data_5VDU # _model_server_result.job_id JiDKJy4F9y52BSmHQRX3XA _model_server_result.datetime_utc '2024-10-15 12:16:11' _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 5vdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 5VDU # _exptl.entry_id 5VDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 157.172 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(pyridin-2-yl)pyrimidine _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.94 _cell.angle_gamma 90 _cell.entry_id 5VDU _cell.length_a 216.415 _cell.length_b 48.019 _cell.length_c 86.466 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,I 1 1 B,E,F,G,H,J 2 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 ? 3 D N N ? 3 F N N ? 3 G N N ? 3 H 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 metalc ? metalc1 A NE2 HIS 231 A HIS 390 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc2 A SG CYS 237 A CYS 396 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc3 A SG CYS 238 A CYS 397 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc4 A SG CYS 245 A CYS 404 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc5 B NE2 HIS 231 B HIS 390 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc6 B SG CYS 237 B CYS 396 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc7 B SG CYS 238 B CYS 397 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc8 B SG CYS 245 B CYS 404 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? # _chem_comp.formula 'C9 H7 N3' _chem_comp.formula_weight 157.172 _chem_comp.id 9BS _chem_comp.mon_nstd_flag . _chem_comp.name 2-(pyridin-2-yl)pyrimidine _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 C7 N2 9BS doub 1 n y C7 C8 9BS sing 2 n y N2 C6 9BS sing 3 n y C5 C1 9BS doub 4 n y C5 C4 9BS sing 5 n y C8 C9 9BS doub 6 n y C1 C2 9BS sing 7 n y C6 C4 9BS sing 8 n n C6 N3 9BS doub 9 n y C4 N1 9BS doub 10 n y C9 N3 9BS sing 11 n y C2 C3 9BS doub 12 n y N1 C3 9BS sing 13 n y C7 H1 9BS sing 14 n n C9 H2 9BS sing 15 n n C8 H3 9BS sing 16 n n C1 H4 9BS sing 17 n n C2 H5 9BS sing 18 n n C3 H6 9BS sing 19 n n C5 H7 9BS sing 20 n n # _atom_sites.entry_id 5VDU _atom_sites.fract_transf_matrix[1][1] 0.004621 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001233 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020825 _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] 0.01197 _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 C 2 ZN A 1 601 601 ZN ZN . D 3 9BS A 1 602 1 9BS PFE . E 2 ZN B 1 601 601 ZN ZN . F 3 9BS B 1 602 1 9BS PFE . G 3 9BS B 1 603 1 9BS PFE . H 3 9BS B 1 604 1 9BS PFE . I 4 HOH A 1 701 53 HOH HOH . I 4 HOH A 2 702 5 HOH HOH . I 4 HOH A 3 703 32 HOH HOH . I 4 HOH A 4 704 24 HOH HOH . I 4 HOH A 5 705 17 HOH HOH . I 4 HOH A 6 706 21 HOH HOH . I 4 HOH A 7 707 45 HOH HOH . I 4 HOH A 8 708 37 HOH HOH . I 4 HOH A 9 709 4 HOH HOH . I 4 HOH A 10 710 26 HOH HOH . I 4 HOH A 11 711 7 HOH HOH . I 4 HOH A 12 712 33 HOH HOH . I 4 HOH A 13 713 22 HOH HOH . I 4 HOH A 14 714 3 HOH HOH . I 4 HOH A 15 715 10 HOH HOH . I 4 HOH A 16 716 50 HOH HOH . I 4 HOH A 17 717 35 HOH HOH . I 4 HOH A 18 718 52 HOH HOH . I 4 HOH A 19 719 34 HOH HOH . I 4 HOH A 20 720 31 HOH HOH . I 4 HOH A 21 721 54 HOH HOH . I 4 HOH A 22 722 9 HOH HOH . I 4 HOH A 23 723 43 HOH HOH . I 4 HOH A 24 724 11 HOH HOH . I 4 HOH A 25 725 41 HOH HOH . I 4 HOH A 26 726 12 HOH HOH . J 4 HOH B 1 701 30 HOH HOH . J 4 HOH B 2 702 15 HOH HOH . J 4 HOH B 3 703 46 HOH HOH . J 4 HOH B 4 704 20 HOH HOH . J 4 HOH B 5 705 42 HOH HOH . J 4 HOH B 6 706 48 HOH HOH . J 4 HOH B 7 707 29 HOH HOH . J 4 HOH B 8 708 2 HOH HOH . J 4 HOH B 9 709 6 HOH HOH . J 4 HOH B 10 710 44 HOH HOH . J 4 HOH B 11 711 51 HOH HOH . J 4 HOH B 12 712 1 HOH HOH . J 4 HOH B 13 713 25 HOH HOH . J 4 HOH B 14 714 14 HOH HOH . J 4 HOH B 15 715 27 HOH HOH . J 4 HOH B 16 716 47 HOH HOH . J 4 HOH B 17 717 13 HOH HOH . J 4 HOH B 18 718 40 HOH HOH . J 4 HOH B 19 719 16 HOH HOH . J 4 HOH B 20 720 36 HOH HOH . J 4 HOH B 21 721 49 HOH HOH . J 4 HOH B 22 722 39 HOH HOH . J 4 HOH B 23 723 38 HOH HOH . J 4 HOH B 24 724 8 HOH HOH . J 4 HOH B 25 725 19 HOH HOH . J 4 HOH B 26 726 18 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 9BS . A . D 3 -30.657 18.868 -24.365 0.56 76.59 ? N3 9BS 602 A 1 HETATM 2 N N3 9BS . B . D 3 -30.499 20.678 -22.793 0.29 75.4 ? N3 9BS 602 A 1 HETATM 3 N N3 9BS . C . D 3 -30.343 19.081 -23.325 0.15 73.75 ? N3 9BS 602 A 1 HETATM 4 C C4 9BS . A . D 3 -30.275 16.534 -23.892 0.56 74.87 ? C4 9BS 602 A 1 HETATM 5 C C4 9BS . B . D 3 -31.094 19.29 -24.674 0.29 75.25 ? C4 9BS 602 A 1 HETATM 6 C C4 9BS . C . D 3 -29.867 16.82 -22.631 0.15 74.94 ? C4 9BS 602 A 1 HETATM 7 N N2 9BS . A . D 3 -31.258 17.224 -25.984 0.56 75.4 ? N2 9BS 602 A 1 HETATM 8 N N2 9BS . B . D 3 -30.182 18.319 -22.663 0.29 74.42 ? N2 9BS 602 A 1 HETATM 9 N N2 9BS . C . D 3 -29.69 18.651 -21.072 0.15 75.54 ? N2 9BS 602 A 1 HETATM 10 C C7 9BS . A . D 3 -31.693 18.209 -26.781 0.56 75.32 ? C7 9BS 602 A 1 HETATM 11 C C7 9BS . B . D 3 -29.708 18.481 -21.42 0.29 75.54 ? C7 9BS 602 A 1 HETATM 12 C C7 9BS . C . D 3 -29.789 19.964 -20.824 0.15 75.7 ? C7 9BS 602 A 1 HETATM 13 C C6 9BS . A . D 3 -30.758 17.607 -24.803 0.56 74.24 ? C6 9BS 602 A 1 HETATM 14 C C6 9BS . B . D 3 -30.558 19.438 -23.294 0.29 74.97 ? C6 9BS 602 A 1 HETATM 15 C C6 9BS . C . D 3 -29.974 18.272 -22.324 0.15 75.18 ? C6 9BS 602 A 1 HETATM 16 C C9 9BS . A . D 3 -31.107 19.814 -25.202 0.56 74.4 ? C9 9BS 602 A 1 HETATM 17 C C9 9BS . B . D 3 -30.017 20.783 -21.547 0.29 75.55 ? C9 9BS 602 A 1 HETATM 18 C C9 9BS . C . D 3 -30.426 20.383 -23.021 0.15 75.41 ? C9 9BS 602 A 1 HETATM 19 C C8 9BS . A . D 3 -31.641 19.539 -26.438 0.56 74.26 ? C8 9BS 602 A 1 HETATM 20 C C8 9BS . B . D 3 -29.601 19.705 -20.804 0.29 75.7 ? C8 9BS 602 A 1 HETATM 21 C C8 9BS . C . D 3 -30.157 20.887 -21.772 0.15 75.55 ? C8 9BS 602 A 1 HETATM 22 C C1 9BS . A . D 3 -29.836 14.243 -23.41 0.56 75.36 ? C1 9BS 602 A 1 HETATM 23 C C1 9BS . B . D 3 -31.826 17.944 -26.498 0.29 75.4 ? C1 9BS 602 A 1 HETATM 24 C C1 9BS . C . D 3 -29.434 14.572 -21.974 0.15 75.43 ? C1 9BS 602 A 1 HETATM 25 C C2 9BS . A . D 3 -29.395 14.617 -22.162 0.56 75.46 ? C2 9BS 602 A 1 HETATM 26 C C2 9BS . B . D 3 -32.089 19.093 -27.207 0.29 78.06 ? C2 9BS 602 A 1 HETATM 27 C C2 9BS . C . D 3 -29.709 14.17 -23.26 0.15 75.37 ? C2 9BS 602 A 1 HETATM 28 C C3 9BS . A . D 3 -29.417 15.957 -21.841 0.56 75.07 ? C3 9BS 602 A 1 HETATM 29 C C3 9BS . B . D 3 -31.834 20.303 -26.597 0.29 75.34 ? C3 9BS 602 A 1 HETATM 30 C C3 9BS . C . D 3 -30.053 15.136 -24.182 0.15 74.96 ? C3 9BS 602 A 1 HETATM 31 N N1 9BS . A . D 3 -29.845 16.917 -22.677 0.56 75.14 ? N1 9BS 602 A 1 HETATM 32 N N1 9BS . B . D 3 -31.345 20.423 -25.353 0.29 74.32 ? N1 9BS 602 A 1 HETATM 33 N N1 9BS . C . D 3 -30.137 16.445 -23.894 0.15 74.8 ? N1 9BS 602 A 1 HETATM 34 C C5 9BS . A . D 3 -30.283 15.206 -24.294 0.56 74.93 ? C5 9BS 602 A 1 HETATM 35 C C5 9BS . B . D 3 -31.321 18.032 -25.215 0.29 74.65 ? C5 9BS 602 A 1 HETATM 36 C C5 9BS . C . D 3 -29.51 15.911 -21.644 0.15 75.13 ? C5 9BS 602 A 1 # _model_server_stats.io_time_ms 93 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #