data_8PT9 # _model_server_result.job_id kfCOg4rsTC-QEdj4o_j4Eg _model_server_result.datetime_utc '2025-01-10 15:54:56' _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 8pt9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 8PT9 # _exptl.entry_id 8PT9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 592.644 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'methyl (1S,3S)-1-methyl-3-[[3-[[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]carbamoyl]phenyl]carbamoyl]-4-oxidanylidene-cyclohexane-1-carboxylate' _entity.pdbx_number_of_molecules 3 _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 8PT9 _cell.length_a 106.552 _cell.length_b 106.552 _cell.length_c 99.795 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PT9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D 1 1 B,E,G 2 1 C,F 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N 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 118 A CYS 116 1_555 D C3 DVI . A DVI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.724 ? covale ? covale2 B SG CYS 118 B CYS 116 1_555 E C3 DVI . B DVI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.723 ? covale ? covale3 C SG CYS 118 C CYS 116 1_555 F C3 DVI . C DVI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? # _chem_comp.formula 'C33 H32 N6 O5' _chem_comp.formula_weight 592.644 _chem_comp.id DVI _chem_comp.mon_nstd_flag . _chem_comp.name 'methyl (1S,3S)-1-methyl-3-[[3-[[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]carbamoyl]phenyl]carbamoyl]-4-oxidanylidene-cyclohexane-1-carboxylate' _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 O C15 DVI sing 83 n n O C14 DVI sing 84 n n C5 C6 DVI sing 85 n n C5 C4 DVI sing 86 n n C7 C4 DVI sing 87 n n C6 C1 DVI sing 88 n n C4 C14 DVI sing 89 n n C4 C3 DVI sing 90 n n C14 O1 DVI doub 91 n n C1 O4 DVI doub 92 n n C1 C2 DVI sing 93 n n C3 C2 DVI sing 94 n n O2 C16 DVI doub 95 n n C2 C16 DVI sing 96 n n C16 N2 DVI sing 97 n n N2 C17 DVI sing 98 n n C43 N44 DVI doub 99 n y C43 C42 DVI sing 100 n y C17 C18 DVI doub 101 n y C17 C22 DVI sing 102 n y C18 C19 DVI sing 103 n y N44 C45 DVI sing 104 n y C42 C41 DVI doub 105 n y C22 C21 DVI doub 106 n y C19 C20 DVI doub 107 n y C21 C20 DVI sing 108 n y C21 C23 DVI sing 109 n n C45 C40 DVI doub 110 n y C41 C40 DVI sing 111 n y C40 C37 DVI sing 112 n n C23 O24 DVI doub 113 n n C23 N25 DVI sing 114 n n N25 C26 DVI sing 115 n n C27 C26 DVI doub 116 n y C27 C28 DVI sing 117 n y C39 C28 DVI sing 118 n n C37 N38 DVI doub 119 n y C37 C36 DVI sing 120 n y C26 C31 DVI sing 121 n y C28 C29 DVI doub 122 n y N38 C33 DVI sing 123 n y C36 C35 DVI doub 124 n y C31 C30 DVI doub 125 n y C29 C30 DVI sing 126 n y C29 N32 DVI sing 127 n n C33 N32 DVI sing 128 n n C33 N34 DVI doub 129 n y C35 N34 DVI sing 130 n y C7 H1 DVI sing 131 n n C7 H2 DVI sing 132 n n C7 H3 DVI sing 133 n n C15 H4 DVI sing 134 n n C15 H5 DVI sing 135 n n C15 H6 DVI sing 136 n n C18 H7 DVI sing 137 n n C19 H8 DVI sing 138 n n C20 H9 DVI sing 139 n n C22 H10 DVI sing 140 n n C27 H11 DVI sing 141 n n C2 H12 DVI sing 142 n n C30 H13 DVI sing 143 n n C31 H14 DVI sing 144 n n C35 H15 DVI sing 145 n n C36 H16 DVI sing 146 n n C39 H17 DVI sing 147 n n C39 H18 DVI sing 148 n n C39 H19 DVI sing 149 n n C41 H20 DVI sing 150 n n C42 H21 DVI sing 151 n n C43 H22 DVI sing 152 n n C45 H23 DVI sing 153 n n C6 H24 DVI sing 154 n n C6 H25 DVI sing 155 n n C5 H26 DVI sing 156 n n C5 H27 DVI sing 157 n n C3 H28 DVI sing 158 n n C3 H29 DVI sing 159 n n N2 H30 DVI sing 160 n n N25 H31 DVI sing 161 n n N32 H32 DVI sing 162 n n # _atom_sites.entry_id 8PT9 _atom_sites.fract_transf_matrix[1][1] 0.009385 _atom_sites.fract_transf_matrix[1][2] 0.005418 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010837 _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] 0.010021 _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 D 2 DVI A 1 401 401 DVI 38B . E 2 DVI B 1 401 401 DVI 38B . F 2 DVI C 1 401 401 DVI 38B . G 3 HOH B 1 501 2 HOH HOH . G 3 HOH B 2 502 1 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 C16 DVI . . . E 2 55.4 -35.39 4.381 1 82.23 ? C16 DVI 401 B 1 HETATM 2 C C7 DVI . . . E 2 53.018 -34.638 0.684 1 78.77 ? C7 DVI 401 B 1 HETATM 3 C C14 DVI . . . E 2 54.666 -33.151 1.722 1 89.15 ? C14 DVI 401 B 1 HETATM 4 C C15 DVI . . . E 2 56.328 -31.553 2.65 1 84.23 ? C15 DVI 401 B 1 HETATM 5 C C17 DVI . . . E 2 56.52 -34.079 6.024 1 75.48 ? C17 DVI 401 B 1 HETATM 6 C C18 DVI . . . E 2 57.507 -34.997 6.192 1 77.51 ? C18 DVI 401 B 1 HETATM 7 C C19 DVI . . . E 2 58.59 -34.729 6.988 1 78.19 ? C19 DVI 401 B 1 HETATM 8 C C20 DVI . . . E 2 58.704 -33.532 7.646 1 75.38 ? C20 DVI 401 B 1 HETATM 9 C C21 DVI . . . E 2 57.73 -32.595 7.501 1 74.09 ? C21 DVI 401 B 1 HETATM 10 C C22 DVI . . . E 2 56.641 -32.874 6.686 1 73.74 ? C22 DVI 401 B 1 HETATM 11 C C23 DVI . . . E 2 57.919 -31.325 8.258 1 75.29 ? C23 DVI 401 B 1 HETATM 12 C C26 DVI . . . E 2 57.018 -29.537 9.373 1 68.4 ? C26 DVI 401 B 1 HETATM 13 C C27 DVI . . . E 2 56.245 -28.517 8.942 1 69.03 ? C27 DVI 401 B 1 HETATM 14 C C28 DVI . . . E 2 56.346 -27.277 9.49 1 67.86 ? C28 DVI 401 B 1 HETATM 15 C C29 DVI . . . E 2 57.237 -27.026 10.488 1 68.46 ? C29 DVI 401 B 1 HETATM 16 C C2 DVI . . . E 2 54.047 -35.802 3.902 1 80.54 ? C2 DVI 401 B 1 HETATM 17 C C30 DVI . . . E 2 58.021 -28.061 10.93 1 69.31 ? C30 DVI 401 B 1 HETATM 18 C C31 DVI . . . E 2 57.919 -29.316 10.372 1 69.35 ? C31 DVI 401 B 1 HETATM 19 C C33 DVI . . . E 2 57.112 -24.671 10.549 1 68.1 ? C33 DVI 401 B 1 HETATM 20 C C35 DVI . . . E 2 56.212 -22.567 10.693 1 68.18 ? C35 DVI 401 B 1 HETATM 21 C C36 DVI . . . E 2 56.553 -22.317 9.391 1 69.37 ? C36 DVI 401 B 1 HETATM 22 C C37 DVI . . . E 2 57.188 -23.302 8.696 1 73.53 ? C37 DVI 401 B 1 HETATM 23 C C39 DVI . . . E 2 55.437 -26.262 8.913 1 66.65 ? C39 DVI 401 B 1 HETATM 24 C C1 DVI . . . E 2 54.128 -37 3.023 1 80.82 ? C1 DVI 401 B 1 HETATM 25 C C40 DVI . . . E 2 57.585 -23.097 7.292 1 78.16 ? C40 DVI 401 B 1 HETATM 26 C C41 DVI . . . E 2 57.184 -21.973 6.618 1 76.62 ? C41 DVI 401 B 1 HETATM 27 C C42 DVI . . . E 2 57.572 -21.815 5.315 1 77.26 ? C42 DVI 401 B 1 HETATM 28 C C43 DVI . . . E 2 58.335 -22.785 4.715 1 77.17 ? C43 DVI 401 B 1 HETATM 29 C C45 DVI . . . E 2 58.35 -24.038 6.641 1 77.2 ? C45 DVI 401 B 1 HETATM 30 C C6 DVI . . . E 2 54.55 -36.832 1.602 1 83.58 ? C6 DVI 401 B 1 HETATM 31 C C5 DVI . . . E 2 55.176 -35.469 1.486 1 84.14 ? C5 DVI 401 B 1 HETATM 32 C C4 DVI . . . E 2 54.074 -34.5 1.743 1 83 ? C4 DVI 401 B 1 HETATM 33 C C3 DVI . . . E 2 53.512 -34.642 3.114 1 79.19 ? C3 DVI 401 B 1 HETATM 34 N N2 DVI . . . E 2 55.462 -34.366 5.233 1 78.8 ? N2 DVI 401 B 1 HETATM 35 N N25 DVI . . . E 2 56.892 -30.731 8.81 1 70.96 ? N25 DVI 401 B 1 HETATM 36 N N32 DVI . . . E 2 57.387 -25.843 11.092 1 69.14 ? N32 DVI 401 B 1 HETATM 37 N N34 DVI . . . E 2 56.49 -23.736 11.235 1 68.83 ? N34 DVI 401 B 1 HETATM 38 N N38 DVI . . . E 2 57.449 -24.462 9.295 1 74.98 ? N38 DVI 401 B 1 HETATM 39 N N44 DVI . . . E 2 58.708 -23.86 5.382 1 75.28 ? N44 DVI 401 B 1 HETATM 40 O O2 DVI . . . E 2 56.365 -35.991 3.964 1 83.79 ? O2 DVI 401 B 1 HETATM 41 O O1 DVI . . . E 2 54.431 -32.412 0.801 1 115.86 ? O1 DVI 401 B 1 HETATM 42 O O DVI . . . E 2 55.525 -32.719 2.804 1 86.73 ? O DVI 401 B 1 HETATM 43 O O4 DVI . . . E 2 53.888 -38.103 3.444 1 80.91 ? O4 DVI 401 B 1 HETATM 44 O O24 DVI . . . E 2 59.033 -30.898 8.377 1 80.48 ? O24 DVI 401 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 44 #