data_3HYF # _model_server_result.job_id -02oiFNrNsEqbKJzn1lafA _model_server_result.datetime_utc '2024-12-01 01:10:04' _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 3hyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":701}' # _entry.id 3HYF # _exptl.entry_id 3HYF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 315.109 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid' _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 3HYF _cell.length_a 39.717 _cell.length_b 90.326 _cell.length_c 113.334 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 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,D,E,F,G,H _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 5 _struct_asym.id G _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 metalc ? metalc1 A OD1 ASP 18 A ASP 443 1_555 B MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc2 A OD2 ASP 18 A ASP 443 1_555 C MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc3 A OE1 GLU 53 A GLU 478 1_555 B MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc4 A OD2 ASP 73 A ASP 498 1_555 B MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc5 A OD2 ASP 138 A ASP 549 1_555 C MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc6 B MN MN . A MN 601 1_555 G O4 ON1 . A ON1 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc7 B MN MN . A MN 601 1_555 G O1 ON1 . A ON1 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc8 C MN MN . A MN 602 1_555 H O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc9 C MN MN . A MN 602 1_555 H O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc10 C MN MN . A MN 602 1_555 G O1 ON1 . A ON1 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc11 C MN MN . A MN 602 1_555 G O2 ON1 . A ON1 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? # _chem_comp.formula 'C12 H8 Cl2 N2 O4' _chem_comp.formula_weight 315.109 _chem_comp.id ON1 _chem_comp.mon_nstd_flag . _chem_comp.name '2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid' _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 C1 C2 ON1 sing 243 n y C1 H1 ON1 sing 244 n n N1 C8 ON1 sing 245 n y O1 C10 ON1 sing 246 n n C2 CL2 ON1 sing 247 n n C3 CL1 ON1 sing 248 n n C3 C2 ON1 doub 249 n y O3 HO3 ON1 sing 250 n n C4 C3 ON1 sing 251 n y C4 H4 ON1 sing 252 n n O4 C12 ON1 doub 253 n n C5 C4 ON1 doub 254 n y C5 C6 ON1 sing 255 n y C5 H5 ON1 sing 256 n n C6 C1 ON1 doub 257 n y C7 C6 ON1 sing 258 n n C7 H7 ON1 sing 259 n n C7 H7A ON1 sing 260 n n C8 N2 ON1 doub 261 n y C8 C7 ON1 sing 262 n n C9 N1 ON1 doub 263 n y C9 C10 ON1 sing 264 n y C10 C11 ON1 doub 265 n y C11 N2 ON1 sing 266 n y C11 O2 ON1 sing 267 n n C12 O3 ON1 sing 268 n n C12 C9 ON1 sing 269 n n O1 H71 ON1 sing 270 n n O2 H8 ON1 sing 271 n n # _atom_sites.entry_id 3HYF _atom_sites.fract_transf_matrix[1][1] 0.025178 _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] 0.011071 _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] 0.008823 _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 MN A 1 601 601 MN MN . C 2 MN A 1 602 602 MN MN . D 3 ACT A 1 650 650 ACT ACT . E 4 GOL A 1 698 698 GOL GOL . F 4 GOL A 1 699 699 GOL GOL . G 5 ON1 A 1 701 701 ON1 ON1 . H 6 HOH A 1 1 1 HOH HOH . H 6 HOH A 2 2 2 HOH HOH . H 6 HOH A 3 3 3 HOH HOH . H 6 HOH A 4 4 4 HOH HOH . H 6 HOH A 5 5 5 HOH HOH . H 6 HOH A 6 6 6 HOH HOH . H 6 HOH A 7 7 7 HOH HOH . H 6 HOH A 8 8 8 HOH HOH . H 6 HOH A 9 9 9 HOH HOH . H 6 HOH A 10 10 10 HOH HOH . H 6 HOH A 11 11 11 HOH HOH . H 6 HOH A 12 12 12 HOH HOH . H 6 HOH A 13 13 13 HOH HOH . H 6 HOH A 14 14 14 HOH HOH . H 6 HOH A 15 15 15 HOH HOH . H 6 HOH A 16 16 16 HOH HOH . H 6 HOH A 17 17 17 HOH HOH . H 6 HOH A 18 18 18 HOH HOH . H 6 HOH A 19 19 19 HOH HOH . H 6 HOH A 20 20 20 HOH HOH . H 6 HOH A 21 21 21 HOH HOH . H 6 HOH A 22 22 22 HOH HOH . H 6 HOH A 23 23 23 HOH HOH . H 6 HOH A 24 24 24 HOH HOH . H 6 HOH A 25 25 25 HOH HOH . H 6 HOH A 26 26 26 HOH HOH . H 6 HOH A 27 27 27 HOH HOH . H 6 HOH A 28 28 28 HOH HOH . H 6 HOH A 29 29 29 HOH HOH . H 6 HOH A 30 30 30 HOH HOH . H 6 HOH A 31 31 31 HOH HOH . H 6 HOH A 32 32 32 HOH HOH . H 6 HOH A 33 33 33 HOH HOH . H 6 HOH A 34 34 34 HOH HOH . H 6 HOH A 35 35 35 HOH HOH . H 6 HOH A 36 36 36 HOH HOH . H 6 HOH A 37 37 37 HOH HOH . H 6 HOH A 38 38 38 HOH HOH . H 6 HOH A 39 39 39 HOH HOH . H 6 HOH A 40 40 40 HOH HOH . H 6 HOH A 41 41 41 HOH HOH . H 6 HOH A 42 42 42 HOH HOH . H 6 HOH A 43 43 43 HOH HOH . H 6 HOH A 44 44 44 HOH HOH . H 6 HOH A 45 45 45 HOH HOH . H 6 HOH A 46 46 46 HOH HOH . H 6 HOH A 47 47 47 HOH HOH . H 6 HOH A 48 48 48 HOH HOH . H 6 HOH A 49 49 49 HOH HOH . H 6 HOH A 50 50 50 HOH HOH . H 6 HOH A 51 51 51 HOH HOH . H 6 HOH A 52 52 52 HOH HOH . H 6 HOH A 53 53 53 HOH HOH . H 6 HOH A 54 54 54 HOH HOH . H 6 HOH A 55 55 55 HOH HOH . H 6 HOH A 56 56 56 HOH HOH . H 6 HOH A 57 57 57 HOH HOH . H 6 HOH A 58 58 58 HOH HOH . H 6 HOH A 59 59 59 HOH HOH . H 6 HOH A 60 60 60 HOH HOH . H 6 HOH A 61 61 61 HOH HOH . H 6 HOH A 62 62 62 HOH HOH . H 6 HOH A 63 63 63 HOH HOH . H 6 HOH A 64 64 64 HOH HOH . H 6 HOH A 65 65 65 HOH HOH . H 6 HOH A 66 66 66 HOH HOH . H 6 HOH A 67 67 67 HOH HOH . H 6 HOH A 68 68 68 HOH HOH . H 6 HOH A 69 69 69 HOH HOH . H 6 HOH A 70 70 70 HOH HOH . H 6 HOH A 71 71 71 HOH HOH . H 6 HOH A 72 72 72 HOH HOH . H 6 HOH A 73 