data_3HNB # _model_server_result.job_id k7zuuV0rs9NVOGYEHsLMcw _model_server_result.datetime_utc '2024-11-26 10:06:53' _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 3hnb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3HNB # _exptl.entry_id 3HNB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 463.4 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R)-1-(2,4-dichlorophenoxy)-3-[(2E)-2-imino-3-(2-piperidin-1-ylethyl)-2,3-dihydro-1H-benzimidazol-1-yl]propan-2-ol _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 3HNB _cell.length_a 42.054 _cell.length_b 55.775 _cell.length_c 67.971 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HNB _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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 5 _struct_conn.ptnr1_auth_asym_id M _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 2174 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 157 _struct_conn.ptnr2_auth_asym_id M _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 2326 _struct_conn.ptnr2_symmetry 1_555 _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 2.033 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C23 H28 Cl2 N4 O2' _chem_comp.formula_weight 463.4 _chem_comp.id 768 _chem_comp.mon_nstd_flag . _chem_comp.name (2R)-1-(2,4-dichlorophenoxy)-3-[(2E)-2-imino-3-(2-piperidin-1-ylethyl)-2,3-dihydro-1H-benzimidazol-1-yl]propan-2-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-(2,4-dichlorophenoxy)-3-{2-imino-3-[2-(1-piperidinyl)ethyl]-2,3-dihydro-1H-benzimidazol-1-yl}-2-propanol # 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 O1 C16 768 sing 1 n n C16 C17 768 sing 2 n n C16 C15 768 sing 3 n n C17 O2 768 sing 4 n n O2 C18 768 sing 5 n n C18 C19 768 doub 6 n y C18 C23 768 sing 7 n y C19 C20 768 sing 8 n y C20 C21 768 doub 9 n y C21 CL1 768 sing 10 n n C21 C22 768 sing 11 n y C22 C23 768 doub 12 n y C23 CL2 768 sing 13 n n C15 N3 768 sing 14 n n N3 C14 768 sing 15 n n N3 C13 768 sing 16 n n C14 N4 768 doub 17 n n C14 N2 768 sing 18 n n C13 C12 768 doub 19 n y C13 C8 768 sing 20 n y C12 C11 768 sing 21 n y C11 C10 768 doub 22 n y C10 C9 768 sing 23 n y C9 C8 768 doub 24 n y C8 N2 768 sing 25 n n N2 C7 768 sing 26 n n C7 C6 768 sing 27 n n C6 N1 768 sing 28 n n N1 C5 768 sing 29 n n N1 C1 768 sing 30 n n C5 C4 768 sing 31 n n C4 C3 768 sing 32 n n C3 C2 768 sing 33 n n C2 C1 768 sing 34 n n O1 HO1 768 sing 35 n n C16 H16 768 sing 36 n n C17 H17 768 sing 37 n n C17 H17A 768 sing 38 n n C19 H19 768 sing 39 n n C20 H20 768 sing 40 n n C22 H22 768 sing 41 n n C15 H15 768 sing 42 n n C15 H15A 768 sing 43 n n N4 HN4 768 sing 44 n n C12 H12 768 sing 45 n n C11 H11 768 sing 46 n n C10 