data_9D17 # _model_server_result.job_id GH_yGqMOmJkbvRM5437DJw _model_server_result.datetime_utc '2025-07-04 04:48:11' _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 9d17 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 9D17 # _exptl.entry_id 9D17 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 295.339 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(2-amino-1H-1,3-benzimidazol-1-yl)-N-(5-ethylpyridin-2-yl)acetamide _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 97.52 _cell.angle_gamma 90 _cell.entry_id 9D17 _cell.length_a 71.84 _cell.length_b 40.81 _cell.length_c 101.5 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9D17 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _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 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 disulf ? disulf1 A SG CYS 4 A CYS 366 1_555 A SG CYS 50 A CYS 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf2 A SG CYS 34 A CYS 396 1_555 A SG CYS 68 A CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf3 A SG CYS 72 A CYS 434 1_555 A SG CYS 190 A CYS 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf4 A SG CYS 236 A CYS 598 1_555 A SG CYS 256 A CYS 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? disulf ? disulf5 A SG CYS 267 A CYS 629 1_555 A SG CYS 298 A CYS 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? # _chem_comp.formula 'C16 H17 N5 O' _chem_comp.formula_weight 295.339 _chem_comp.id A1A1X _chem_comp.mon_nstd_flag . _chem_comp.name 2-(2-amino-1H-1,3-benzimidazol-1-yl)-N-(5-ethylpyridin-2-yl)acetamide _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 A1A1X sing 1 n n N1 C4 A1A1X doub 2 n y N1 C5 A1A1X sing 3 n y O1 C6 A1A1X doub 4 n n C2 C3 A1A1X sing 5 n n N2 C5 A1A1X sing 6 n n N2 C6 A1A1X sing 7 n n C3 C4 A1A1X sing 8 n y C3 C16 A1A1X doub 9 n y N3 C7 A1A1X sing 10 n n N3 C8 A1A1X sing 11 n y N3 C10 A1A1X sing 12 n y N4 C8 A1A1X doub 13 n y N4 C9 A1A1X sing 14 n y C5 C15 A1A1X doub 15 n y N5 C8 A1A1X sing 16 n n C6 C7 A1A1X sing 17 n n C9 C10 A1A1X doub 18 n y C9 C14 A1A1X sing 19 n y C10 C11 A1A1X sing 20 n y C11 C12 A1A1X doub 21 n y C12 C13 A1A1X sing 22 n y C13 C14 A1A1X doub 23 n y C15 C16 A1A1X sing 24 n y C13 HC13 A1A1X sing 25 n n C15 HC15 A1A1X sing 26 n n C11 HC11 A1A1X sing 27 n n C12 HC12 A1A1X sing 28 n n C14 HC14 A1A1X sing 29 n n C16 HC16 A1A1X sing 30 n n C1 H1_3 A1A1X sing 31 n n C1 H1_2 A1A1X sing 32 n n C1 H1_1 A1A1X sing 33 n n C2 H2_1 A1A1X sing 34 n n C2 H2_2 A1A1X sing 35 n n C4 HC4 A1A1X sing 36 n n C7 H7_2 A1A1X sing 37 n n C7 H7_1 A1A1X sing 38 n n N2 HN2 A1A1X sing 39 n n N5 H5_1 A1A1X sing 40 n n N5 H5_2 A1A1X sing 41 n n # _atom_sites.entry_id 9D17 _atom_sites.fract_transf_matrix[1][1] 0.01392 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001838 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024504 _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] 0.009938 _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 A1A1X A 1 701 1 A1A1X ENI . C 3 GOL A 1 702 1 GOL GOL . D 3 GOL A 1 703 2 GOL GOL . E 4 DMS A 1 704 3 DMS DMS . F 4 DMS A 1 705 4 DMS DMS . G 4 DMS A 1 706 5 DMS DMS . H 5 HOH A 1 801 59 HOH HOH . H 5 HOH A 2 802 8 HOH HOH . H 5 HOH A 3 803 48 HOH HOH . H 5 HOH A 4 804 31 HOH HOH . H 5 HOH A 5 805 39 HOH HOH . H 5 HOH A 6 806 24 HOH HOH . H 5 HOH A 7 807 26 HOH HOH . H 5 HOH A 8 808 47 HOH HOH . H 5 HOH A 9 809 21 HOH HOH . H 5 HOH A 10 810 35 HOH HOH . H 5 HOH A 11 811 37 HOH HOH . H 5 HOH A 12 812 36 HOH HOH . H 5 HOH A 13 813 25 HOH HOH . H 5 HOH A 14 814 5 HOH HOH . H 5 HOH A 15 815 55 HOH HOH . H 5 HOH A 16 816 42 HOH HOH . H 5 HOH A 17 817 9 HOH HOH . H 5 HOH A 18 818 19 HOH HOH . H 5 HOH A 19 819 15 HOH HOH . H 5 HOH A 20 820 49 HOH HOH . H 5 HOH A 21 821 23 HOH HOH . H 5 HOH A 22 822 40 HOH HOH . H 5 HOH A 23 823 10 HOH HOH . H 5 HOH A 24 824 41 HOH HOH . H 5 HOH A 25 825 6 HOH HOH . H 5 HOH A 26 826 12 HOH HOH . H 5 HOH A 27 827 30 HOH HOH . H 5 HOH A 28 828 43 HOH HOH . H 5 HOH A 29 829 20 HOH HOH . H 5 HOH A 30 830 60 HOH HOH . H 5 HOH A 31 831 52 HOH HOH . H 5 HOH A 32 832 29 HOH HOH . H 5 HOH A 33 833 16 HOH HOH . H 5 HOH A 34 834 17 HOH HOH . H 5 HOH A 35 835 34 HOH HOH . H 5 HOH A 36 836 51 HOH HOH . H 5 HOH A 37 837 53 HOH HOH . H 5 HOH A 38 838 13 HOH HOH . H 5 HOH A 39 839 45 HOH HOH . H 5 HOH A 40 840 22 HOH HOH . H 5 HOH A 41 841 57 HOH HOH . H 5 HOH A 42 842 33 HOH HOH . H 5 HOH A 43 843 27 HOH HOH . H 5 HOH A 44 844 4 HOH HOH . H 5 HOH A 45 845 3 HOH HOH . H 5 HOH A 46 846 32 HOH HOH . H 5 HOH A 47 847 50 HOH HOH . H 5 HOH A 48 848 14 HOH HOH . H 5 HOH A 49 849 2 HOH HOH . H 5 HOH A 50 850 18 HOH HOH . H 5 HOH A 51 851 46 HOH HOH . H 5 HOH A 52 852 28 HOH HOH . H 5 HOH A 53 853 11 HOH HOH . H 5 HOH A 54 854 1 HOH HOH . H 5 HOH A 55 855 7 HOH HOH . H 5 HOH A 56 856 38 HOH HOH . H 5 HOH A 57 857 44 HOH HOH . H 5 HOH A 58 858 54 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 C13 A1A1X . . . B 2 13.808 5.514 39.862 1 40.55 ? C13 A1A1X 701 A 1 HETATM 2 C C15 A1A1X . . . B 2 11.926 8.662 48.969 1 74.39 ? C15 A1A1X 701 A 1 HETATM 3 C C11 A1A1X . . . B 2 14.276 6.19 42.083 1 43.89 ? C11 A1A1X 701 A 1 HETATM 4 C C12 A1A1X . . . B 2 14.538 5.393 41.013 1 46.98 ? C12 A1A1X 701 A 1 HETATM 5 C C14 A1A1X . . . B 2 12.798 6.411 39.736 1 42.56 ? C14 A1A1X 701 A 1 HETATM 6 C C16 A1A1X . . . B 2 11.4 8.331 50.216 1 69.94 ? C16 A1A1X 701 A 1 HETATM 7 C C1 A1A1X . . . B 2 8.865 6.507 51.961 1 51.25 ? C1 A1A1X 701 A 1 HETATM 8 C C10 A1A1X . . . B 2 13.256 7.086 41.947 1 36.6 ? C10 A1A1X 701 A 1 HETATM 9 C C2 A1A1X . . . B 2 10.301 6.738 51.79 1 61.12 ? C2 A1A1X 701 A 1 HETATM 10 C C3 A1A1X . . . B 2 10.835 7.093 50.439 1 69.49 ? C3 A1A1X 701 A 1 HETATM 11 C C4 A1A1X . . . B 2 10.85 6.204 49.316 1 65.81 ? C4 A1A1X 701 A 1 HETATM 12 C C5 A1A1X . . . B 2 11.882 7.742 47.888 1 66.64 ? C5 A1A1X 701 A 1 HETATM 13 C C6 A1A1X . . . B 2 12.313 7.619 45.364 1 51.48 ? C6 A1A1X 701 A 1 HETATM 14 C C7 A1A1X . . . B 2 13.212 8.253 44.23 1 51.53 ? C7 A1A1X 701 A 1 HETATM 15 C C8 A1A1X . . . B 2 11.671 8.675 42.134 1 56.24 ? C8 A1A1X 701 A 1 HETATM 16 C C9 A1A1X . . . B 2 12.509 7.202 40.788 1 41.66 ? C9 A1A1X 701 A 1 HETATM 17 N N1 A1A1X . . . B 2 11.361 6.477 48.075 1 57.26 ? N1 A1A1X 701 A 1 HETATM 18 N N2 A1A1X . . . B 2 12.478 8.117 46.645 1 61.01 ? N2 A1A1X 701 A 1 HETATM 19 N N3 A1A1X . . . B 2 12.745 8.012 42.857 1 54.66 ? N3 A1A1X 701 A 1 HETATM 20 N N4 A1A1X . . . B 2 11.505 8.206 40.872 1 52.19 ? N4 A1A1X 701 A 1 HETATM 21 N N5 A1A1X . . . B 2 10.923 9.69 42.73 1 67.34 ? N5 A1A1X 701 A 1 HETATM 22 O O1 A1A1X . . . B 2 11.49 6.736 45.144 1 50.03 ? O1 A1A1X 701 A 1 HETATM 23 H HC13 A1A1X . . . B 2 14.061 4.859 39.024 1 48.67 ? HC13 A1A1X 701 A 1 HETATM 24 H HC15 A1A1X . . . B 2 12.373 9.651 48.851 1 89.28 ? HC15 A1A1X 701 A 1 HETATM 25 H HC11 A1A1X . . . B 2 14.846 6.127 43.008 1 52.68 ? HC11 A1A1X 701 A 1 HETATM 26 H HC12 A1A1X . . . B 2 15.336 4.652 41.078 1 56.39 ? HC12 A1A1X 701 A 1 HETATM 27 H HC14 A1A1X . . . B 2 12.243 6.477 38.8 1 51.08 ? HC14 A1A1X 701 A 1 HETATM 28 H HC16 A1A1X . . . B 2 11.435 9.063 51.029 1 83.93 ? HC16 A1A1X 701 A 1 HETATM 29 H H1_3 A1A1X . . . B 2 8.612 6.315 53.019 1 61.52 ? H1_3 A1A1X 701 A 1 HETATM 30 H H1_2 A1A1X . . . B 2 8.526 5.634 51.373 1 61.52 ? H1_2 A1A1X 701 A 1 HETATM 31 H H1_1 A1A1X . . . B 2 8.275 7.381 51.63 1 61.52 ? H1_1 A1A1X 701 A 1 HETATM 32 H H2_1 A1A1X . . . B 2 10.816 5.832 52.182 1 73.35 ? H2_1 A1A1X 701 A 1 HETATM 33 H H2_2 A1A1X . . . B 2 10.587 7.515 52.533 1 73.35 ? H2_2 A1A1X 701 A 1 HETATM 34 H HC4 A1A1X . . . B 2 10.424 5.199 49.409 1 78.99 ? HC4 A1A1X 701 A 1 HETATM 35 H H7_2 A1A1X . . . B 2 13.308 9.357 44.37 1 61.84 ? H7_2 A1A1X 701 A 1 HETATM 36 H H7_1 A1A1X . . . B 2 14.263 7.881 44.303 1 61.84 ? H7_1 A1A1X 701 A 1 HETATM 37 H HN2 A1A1X . . . B 2 13.133 8.887 46.755 1 73.22 ? HN2 A1A1X 701 A 1 HETATM 38 H H5_1 A1A1X . . . B 2 10.135 9.46 43.29 1 80.82 ? H5_1 A1A1X 701 A 1 HETATM 39 H H5_2 A1A1X . . . B 2 11.172 10.649 42.603 1 80.82 ? H5_2 A1A1X 701 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 26 _model_server_stats.element_count 39 #