73 73 HOH HOH . H 6 HOH A 74 74 74 HOH HOH . H 6 HOH A 75 75 75 HOH HOH . H 6 HOH A 76 76 76 HOH HOH . H 6 HOH A 77 77 77 HOH HOH . H 6 HOH A 78 78 78 HOH HOH . H 6 HOH A 79 103 103 HOH HOH . H 6 HOH A 80 104 104 HOH HOH . H 6 HOH A 81 105 105 HOH HOH . H 6 HOH A 82 106 106 HOH HOH . H 6 HOH A 83 107 107 HOH HOH . H 6 HOH A 84 108 108 HOH HOH . H 6 HOH A 85 109 109 HOH HOH . H 6 HOH A 86 110 110 HOH HOH . H 6 HOH A 87 111 111 HOH HOH . H 6 HOH A 88 112 112 HOH HOH . H 6 HOH A 89 113 113 HOH HOH . H 6 HOH A 90 114 114 HOH HOH . H 6 HOH A 91 115 115 HOH HOH . H 6 HOH A 92 116 116 HOH HOH . H 6 HOH A 93 117 117 HOH HOH . H 6 HOH A 94 118 118 HOH HOH . H 6 HOH A 95 119 119 HOH HOH . H 6 HOH A 96 120 120 HOH HOH . H 6 HOH A 97 121 121 HOH HOH . H 6 HOH A 98 122 122 HOH HOH . H 6 HOH A 99 123 123 HOH HOH . H 6 HOH A 100 124 124 HOH HOH . H 6 HOH A 101 125 125 HOH HOH . H 6 HOH A 102 126 126 HOH HOH . H 6 HOH A 103 127 127 HOH HOH . H 6 HOH A 104 128 128 HOH HOH . H 6 HOH A 105 129 129 HOH HOH . H 6 HOH A 106 130 130 HOH HOH . H 6 HOH A 107 131 131 HOH HOH . H 6 HOH A 108 132 132 HOH HOH . H 6 HOH A 109 133 133 HOH HOH . H 6 HOH A 110 134 134 HOH HOH . H 6 HOH A 111 135 135 HOH HOH . H 6 HOH A 112 136 136 HOH HOH . H 6 HOH A 113 137 137 HOH HOH . H 6 HOH A 114 138 138 HOH HOH . H 6 HOH A 115 139 139 HOH HOH . H 6 HOH A 116 140 140 HOH HOH . H 6 HOH A 117 141 141 HOH HOH . H 6 HOH A 118 142 142 HOH HOH . H 6 HOH A 119 143 143 HOH HOH . H 6 HOH A 120 144 144 HOH HOH . H 6 HOH A 121 145 145 HOH HOH . H 6 HOH A 122 146 146 HOH HOH . H 6 HOH A 123 147 147 HOH HOH . H 6 HOH A 124 148 148 HOH HOH . H 6 HOH A 125 149 149 HOH HOH . H 6 HOH A 126 150 150 HOH HOH . H 6 HOH A 127 151 151 HOH HOH . H 6 HOH A 128 152 152 HOH HOH . H 6 HOH A 129 153 153 HOH HOH . H 6 HOH A 130 154 154 HOH HOH . H 6 HOH A 131 155 155 HOH HOH . H 6 HOH A 132 156 156 HOH HOH . H 6 HOH A 133 157 157 HOH HOH . H 6 HOH A 134 158 158 HOH HOH . H 6 HOH A 135 159 159 HOH HOH . H 6 HOH A 136 160 160 HOH HOH . H 6 HOH A 137 161 161 HOH HOH . H 6 HOH A 138 162 162 HOH HOH . H 6 HOH A 139 163 163 HOH HOH . H 6 HOH A 140 164 164 HOH HOH . H 6 HOH A 141 165 165 HOH HOH . H 6 HOH A 142 166 166 HOH HOH . H 6 HOH A 143 167 167 HOH HOH . H 6 HOH A 144 168 168 HOH HOH . H 6 HOH A 145 169 169 HOH HOH . H 6 HOH A 146 170 170 HOH HOH . H 6 HOH A 147 171 171 HOH HOH . H 6 HOH A 148 172 172 HOH HOH . H 6 HOH A 149 173 173 HOH HOH . H 6 HOH A 150 174 174 HOH HOH . H 6 HOH A 151 175 175 HOH HOH . H 6 HOH A 152 176 176 HOH HOH . H 6 HOH A 153 177 177 HOH HOH . H 6 HOH A 154 178 178 HOH HOH . H 6 HOH A 155 179 179 HOH HOH . H 6 HOH A 156 180 180 HOH HOH . H 6 HOH A 157 181 181 HOH HOH . H 6 HOH A 158 182 182 HOH HOH . H 6 HOH A 159 183 183 HOH HOH . H 6 HOH A 160 184 184 HOH HOH . H 6 HOH A 161 185 185 HOH HOH . H 6 HOH A 162 186 186 HOH HOH . H 6 HOH A 163 187 187 HOH HOH . H 6 HOH A 164 603 603 HOH HOH . H 6 HOH A 165 604 604 HOH HOH . H 6 HOH A 166 605 79 HOH HOH . H 6 HOH A 167 606 80 HOH HOH . H 6 HOH A 168 607 81 HOH HOH . H 6 HOH A 169 608 82 HOH HOH . H 6 HOH A 170 609 83 HOH HOH . H 6 HOH A 171 610 84 HOH HOH . H 6 HOH A 172 611 85 HOH HOH . H 6 HOH A 173 612 86 HOH HOH . H 6 HOH A 174 613 87 HOH HOH . H 6 HOH A 175 614 88 HOH HOH . H 6 HOH A 176 615 89 HOH HOH . H 6 HOH A 177 616 90 HOH HOH . H 6 HOH A 178 617 91 HOH HOH . H 6 HOH A 179 618 92 HOH HOH . H 6 HOH A 180 619 93 HOH HOH . H 6 HOH A 181 620 94 HOH HOH . H 6 HOH A 182 621 95 HOH HOH . H 6 HOH A 183 622 96 HOH HOH . H 6 HOH A 184 623 97 HOH HOH . H 6 HOH A 185 624 98 HOH HOH . H 6 HOH A 186 625 99 HOH HOH . H 6 HOH A 187 626 100 HOH HOH . H 6 HOH A 188 627 101 HOH HOH . H 6 HOH A 189 628 102 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 ON1 . . . G 5 3.786 49.407 34.646 1 19.69 ? C1 ON1 701 A 1 HETATM 2 N N1 ON1 . . . G 5 3.426 49.145 29.934 1 18.28 ? N1 ON1 701 A 1 HETATM 3 O O1 ON1 . . . G 5 3.18 52.362 28.019 1 15.32 ? O1 ON1 701 A 1 HETATM 4 CL CL1 ON1 . . . G 5 7.479 50.023 36.395 1 6.92 ? CL1 ON1 701 A 1 HETATM 5 C C2 ON1 . . . G 5 4.791 49.723 35.621 1 17.94 ? C2 ON1 701 A 1 HETATM 6 N N2 ON1 . . . G 5 2.867 50.944 31.395 1 17.48 ? N2 ON1 701 A 1 HETATM 7 O O2 ON1 . . . G 5 2.62 53.085 30.599 1 13.04 ? O2 ON1 701 A 1 HETATM 8 CL CL2 ON1 . . . G 5 4.244 50.164 37.191 1 10.09 ? CL2 ON1 701 A 1 HETATM 9 C C3 ON1 . . . G 5 6.221 49.659 35.269 1 17.95 ? C3 ON1 701 A 1 HETATM 10 O O3 ON1 . . . G 5 3.987 48.077 27.59 1 19.62 ? O3 ON1 701 A 1 HETATM 11 C C4 ON1 . . . G 5 6.611 49.278 33.934 1 18.96 ? C4 ON1 701 A 1 HETATM 12 O O4 ON1 . . . G 5 3.832 49.93 26.476 1 15.83 ? O4 ON1 701 A 1 HETATM 13 C C5 ON1 . . . G 5 5.602 48.962 32.965 1 21.34 ? C5 ON1 701 A 1 HETATM 14 C C6 ON1 . . . G 5 4.19 49.023 33.309 1 18.59 ? C6 ON1 701 A 1 HETATM 15 C C7 ON1 . . . G 5 3.13 48.685 32.281 1 18.84 ? C7 ON1 701 A 1 HETATM 16 C C8 ON1 . . . G 5 3.139 49.652 31.135 1 18.63 ? C8 ON1 701 A 1 HETATM 17 C C9 ON1 . . . G 5 3.453 49.998 28.834 1 18.48 ? C9 ON1 701 A 1 HETATM 18 C C10 ON1 . . . G 5 3.179 51.42 28.999 1 17.78 ? C10 ON1 701 A 1 HETATM 19 C C11 ON1 . . . G 5 2.887 51.822 30.333 1 16.71 ? C11 ON1 701 A 1 HETATM 20 C C12 ON1 . . . G 5 3.778 49.31 27.543 1 19.08 ? C12 ON1 701 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #