data_6DBM # _model_server_result.job_id PwR5BPlOxkTsm5THgA8Oyw _model_server_result.datetime_utc '2025-04-23 05:29:58' _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 6dbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":4000}' # _entry.id 6DBM # _exptl.entry_id 6DBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 389.402 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(1S)-2,2-difluorocyclopropyl][(1R,5S)-3-{2-[(1-methyl-1H-pyrazol-4-yl)amino]pyrimidin-4-yl}-3,8-diazabicyclo[3.2.1]octan-8-yl]methanone' _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 6DBM _cell.length_a 36.238 _cell.length_b 73.317 _cell.length_c 101.224 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 2 _struct_asym.id B _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 GLU 189 A GLU 1053 1_555 A N PTR 190 A PTR 1054 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C PTR 190 A PTR 1054 1_555 A N TYR 191 A TYR 1055 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C18 H21 F2 N7 O' _chem_comp.formula_weight 389.402 _chem_comp.id G4J _chem_comp.mon_nstd_flag . _chem_comp.name '[(1S)-2,2-difluorocyclopropyl][(1R,5S)-3-{2-[(1-methyl-1H-pyrazol-4-yl)amino]pyrimidin-4-yl}-3,8-diazabicyclo[3.2.1]octan-8-yl]methanone' _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 F1 C18 G4J sing 83 n n O1 C15 G4J doub 84 n n C17 C18 G4J sing 85 n n C17 C16 G4J sing 86 n n C18 F2 G4J sing 87 n n C18 C16 G4J sing 88 n n C15 C16 G4J sing 89 n n C15 N7 G4J sing 90 n n C1 N1 G4J sing 91 n n C10 N7 G4J sing 92 n n C10 C11 G4J sing 93 n n C10 C9 G4J sing 94 n n N7 C13 G4J sing 95 n n C11 C12 G4J sing 96 n n N1 N2 G4J sing 97 n y N1 C2 G4J sing 98 n y C9 N6 G4J sing 99 n n C12 C13 G4J sing 100 n n C13 C14 G4J sing 101 n n N2 C4 G4J doub 102 n y C2 C3 G4J doub 103 n y N6 C14 G4J sing 104 n n N6 C8 G4J sing 105 n n C4 C3 G4J sing 106 n y C3 N3 G4J sing 107 n n N5 C8 G4J doub 108 n y N5 C5 G4J sing 109 n y C8 C7 G4J sing 110 n y N3 C5 G4J sing 111 n n C5 N4 G4J doub 112 n y C7 C6 G4J doub 113 n y N4 C6 G4J sing 114 n y N3 H9 G4J sing 115 n n C4 H8 G4J sing 116 n n C7 H11 G4J sing 117 n n C6 H10 G4J sing 118 n n C9 H13 G4J sing 119 n n C9 H12 G4J sing 120 n n C13 H2 G4J sing 121 n n C16 H3 G4J sing 122 n n C1 H4 G4J sing 123 n n C1 H5 G4J sing 124 n n C1 H6 G4J sing 125 n n C2 H7 G4J sing 126 n n C10 H1 G4J sing 127 n n C11 H15 G4J sing 128 n n C11 H14 G4J sing 129 n n C12 H17 G4J sing 130 n n C12 H16 G4J sing 131 n n C14 H19 G4J sing 132 n n C14 H18 G4J sing 133 n n C17 H20 G4J sing 134 n n C17 H21 G4J sing 135 n n # _atom_sites.entry_id 6DBM _atom_sites.fract_transf_matrix[1][1] 0.027595 _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] 0.013639 _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] 0.009879 _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 G4J A 1 4000 4000 G4J PFE . C 3 HOH A 1 4101 91 HOH HOH . C 3 HOH A 2 4102 90 HOH HOH . C 3 HOH A 3 4103 93 HOH HOH . C 3 HOH A 4 4104 89 HOH HOH . C 3 HOH A 5 4105 79 HOH HOH . C 3 HOH A 6 4106 41 HOH HOH . C 3 HOH A 7 4107 85 HOH HOH . C 3 HOH A 8 4108 68 HOH HOH . C 3 HOH A 9 4109 67 HOH HOH . C 3 HOH A 10 4110 51 HOH HOH . C 3 HOH A 11 4111 73 HOH HOH . C 3 HOH A 12 4112 21 HOH HOH . C 3 HOH A 13 4113 6 HOH HOH . C 3 HOH A 14 4114 1 HOH HOH . C 3 HOH A 15 4115 12 HOH HOH . C 3 HOH A 16 4116 24 HOH HOH . C 3 HOH A 17 4117 31 HOH HOH . C 3 HOH A 18 4118 98 HOH HOH . C 3 HOH A 19 4119 17 HOH HOH . C 3 HOH A 20 4120 74 HOH HOH . C 3 HOH A 21 4121 7 HOH HOH . C 3 HOH A 22 4122 63 HOH HOH . C 3 HOH A 23 4123 9 HOH HOH . C 3 HOH A 24 4124 30 HOH HOH . C 3 HOH A 25 4125 22 HOH HOH . C 3 HOH A 26 4126 18 HOH HOH . C 3 HOH A 27 4127 81 HOH HOH . C 3 HOH A 28 4128 2 HOH HOH . C 3 HOH A 29 4129 37 HOH HOH . C 3 HOH A 30 4130 20 HOH HOH . C 3 HOH A 31 4131 25 HOH HOH . C 3 HOH A 32 4132 69 HOH HOH . C 3 HOH A 33 4133 8 HOH HOH . C 3 HOH A 34 4134 32 HOH HOH . C 3 HOH A 35 4135 26 HOH HOH . C 3 HOH A 36 4136 36 HOH HOH . C 3 HOH A 37 4137 23 HOH HOH . C 3 HOH A 38 4138 46 HOH HOH . C 3 HOH A 39 4139 10 HOH HOH . C 3 HOH A 40 4140 71 HOH HOH . C 3 HOH A 41 4141 55 HOH HOH . C 3 HOH A 42 4142 47 HOH HOH . C 3 HOH A 43 4143 14 HOH HOH . C 3 HOH A 44 4144 64 HOH HOH . C 3 HOH A 45 4145 27 HOH HOH . C 3 HOH A 46 4146 59 HOH HOH . C 3 HOH A 47 4147 3 HOH HOH . C 3 HOH A 48 4148 84 HOH HOH . C 3 HOH A 49 4149 48 HOH HOH . C 3 HOH A 50 4150 97 HOH HOH . C 3 HOH A 51 4151 87 HOH HOH . C 3 HOH A 52 4152 13 HOH HOH . C 3 HOH A 53 4153 94 HOH HOH . C 3 HOH A 54 4154 61 HOH HOH . C 3 HOH A 55 4155 62 HOH HOH . C 3 HOH A 56 4156 70 HOH HOH . C 3 HOH A 57 4157 15 HOH HOH . C 3 HOH A 58 4158 44 HOH HOH . C 3 HOH A 59 4159 52 HOH HOH . C 3 HOH A 60 4160 57 HOH HOH . C 3 HOH A 61 4161 65 HOH HOH . C 3 HOH A 62 4162 49 HOH HOH . C 3 HOH A 63 4163 40 HOH HOH . C 3 HOH A 64 4164 11 HOH HOH . C 3 HOH A 65 4165 5 HOH HOH . C 3 HOH A 66 4166 34 HOH HOH . C 3 HOH A 67 4167 66 HOH HOH . C 3 HOH A 68 4168 72 HOH HOH . C 3 HOH A 69 4169 39 HOH HOH . C 3 HOH A 70 4170 33 HOH HOH . C 3 HOH A 71 4171 43 HOH HOH . C 3 HOH A 72 4172 45 HOH HOH . C 3 HOH A 73 4173 38 HOH HOH . C 3 HOH A 74 4174 28 HOH HOH . C 3 HOH A 75 4175 75 HOH HOH . C 3 HOH A 76 4176 60 HOH HOH . C 3 HOH A 77 4177 99 HOH HOH . C 3 HOH A 78 4178 95 HOH HOH . C 3 HOH A 79 4179 50 HOH HOH . C 3 HOH A 80 4180 82 HOH HOH . C 3 HOH A 81 4181 4 HOH HOH . C 3 HOH A 82 4182 100 HOH HOH . C 3 HOH A 83 4183 96 HOH HOH . C 3 HOH A 84 4184 53 HOH HOH . C 3 HOH A 85 4185 76 HOH HOH . C 3 HOH A 86 4186 42 HOH HOH . C 3 HOH A 87 4187 19 HOH HOH . C 3 HOH A 88 4188 16 HOH HOH . C 3 HOH A 89 4189 35 HOH HOH . C 3 HOH A 90 4190 58 HOH HOH . C 3 HOH A 91 4191 54 HOH HOH . C 3 HOH A 92 4192 56 HOH HOH . C 3 HOH A 93 4193 88 HOH HOH . C 3 HOH A 94 4194 80 HOH HOH . C 3 HOH A 95 4195 29 HOH HOH . C 3 HOH A 96 4196 77 HOH HOH . C 3 HOH A 97 4197 83 HOH HOH . C 3 HOH A 98 4198 78 HOH HOH . C 3 HOH A 99 4199 86 HOH HOH . C 3 HOH A 100 4200 92 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 N N3 G4J . . . B 2 9.224 -11.32 17.259 1 16.56 ? N3 G4J 4000 A 1 HETATM 2 C C4 G4J . . . B 2 8.033 -12.32 19.301 1 16.71 ? C4 G4J 4000 A 1 HETATM 3 N N2 G4J . . . B 2 6.884 -12.061 19.986 1 15.59 ? N2 G4J 4000 A 1 HETATM 4 C C7 G4J . . . B 2 9.257 -9.537 13.535 1 17.41 ? C7 G4J 4000 A 1 HETATM 5 C C6 G4J . . . B 2 10.066 -10.624 13.838 1 22.01 ? C6 G4J 4000 A 1 HETATM 6 C C9 G4J . . . B 2 6.442 -7.754 15.242 1 13.74 ? C9 G4J 4000 A 1 HETATM 7 C C13 G4J . . . B 2 7.233 -5.75 13.456 1 15.6 ? C13 G4J 4000 A 1 HETATM 8 C C8 G4J . . . B 2 8.385 -9.049 14.562 1 18.03 ? C8 G4J 4000 A 1 HETATM 9 N N5 G4J . . . B 2 8.372 -9.665 15.809 1 19.56 ? N5 G4J 4000 A 1 HETATM 10 C C18 G4J . . . B 2 3.395 -4.684 11.49 1 22.92 ? C18 G4J 4000 A 1 HETATM 11 C C16 G4J . . . B 2 4.624 -4.5 12.255 1 20.43 ? C16 G4J 4000 A 1 HETATM 12 C C1 G4J . . . B 2 5.034 -10.428 19.788 1 18.15 ? C1 G4J 4000 A 1 HETATM 13 N N1 G4J . . . B 2 6.302 -11.022 19.343 1 18.32 ? N1 G4J 4000 A 1 HETATM 14 C C2 G4J . . . B 2 7.03 -10.584 18.244 1 16.94 ? C2 G4J 4000 A 1 HETATM 15 C C3 G4J . . . B 2 8.171 -11.414 18.196 1 17.14 ? C3 G4J 4000 A 1 HETATM 16 C C5 G4J . . . B 2 9.225 -10.741 15.984 1 18.75 ? C5 G4J 4000 A 1 HETATM 17 N N4 G4J . . . B 2 10.088 -11.261 15.03 1 21.06 ? N4 G4J 4000 A 1 HETATM 18 N N6 G4J . . . B 2 7.592 -8.008 14.377 1 15.4 ? N6 G4J 4000 A 1 HETATM 19 C C10 G4J . . . B 2 6.209 -6.271 15.418 1 19.89 ? C10 G4J 4000 A 1 HETATM 20 C C11 G4J . . . B 2 7.494 -5.555 15.846 1 12.58 ? C11 G4J 4000 A 1 HETATM 21 C C12 G4J . . . B 2 8.17 -5.177 14.517 1 11.37 ? C12 G4J 4000 A 1 HETATM 22 C C14 G4J . . . B 2 7.605 -7.187 13.166 1 17.41 ? C14 G4J 4000 A 1 HETATM 23 N N7 G4J . . . B 2 5.927 -5.656 14.121 1 15.92 ? N7 G4J 4000 A 1 HETATM 24 C C15 G4J . . . B 2 4.711 -5.096 13.631 1 21.87 ? C15 G4J 4000 A 1 HETATM 25 O O1 G4J . . . B 2 3.72 -5.112 14.351 1 20.73 ? O1 G4J 4000 A 1 HETATM 26 C C17 G4J . . . B 2 3.606 -3.389 12.118 1 21.09 ? C17 G4J 4000 A 1 HETATM 27 F F1 G4J . . . B 2 3.44 -4.808 10.132 1 26.07 ? F1 G4J 4000 A 1 HETATM 28 F F2 G4J . . . B 2 2.423 -5.523 11.947 1 21.99 ? F2 G4J 4000 A 1 HETATM 29 H H9 G4J . . . B 2 10.099 -11.735 17.561 0 19.87 ? H9 G4J 4000 A 1 HETATM 30 H H8 G4J . . . B 2 8.699 -13.123 19.617 0 20.05 ? H8 G4J 4000 A 1 HETATM 31 H H11 G4J . . . B 2 9.291 -9.078 12.548 0 20.89 ? H11 G4J 4000 A 1 HETATM 32 H H10 G4J . . . B 2 10.753 -11.037 13.101 0 26.41 ? H10 G4J 4000 A 1 HETATM 33 H H13 G4J . . . B 2 6.583 -8.221 16.216 0 16.48 ? H13 G4J 4000 A 1 HETATM 34 H H12 G4J . . . B 2 5.552 -8.23 14.832 0 16.48 ? H12 G4J 4000 A 1 HETATM 35 H H2 G4J . . . B 2 7.242 -5.168 12.536 0 18.72 ? H2 G4J 4000 A 1 HETATM 36 H H3 G4J . . . B 2 5.569 -4.422 11.719 0 24.51 ? H3 G4J 4000 A 1 HETATM 37 H H4 G4J . . . B 2 4.279 -11.198 19.94 0 21.78 ? H4 G4J 4000 A 1 HETATM 38 H H5 G4J . . . B 2 5.172 -9.901 20.731 0 21.78 ? H5 G4J 4000 A 1 HETATM 39 H H6 G4J . . . B 2 4.649 -9.718 19.057 0 21.78 ? H6 G4J 4000 A 1 HETATM 40 H H7 G4J . . . B 2 6.721 -9.763 17.599 0 20.33 ? H7 G4J 4000 A 1 HETATM 41 H H1 G4J . . . B 2 5.396 -6.103 16.123 0 23.87 ? H1 G4J 4000 A 1 HETATM 42 H H15 G4J . . . B 2 8.129 -6.181 16.471 0 15.1 ? H15 G4J 4000 A 1 HETATM 43 H H14 G4J . . . B 2 7.277 -4.677 16.452 0 15.1 ? H14 G4J 4000 A 1 HETATM 44 H H17 G4J . . . B 2 8.305 -4.101 14.414 0 13.64 ? H17 G4J 4000 A 1 HETATM 45 H H16 G4J . . . B 2 9.172 -5.596 14.441 0 13.64 ? H16 G4J 4000 A 1 HETATM 46 H H19 G4J . . . B 2 6.951 -7.61 12.405 0 20.89 ? H19 G4J 4000 A 1 HETATM 47 H H18 G4J . . . B 2 8.595 -7.204 12.712 0 20.89 ? H18 G4J 4000 A 1 HETATM 48 H H20 G4J . . . B 2 3.841 -2.508 11.522 0 25.31 ? H20 G4J 4000 A 1 HETATM 49 H H21 G4J . . . B 2 3.018 -3.075 12.979 0 25.31 ? H21 G4J 4000 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 114 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 49 #