data_9D4D # _model_server_result.job_id pUoGeqRRuX1xcmt9rDAD0g _model_server_result.datetime_utc '2025-07-02 15:05:28' _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 9d4d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":708}' # _entry.id 9D4D # _exptl.entry_id 9D4D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 357.408 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(2-amino-1H-1,3-benzimidazol-4-yl)-N-{4-[(pyridin-4-yl)methyl]phenyl}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 98.22 _cell.angle_gamma 90 _cell.entry_id 9D4D _cell.length_a 72.65 _cell.length_b 41.11 _cell.length_c 103.13 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9D4D _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,I,J _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 3 _struct_asym.id I _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 34 A CYS 396 1_555 A SG CYS 68 A CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 72 A CYS 434 1_555 A SG CYS 190 A CYS 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf4 A SG CYS 236 A CYS 598 1_555 A SG CYS 256 A CYS 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 267 A CYS 629 1_555 A SG CYS 298 A CYS 660 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 A SG CYS 267 A CYS 629 1_555 A SG CYS 298 A CYS 660 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.019 ? # _chem_comp.formula 'C21 H19 N5 O' _chem_comp.formula_weight 357.408 _chem_comp.id A1A10 _chem_comp.mon_nstd_flag . _chem_comp.name 2-(2-amino-1H-1,3-benzimidazol-4-yl)-N-{4-[(pyridin-4-yl)methyl]phenyl}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 C02 N01 A1A10 sing 1 n n N03 C02 A1A10 doub 2 n y C04 N03 A1A10 sing 3 n y C05 C04 A1A10 doub 4 n y N06 C05 A1A10 sing 5 n y C07 C05 A1A10 sing 6 n y C08 C07 A1A10 doub 7 n y C09 C08 A1A10 sing 8 n y C10 C09 A1A10 doub 9 n y C11 C10 A1A10 sing 10 n n C12 C11 A1A10 sing 11 n n O13 C12 A1A10 doub 12 n n N14 C12 A1A10 sing 13 n n C15 N14 A1A10 sing 14 n n C16 C15 A1A10 doub 15 n y C17 C16 A1A10 sing 16 n y C18 C17 A1A10 doub 17 n y C20 C19 A1A10 sing 18 n n C21 C20 A1A10 doub 19 n y C22 C21 A1A10 sing 20 n y N23 C22 A1A10 doub 21 n y C24 N23 A1A10 sing 22 n y C25 C24 A1A10 doub 23 n y C19 C18 A1A10 sing 24 n n C26 C18 A1A10 sing 25 n y C27 C26 A1A10 doub 26 n y C02 N06 A1A10 sing 27 n y C04 C10 A1A10 sing 28 n y C15 C27 A1A10 sing 29 n y C20 C25 A1A10 sing 30 n y C07 H071 A1A10 sing 31 n n C08 H081 A1A10 sing 32 n n C09 H091 A1A10 sing 33 n n C11 H111 A1A10 sing 34 n n C11 H112 A1A10 sing 35 n n C16 H161 A1A10 sing 36 n n C17 H171 A1A10 sing 37 n n C19 H191 A1A10 sing 38 n n C19 H192 A1A10 sing 39 n n C21 H211 A1A10 sing 40 n n C22 H221 A1A10 sing 41 n n C24 H241 A1A10 sing 42 n n C25 H251 A1A10 sing 43 n n C26 H261 A1A10 sing 44 n n C27 H271 A1A10 sing 45 n n N01 H011 A1A10 sing 46 n n N01 H012 A1A10 sing 47 n n N06 H061 A1A10 sing 48 n n N14 