H10 768 sing 47 n n C9 H9 768 sing 48 n n C7 H7 768 sing 49 n n C7 H7A 768 sing 50 n n C6 H6 768 sing 51 n n C6 H6A 768 sing 52 n n C5 H5 768 sing 53 n n C5 H5A 768 sing 54 n n C4 H4 768 sing 55 n n C4 H4A 768 sing 56 n n C3 H3 768 sing 57 n n C3 H3A 768 sing 58 n n C2 H2 768 sing 59 n n C2 H2A 768 sing 60 n n C1 H1 768 sing 61 n n C1 H1A 768 sing 62 n n # _atom_sites.entry_id 3HNB _atom_sites.fract_transf_matrix[1][1] 0.023779 _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] 0.017929 _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] 0.014712 _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 2 768 M 1 1 1 768 768 . C 3 HOH M 1 2 2 HOH HOH . C 3 HOH M 2 5 5 HOH HOH . C 3 HOH M 3 6 6 HOH HOH . C 3 HOH M 4 7 7 HOH HOH . C 3 HOH M 5 8 8 HOH HOH . C 3 HOH M 6 9 9 HOH HOH . C 3 HOH M 7 10 10 HOH HOH . C 3 HOH M 8 13 13 HOH HOH . C 3 HOH M 9 14 14 HOH HOH . C 3 HOH M 10 16 16 HOH HOH . C 3 HOH M 11 17 17 HOH HOH . C 3 HOH M 12 18 18 HOH HOH . C 3 HOH M 13 19 19 HOH HOH . C 3 HOH M 14 20 20 HOH HOH . C 3 HOH M 15 21 21 HOH HOH . C 3 HOH M 16 22 22 HOH HOH . C 3 HOH M 17 23 23 HOH HOH . C 3 HOH M 18 24 24 HOH HOH . C 3 HOH M 19 25 25 HOH HOH . C 3 HOH M 20 26 26 HOH HOH . C 3 HOH M 21 27 27 HOH HOH . C 3 HOH M 22 28 28 HOH HOH . C 3 HOH M 23 29 29 HOH HOH . C 3 HOH M 24 30 30 HOH HOH . C 3 HOH M 25 31 31 HOH HOH . C 3 HOH M 26 32 32 HOH HOH . C 3 HOH M 27 33 33 HOH HOH . C 3 HOH M 28 34 34 HOH HOH . C 3 HOH M 29 36 36 HOH HOH . C 3 HOH M 30 37 37 HOH HOH . C 3 HOH M 31 38 38 HOH HOH . C 3 HOH M 32 39 39 HOH HOH . C 3 HOH M 33 40 40 HOH HOH . C 3 HOH M 34 41 41 HOH HOH . C 3 HOH M 35 42 42 HOH HOH . C 3 HOH M 36 43 43 HOH HOH . C 3 HOH M 37 44 44 HOH HOH . C 3 HOH M 38 46 46 HOH HOH . C 3 HOH M 39 47 47 HOH HOH . C 3 HOH M 40 48 48 HOH HOH . C 3 HOH M 41 49 49 HOH HOH . C 3 HOH M 42 50 50 HOH HOH . C 3 HOH M 43 51 51 HOH HOH . C 3 HOH M 44 52 52 HOH HOH . C 3 HOH M 45 53 53 HOH HOH . C 3 HOH M 46 54 54 HOH HOH . C 3 HOH M 47 55 55 HOH HOH . C 3 HOH M 48 56 56 HOH HOH . C 3 HOH M 49 58 58 HOH HOH . C 3 HOH M 50 59 59 HOH HOH . C 3 HOH M 51 60 60 HOH HOH . C 3 HOH M 52 61 61 HOH HOH . C 3 HOH M 53 62 62 HOH HOH . C 3 HOH M 54 63 63 HOH HOH . C 3 HOH M 55 64 64 HOH HOH . C 3 HOH M 56 65 65 HOH HOH . C 3 HOH M 57 66 66 HOH HOH . C 3 HOH M 58 67 67 HOH HOH . C 3 HOH M 59 68 68 HOH HOH . C 3 HOH M 60 69 69 HOH HOH . C 3 HOH M 61 70 70 HOH HOH . C 3 HOH M 62 71 71 HOH HOH . C 3 HOH M 63 72 72 HOH HOH . C 3 HOH M 64 73 73 HOH HOH . C 3 HOH M 65 74 74 HOH HOH . C 3 HOH M 66 75 75 HOH HOH . C 3 HOH M 67 76 76 HOH HOH . C 3 HOH M 68 77 77 HOH HOH . C 3 HOH M 69 78 78 HOH HOH . C 3 HOH M 70 79 79 HOH HOH . C 3 HOH M 71 83 83 HOH HOH . C 3 HOH M 72 85 85 HOH HOH . C 3 HOH M 73 86 86 HOH HOH . C 3 HOH M 74 87 87 HOH HOH . C 3 HOH M 75 91 91 HOH HOH . C 3 HOH M 76 92 92 HOH HOH . C 3 HOH M 77 94 94 HOH HOH . C 3 HOH M 78 96 96 HOH HOH . C 3 HOH M 79 97 97 HOH HOH . C 3 HOH M 80 98 98 HOH HOH . C 3 HOH M 81 99 99 HOH HOH . C 3 HOH M 82 100 100 HOH HOH . C 3 HOH M 83 104 104 HOH HOH . C 3 HOH M 84 106 106 HOH HOH . C 3 HOH M 85 107 107 HOH HOH . C 3 HOH M 86 109 109 HOH HOH . C 3 HOH M 87 110 110 HOH HOH . C 3 HOH M 88 111 111 HOH HOH . C 3 HOH M 89 113 113 HOH HOH . C 3 HOH M 90 114 114 HOH HOH . C 3 HOH M 91 115 115 HOH HOH . C 3 HOH M 92 116 116 HOH HOH . C 3 HOH M 93 117 117 HOH HOH . C 3 HOH M 94 118 118 HOH HOH . C 3 HOH M 95 119 119 HOH HOH . C 3 HOH M 96 120 120 HOH HOH . C 3 HOH M 97 121 121 HOH HOH . C 3 HOH M 98 123 123 HOH HOH . C 3 HOH M 99 125 125 HOH HOH . C 3 HOH M 100 127 127 HOH HOH . C 3 HOH M 101 128 128 HOH HOH . C 3 HOH M 102 130 130 HOH HOH . C 3 HOH M 103 131 131 HOH HOH . C 3 HOH M 104 133 133 HOH HOH . C 3 HOH M 105 137 137 HOH HOH . C 3 HOH M 106 138 138 HOH HOH . C 3 HOH M 107 140 140 HOH HOH . C 3 HOH M 108 141 141 HOH HOH . C 3 HOH M 109 142 142 HOH HOH . C 3 HOH M 110 143 143 HOH HOH . C 3 HOH M 111 144 144 HOH HOH . C 3 HOH M 112 145 145 HOH HOH . C 3 HOH M 113 150 150 HOH HOH . C 3 HOH M 114 154 154 HOH HOH . C 3 HOH M 115 160 160 HOH HOH . C 3 HOH M 116 162 162 HOH HOH . C 3 HOH M 117 164 164 HOH HOH . C 3 HOH M 118 165 165 HOH HOH . C 3 HOH M 119 166 166 HOH HOH . C 3 HOH M 120 167 167 HOH HOH . C 3 HOH M 121 174 174 HOH HOH . C 3 HOH M 122 176 176 HOH HOH . C 3 HOH M 123 179 179 HOH HOH . C 3 HOH M 124 183 183 HOH HOH . C 3 HOH M 125 193 193 HOH HOH . C 3 HOH M 126 194 194 HOH HOH . C 3 HOH M 127 195 195 HOH HOH . C 3 HOH M 128 196 196 HOH HOH . C 3 HOH M 129 197 197 HOH HOH . C 3 HOH M 130 198 198 HOH HOH . C 3 HOH M 131 199 199 HOH HOH . C 3 HOH M 132 201 201 HOH HOH . C 3 HOH M 133 205 205 HOH HOH . C 3 HOH M 134 207 207 HOH HOH . C 3 HOH M 135 211 211 HOH HOH . C 3 HOH M 136 214 214 HOH HOH . C 3 HOH M 137 215 215 HOH HOH . C 3 HOH M 138 216 216 HOH HOH . C 3 HOH M 139 217 217 HOH HOH . C 3 HOH M 140 218 218 HOH HOH . C 3 HOH M 141 219 219 HOH HOH . C 3 HOH M 142 221 221 HOH HOH . C 3 HOH M 143 222 222 HOH HOH . C 3 HOH M 144 223 223 HOH HOH . C 3 HOH M 145 225 225 HOH HOH . C 3 HOH M 146 228 228 HOH HOH . C 3 HOH M 147 229 229 HOH HOH . C 3 HOH M 148 230 230 HOH HOH . C 3 HOH M 149 231 231 HOH HOH . C 3 HOH M 150 239 239 HOH HOH . C 3 HOH M 151 246 246 HOH HOH . C 3 HOH M 152 247 247 HOH HOH . C 3 HOH M 153 250 250 HOH HOH . C 3 HOH M 154 252 252 HOH HOH . C 3 HOH M 155 253 253 HOH HOH . C 3 HOH M 156 254 254 HOH HOH . C 3 HOH M 157 256 256 HOH HOH . C 3 HOH M 158 260 260 HOH HOH . C 3 HOH M 159 262 262 HOH HOH . C 3 HOH M 160 264 264 HOH HOH . C 3 HOH M 161 268 268 HOH HOH . C 3 HOH M 162 269 269 HOH HOH . C 3 HOH M 163 271 271 HOH HOH . C 3 HOH M 164 272 272 HOH HOH . C 3 HOH M 165 273 273 HOH HOH . C 3 HOH M 166 274 274 HOH HOH . C 3 HOH M 167 275 275 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 O O1 768 . . . B 2 -5.235 5.334 28.512 1 30.99 ? O1 768 1 M 1 HETATM 2 C C16 768 . . . B 2 -3.949 5.106 29.089 1 30.47 ? C16 768 1 M 1 HETATM 3 C C17 768 . . . B 2 -3.845 3.651 29.573 1 30.74 ? C17 768 1 M 1 HETATM 4 O O2 768 . . . B 2 -2.518 3.131 29.473 1 31.05 ? O2 768 1 M 1 HETATM 5 C C18 768 . . . B 2 -1.811 2.544 30.499 1 30.69 ? C18 768 1 M 1 HETATM 6 C C19 768 . . . B 2 -2.126 1.264 30.949 1 30.64 ? C19 768 1 M 1 HETATM 7 C C20 768 . . . B 2 -1.366 0.683 31.969 1 30.55 ? C20 768 1 M 1 HETATM 8 C C21 768 . . . B 2 -0.275 1.372 32.529 1 30.69 ? C21 768 1 M 1 HETATM 9 CL CL1 768 . . . B 2 0.547 0.777 33.638 1 31.01 ? CL1 768 1 M 1 HETATM 10 C C22 768 . . . B 2 0.091 2.651 32.1 1 30.71 ? C22 768 1 M 1 HETATM 11 C C23 768 . . . B 2 -0.621 3.243 31.087 1 30.32 ? C23 768 1 M 1 HETATM 12 CL CL2 768 . . . B 2 -0.209 4.61 30.666 1 30.18 ? CL2 768 1 M 1 HETATM 13 C C15 768 . . . B 2 -2.974 5.461 27.96 1 29.4 ? C15 768 1 M 1 HETATM 14 N N3 768 . . . B 2 -2.877 6.922 28.011 1 28.7 ? N3 768 1 M 1 HETATM 15 C C14 768 . . . B 2 -3.478 7.802 27.295 1 28.31 ? C14 768 1 M 1 HETATM 16 N N4 768 . . . B 2 -4.308 7.354 26.314 1 29 ? N4 768 1 M 1 HETATM 17 C C13 768 . . . B 2 -2.185 7.606 28.907 1 28.62 ? C13 768 1 M 1 HETATM 18 C C12 768 . . . B 2 -1.335 7.215 29.924 1 28.66 ? C12 768 1 M 1 HETATM 19 C C11 768 . . . B 2 -0.691 8.175 30.695 1 28.8 ? C11 768 1 M 1 HETATM 20 C C10 768 . . . B 2 -0.89 9.54 30.446 1 28.84 ? C10 768 1 M 1 HETATM 21 C C9 768 . . . B 2 -1.736 9.985 29.426 1 28.86 ? C9 768 1 M 1 HETATM 22 C C8 768 . . . B 2 -2.393 9.052 28.632 1 28.56 ? C8 768 1 M 1 HETATM 23 N N2 768 . . . B 2 -3.255 9.105 27.622 1 28.64 ? N2 768 1 M 1 HETATM 24 C C7 768 . . . B 2 -3.754 10.322 27.001 1 28.78 ? C7 768 1 M 1 HETATM 25 C C6 768 . . . B 2 -4.713 10.088 25.844 1 29.05 ? C6 768 1 M 1 HETATM 26 N N1 768 . . . B 2 -6.05 10.105 26.399 1 29.18 ? N1 768 1 M 1 HETATM 27 C C5 768 . . . B 2 -6.396 9.302 27.564 1 29.47 ? C5 768 1 M 1 HETATM 28 C C4 768 . . . B 2 -6.398 10.375 28.651 1 29.4 ? C4 768 1 M 1 HETATM 29 C C3 768 . . . B 2 -7.294 11.567 28.296 1 29.61 ? C3 768 1 M 1 HETATM 30 C C2 768 . . . B 2 -7.175 12.072 26.841 1 29.51 ? C2 768 1 M 1 HETATM 31 C C1 768 . . . B 2 -7.119 10.931 25.827 1 29.58 ? C1 768 1 M 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #