0.009029 _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] 0.008681 _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 1 1 MG MG . C 2 MG A 1 2 2 MG MG . D 3 92M A 1 809 1 92M 92M . E 4 HOH A 1 3 3 HOH HOH . E 4 HOH A 2 4 4 HOH HOH . E 4 HOH A 3 5 5 HOH HOH . E 4 HOH A 4 6 6 HOH HOH . E 4 HOH A 5 7 7 HOH HOH . E 4 HOH A 6 8 8 HOH HOH . E 4 HOH A 7 9 9 HOH HOH . E 4 HOH A 8 10 10 HOH HOH . E 4 HOH A 9 11 11 HOH HOH . E 4 HOH A 10 810 1 HOH HOH . E 4 HOH A 11 811 2 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 C4 92M . . . D 3 1.609 20.611 45.904 1 38.85 ? C4 92M 809 A 1 HETATM 2 C C5 92M . . . D 3 1.879 21.936 45.624 1 40.07 ? C5 92M 809 A 1 HETATM 3 C C6 92M . . . D 3 1.269 22.926 46.381 1 43.85 ? C6 92M 809 A 1 HETATM 4 N N1 92M . . . D 3 0.448 22.569 47.345 1 50.02 ? N1 92M 809 A 1 HETATM 5 N N3 92M . . . D 3 0.764 20.312 46.893 1 32.24 ? N3 92M 809 A 1 HETATM 6 C CAT 92M . . . D 3 -1.492 15.729 52.268 1 68.8 ? CAT 92M 809 A 1 HETATM 7 C CAU 92M . . . D 3 -0.951 14.324 52.55 1 69.08 ? CAU 92M 809 A 1 HETATM 8 C CAV 92M . . . D 3 -1.918 13.292 51.924 1 71.27 ? CAV 92M 809 A 1 HETATM 9 O OAW 92M . . . D 3 -1.423 11.946 52.062 1 68.43 ? OAW 92M 809 A 1 HETATM 10 C CAX 92M . . . D 3 -2.145 13.624 50.43 1 54.06 ? CAX 92M 809 A 1 HETATM 11 C CAY 92M . . . D 3 -1.233 14.757 49.932 1 42.35 ? CAY 92M 809 A 1 HETATM 12 N NAS 92M . . . D 3 -1.291 15.94 50.822 1 44.57 ? NAS 92M 809 A 1 HETATM 13 C CAR 92M . . . D 3 -1.128 17.214 50.281 1 40.44 ? CAR 92M 809 A 1 HETATM 14 C CAZ 92M . . . D 3 -0.955 18.33 51.102 1 39.15 ? CAZ 92M 809 A 1 HETATM 15 C CBA 92M . . . D 3 -0.765 19.586 50.515 1 52.55 ? CBA 92M 809 A 1 HETATM 16 O OBB 92M . . . D 3 -0.574 20.693 51.257 1 46.76 ? OBB 92M 809 A 1 HETATM 17 C CBC 92M . . . D 3 -0.649 20.483 52.649 1 37.99 ? CBC 92M 809 A 1 HETATM 18 C CAQ 92M . . . D 3 -1.122 17.38 48.897 1 43.79 ? CAQ 92M 809 A 1 HETATM 19 C CAP 92M . . . D 3 -0.954 18.64 48.317 1 45.08 ? CAP 92M 809 A 1 HETATM 20 C CAO 92M . . . D 3 -0.757 19.748 49.128 1 50.44 ? CAO 92M 809 A 1 HETATM 21 N NAN 92M . . . D 3 -0.622 20.975 48.621 1 46.18 ? NAN 92M 809 A 1 HETATM 22 C C2 92M . . . D 3 0.197 21.274 47.616 1 52.38 ? C2 92M 809 A 1 HETATM 23 N NBG 92M . . . D 3 2.678 22.416 44.683 1 40 ? NBG 92M 809 A 1 HETATM 24 C CBH 92M . . . D 3 3.469 23.624 44.978 1 33.52 ? CBH 92M 809 A 1 HETATM 25 C CAB 92M . . . D 3 2.832 21.859 43.487 1 33.36 ? CAB 92M 809 A 1 HETATM 26 O OAA 92M . . . D 3 3.615 22.374 42.677 1 45.36 ? OAA 92M 809 A 1 HETATM 27 C CAC 92M . . . D 3 2.074 20.629 43.108 1 36.11 ? CAC 92M 809 A 1 HETATM 28 C CAD 92M . . . D 3 2.603 19.457 43.937 1 33.91 ? CAD 92M 809 A 1 HETATM 29 N NAE 92M . . . D 3 2.055 19.514 45.292 1 40.64 ? NAE 92M 809 A 1 HETATM 30 C CAF 92M . . . D 3 1.83 18.195 45.935 1 38.13 ? CAF 92M 809 A 1 HETATM 31 C CAG 92M . . . D 3 3.062 17.288 45.828 1 33.4 ? CAG 92M 809 A 1 HETATM 32 C CAH 92M . . . D 3 2.532 15.876 45.736 1 42.48 ? CAH 92M 809 A 1 HETATM 33 C CAI 92M . . . D 3 1.141 15.993 45.152 1 33.31 ? CAI 92M 809 A 1 HETATM 34 C CAJ 92M . . . D 3 0.785 17.487 45.13 1 40.67 ? CAJ 92M 809 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 1160 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 34 #