H141 A1A10 sing 49 n n # _atom_sites.entry_id 9D4D _atom_sites.fract_transf_matrix[1][1] 0.013765 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001988 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024325 _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] 0.009797 _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 GOL A 1 701 1 GOL GOL . C 2 GOL A 1 702 2 GOL GOL . D 2 GOL A 1 703 3 GOL GOL . E 2 GOL A 1 704 4 GOL GOL . F 2 GOL A 1 705 5 GOL GOL . G 2 GOL A 1 706 6 GOL GOL . H 2 GOL A 1 707 7 GOL GOL . I 3 A1A10 A 1 708 1 A1A10 SD0 . J 4 HOH A 1 801 42 HOH HOH . J 4 HOH A 2 802 1 HOH HOH . J 4 HOH A 3 803 19 HOH HOH . J 4 HOH A 4 804 5 HOH HOH . J 4 HOH A 5 805 22 HOH HOH . J 4 HOH A 6 806 7 HOH HOH . J 4 HOH A 7 807 3 HOH HOH . J 4 HOH A 8 808 11 HOH HOH . J 4 HOH A 9 809 37 HOH HOH . J 4 HOH A 10 810 2 HOH HOH . J 4 HOH A 11 811 8 HOH HOH . J 4 HOH A 12 812 9 HOH HOH . J 4 HOH A 13 813 12 HOH HOH . J 4 HOH A 14 814 4 HOH HOH . J 4 HOH A 15 815 43 HOH HOH . J 4 HOH A 16 816 28 HOH HOH . J 4 HOH A 17 817 16 HOH HOH . J 4 HOH A 18 818 13 HOH HOH . J 4 HOH A 19 819 17 HOH HOH . J 4 HOH A 20 820 20 HOH HOH . J 4 HOH A 21 821 27 HOH HOH . J 4 HOH A 22 822 40 HOH HOH . J 4 HOH A 23 823 18 HOH HOH . J 4 HOH A 24 824 25 HOH HOH . J 4 HOH A 25 825 15 HOH HOH . J 4 HOH A 26 826 48 HOH HOH . J 4 HOH A 27 827 6 HOH HOH . J 4 HOH A 28 828 38 HOH HOH . J 4 HOH A 29 829 23 HOH HOH . J 4 HOH A 30 830 32 HOH HOH . J 4 HOH A 31 831 33 HOH HOH . J 4 HOH A 32 832 21 HOH HOH . J 4 HOH A 33 833 14 HOH HOH . J 4 HOH A 34 834 29 HOH HOH . J 4 HOH A 35 835 39 HOH HOH . J 4 HOH A 36 836 10 HOH HOH . J 4 HOH A 37 837 24 HOH HOH . J 4 HOH A 38 838 36 HOH HOH . J 4 HOH A 39 839 49 HOH HOH . J 4 HOH A 40 840 47 HOH HOH . J 4 HOH A 41 841 46 HOH HOH . J 4 HOH A 42 842 45 HOH HOH . J 4 HOH A 43 843 26 HOH HOH . J 4 HOH A 44 844 44 HOH HOH . J 4 HOH A 45 845 30 HOH HOH . J 4 HOH A 46 846 41 HOH HOH . J 4 HOH A 47 847 34 HOH HOH . J 4 HOH A 48 848 31 HOH HOH . J 4 HOH A 49 849 35 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 C02 A1A10 . . . I 3 15.506 5.797 42.539 1 72.61 ? C02 A1A10 708 A 1 HETATM 2 C C04 A1A10 . . . I 3 13.755 7.124 42.302 1 60.12 ? C04 A1A10 708 A 1 HETATM 3 C C05 A1A10 . . . I 3 13.799 6.263 41.166 1 57.03 ? C05 A1A10 708 A 1 HETATM 4 C C07 A1A10 . . . I 3 12.877 6.302 40.133 1 52.87 ? C07 A1A10 708 A 1 HETATM 5 C C08 A1A10 . . . I 3 11.878 7.244 40.261 1 48.38 ? C08 A1A10 708 A 1 HETATM 6 C C09 A1A10 . . . I 3 11.813 8.101 41.368 1 56.37 ? C09 A1A10 708 A 1 HETATM 7 C C10 A1A10 . . . I 3 12.737 8.081 42.403 1 64.88 ? C10 A1A10 708 A 1 HETATM 8 C C11 A1A10 . . . I 3 12.598 9.019 43.564 1 61.52 ? C11 A1A10 708 A 1 HETATM 9 C C12 A1A10 . . . I 3 11.807 8.411 44.693 1 56.64 ? C12 A1A10 708 A 1 HETATM 10 C C15 A1A10 . . . I 3 11.357 8.11 47.117 1 66.6 ? C15 A1A10 708 A 1 HETATM 11 C C16 A1A10 . . . I 3 11.999 7.369 48.118 1 54.76 ? C16 A1A10 708 A 1 HETATM 12 C C17 A1A10 . . . I 3 11.301 6.811 49.177 1 60.87 ? C17 A1A10 708 A 1 HETATM 13 C C18 A1A10 . . . I 3 9.925 6.946 49.316 1 66.61 ? C18 A1A10 708 A 1 HETATM 14 C C19 A1A10 . . . I 3 9.189 6.341 50.464 1 60.8 ? C19 A1A10 708 A 1 HETATM 15 C C20 A1A10 . . . I 3 8.588 4.991 50.246 1 48.87 ? C20 A1A10 708 A 1 HETATM 16 C C21 A1A10 . . . I 3 9.211 4.035 49.437 1 56.89 ? C21 A1A10 708 A 1 HETATM 17 C C22 A1A10 . . . I 3 8.612 2.781 49.265 1 55.59 ? C22 A1A10 708 A 1 HETATM 18 C C24 A1A10 . . . I 3 6.862 3.363 50.634 1 69.37 ? C24 A1A10 708 A 1 HETATM 19 C C25 A1A10 . . . I 3 7.388 4.637 50.853 1 44.49 ? C25 A1A10 708 A 1 HETATM 20 C C26 A1A10 . . . I 3 9.278 7.677 48.322 1 72.55 ? C26 A1A10 708 A 1 HETATM 21 C C27 A1A10 . . . I 3 9.964 8.241 47.253 1 53.62 ? C27 A1A10 708 A 1 HETATM 22 N N01 A1A10 . . . I 3 16.642 5.159 42.978 1 74.1 ? N01 A1A10 708 A 1 HETATM 23 N N03 A1A10 . . . I 3 14.842 6.822 43.166 1 69.14 ? N03 A1A10 708 A 1 HETATM 24 N N06 A1A10 . . . I 3 14.906 5.422 41.311 1 66.57 ? N06 A1A10 708 A 1 HETATM 25 N N14 A1A10 . . . I 3 12.067 8.673 46.035 1 64.94 ? N14 A1A10 708 A 1 HETATM 26 N N23 A1A10 . . . I 3 7.444 2.427 49.848 1 54.02 ? N23 A1A10 708 A 1 HETATM 27 O O13 A1A10 . . . I 3 10.911 7.639 44.413 1 65.32 ? O13 A1A10 708 A 1 HETATM 28 H H071 A1A10 . . . I 3 12.956 5.62 39.283 1 63.5 ? H071 A1A10 708 A 1 HETATM 29 H H081 A1A10 . . . I 3 11.128 7.31 39.47 1 58.12 ? H081 A1A10 708 A 1 HETATM 30 H H091 A1A10 . . . I 3 10.983 8.808 41.389 1 67.7 ? H091 A1A10 708 A 1 HETATM 31 H H111 A1A10 . . . I 3 12.121 9.971 43.24 1 73.89 ? H111 A1A10 708 A 1 HETATM 32 H H112 A1A10 . . . I 3 13.6 9.333 43.932 1 73.89 ? H112 A1A10 708 A 1 HETATM 33 H H161 A1A10 . . . I 3 13.08 7.204 48.097 1 65.77 ? H161 A1A10 708 A 1 HETATM 34 H H171 A1A10 . . . I 3 11.839 6.239 49.942 1 73.11 ? H171 A1A10 708 A 1 HETATM 35 H H191 A1A10 . . . I 3 9.847 6.289 51.363 1 73.02 ? H191 A1A10 708 A 1 HETATM 36 H H192 A1A10 . . . I 3 8.385 7.028 50.817 1 73.02 ? H192 A1A10 708 A 1 HETATM 37 H H211 A1A10 . . . I 3 10.156 4.243 48.935 1 68.33 ? H211 A1A10 708 A 1 HETATM 38 H H221 A1A10 . . . I 3 9.058 1.998 48.639 1 66.77 ? H221 A1A10 708 A 1 HETATM 39 H H241 A1A10 . . . I 3 5.921 3.034 51.096 1 83.31 ? H241 A1A10 708 A 1 HETATM 40 H H251 A1A10 . . . I 3 6.842 5.327 51.497 1 53.45 ? H251 A1A10 708 A 1 HETATM 41 H H261 A1A10 . . . I 3 8.195 7.823 48.366 1 87.13 ? H261 A1A10 708 A 1 HETATM 42 H H271 A1A10 . . . I 3 9.385 8.794 46.515 1 64.41 ? H271 A1A10 708 A 1 HETATM 43 H H011 A1A10 . . . I 3 17.13 5.483 43.788 1 88.98 ? H011 A1A10 708 A 1 HETATM 44 H H012 A1A10 . . . I 3 16.992 4.368 42.488 1 88.98 ? H012 A1A10 708 A 1 HETATM 45 H H061 A1A10 . . . I 3 15.193 4.708 40.663 1 79.95 ? H061 A1A10 708 A 1 HETATM 46 H H141 A1A10 . . . I 3 12.816 9.311 46.285 1 77.99 ? H141 A1A10 708 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #