data_A1EMG # _chem_comp.id A1EMG _chem_comp.name "3-(1H-benzimidazol-5-yl)-5-[1-[2-(3,4-dimethoxyphenyl)ethanoyl]piperidin-4-yl]oxy-1H-benzimidazol-2-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C29 H29 N5 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-02-27 _chem_comp.pdbx_modified_date 2026-02-27 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 527.571 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1EMG _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 9LZV _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _chem_comp.pdbx_pcm ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal A1EMG C13 C1 C 0 1 N N N N N N 51.732 14.409 182.137 -0.248 -1.131 0.710 C13 A1EMG 1 A1EMG C15 C2 C 0 1 N N N N N N 50.159 13.727 180.509 -2.225 -1.910 -0.604 C15 A1EMG 2 A1EMG C20 C3 C 0 1 Y N N N N N 53.015 15.454 187.049 4.283 -2.652 -0.549 C20 A1EMG 3 A1EMG C22 C4 C 0 1 N N N N N N 54.249 17.073 188.176 6.441 -2.138 -0.686 C22 A1EMG 4 A1EMG C04 C5 C 0 1 Y N N N N N 56.011 10.741 180.288 -8.787 -0.542 0.259 C04 A1EMG 5 A1EMG C06 C6 C 0 1 Y N N N N N 53.869 11.199 179.331 -6.514 0.051 0.731 C06 A1EMG 6 A1EMG C11 C7 C 0 1 N N N N N N 51.451 12.051 181.572 -2.495 -1.179 1.802 C11 A1EMG 7 A1EMG C18 C8 C 0 1 Y N N N N N 51.832 14.195 185.329 1.925 -2.483 -0.161 C18 A1EMG 8 A1EMG C27 C9 C 0 1 Y N N N N N 54.438 20.840 185.172 7.030 1.825 1.729 C27 A1EMG 9 A1EMG C01 C10 C 0 1 N N N N N N 58.704 11.377 180.306 -11.247 0.042 -0.701 C01 A1EMG 10 A1EMG C26 C11 C 0 1 Y N N N N N 53.880 19.638 185.546 6.440 0.623 1.406 C26 A1EMG 11 A1EMG C08 C12 C 0 1 N N N N N N 51.511 12.006 178.928 -4.317 -0.916 0.189 C08 A1EMG 12 A1EMG C33 C13 C 0 1 Y N N N N N 55.794 19.077 186.828 6.972 0.952 -0.919 C33 A1EMG 13 A1EMG O02 O1 O 0 1 N N N N N N 57.742 12.417 180.094 -10.231 1.045 -0.768 O02 A1EMG 14 A1EMG C03 C14 C 0 1 Y N N N N N 56.440 11.978 179.848 -9.007 0.717 -0.277 C03 A1EMG 15 A1EMG C05 C15 C 0 1 Y N N N N N 54.714 10.363 180.025 -7.543 -0.871 0.763 C05 A1EMG 16 A1EMG C07 C16 C 0 1 N N N N N N 52.433 10.778 179.020 -5.160 -0.313 1.283 C07 A1EMG 17 A1EMG O09 O2 O 0 1 N N N N N N 51.104 12.537 177.974 -4.772 -1.038 -0.929 O09 A1EMG 18 A1EMG N10 N1 N 0 1 N N N N N N 51.095 12.537 180.148 -3.059 -1.320 0.452 N10 A1EMG 19 A1EMG C12 C17 C 0 1 N N N N N N 51.530 13.155 182.616 -1.168 -0.419 1.705 C12 A1EMG 20 A1EMG C14 C18 C 0 1 N N N N N N 50.775 14.880 181.296 -0.902 -1.141 -0.674 C14 A1EMG 21 A1EMG O16 O3 O 0 1 N N N N N N 51.767 15.400 183.135 1.002 -0.442 0.641 O16 A1EMG 22 A1EMG C17 C19 C 0 1 Y N N N N N 52.147 15.235 184.445 2.084 -1.166 0.248 C17 A1EMG 23 A1EMG C19 C20 C 0 1 Y N N N N N 52.293 14.306 186.649 3.020 -3.225 -0.557 C19 A1EMG 24 A1EMG N21 N2 N 0 1 N N N N N N 53.604 15.820 188.330 5.551 -3.129 -0.882 N21 A1EMG 25 A1EMG O23 O4 O 0 1 N N N N N N 54.776 17.674 189.021 7.639 -2.223 -0.883 O23 A1EMG 26 A1EMG N24 N3 N 0 1 N N N N N N 54.066 17.501 186.842 5.806 -1.041 -0.232 N24 A1EMG 27 A1EMG C25 C21 C 0 1 Y N N N N N 54.560 18.753 186.366 6.410 0.185 0.083 C25 A1EMG 28 A1EMG C28 C22 C 0 1 Y N N N N N 55.734 21.149 185.654 7.599 2.607 0.733 C28 A1EMG 29 A1EMG N29 N4 N 0 1 Y N N N N N 56.574 22.160 185.465 8.249 3.826 0.724 N29 A1EMG 30 A1EMG C30 C23 C 0 1 Y N N N N N 57.641 21.971 186.146 8.589 4.094 -0.565 C30 A1EMG 31 A1EMG N31 N5 N 0 1 Y N N N N N 57.592 20.823 186.788 8.194 3.128 -1.342 N31 A1EMG 32 A1EMG C32 C24 C 0 1 Y N N N N N 56.404 20.294 186.465 7.573 2.173 -0.603 C32 A1EMG 33 A1EMG C34 C25 C 0 1 Y N N N N N 53.292 16.478 186.159 4.445 -1.329 -0.137 C34 A1EMG 34 A1EMG C35 C26 C 0 1 Y N N N N N 52.842 16.368 184.860 3.344 -0.589 0.264 C35 A1EMG 35 A1EMG C36 C27 C 0 1 Y N N N N N 54.307 12.431 178.880 -6.725 1.308 0.193 C36 A1EMG 36 A1EMG C37 C28 C 0 1 Y N N N N N 55.600 12.818 179.143 -7.970 1.646 -0.309 C37 A1EMG 37 A1EMG O38 O5 O 0 1 N N N N N N 56.113 14.040 178.725 -8.179 2.881 -0.839 O38 A1EMG 38 A1EMG C39 C29 C 0 1 N N N N N N 55.213 15.011 178.279 -7.068 3.781 -0.845 C39 A1EMG 39 A1EMG H1 H1 H 0 1 N N N N N N 52.698 14.429 181.611 -0.081 -2.156 1.040 H1 A1EMG 40 A1EMG H2 H2 H 0 1 N N N N N N 49.769 14.140 179.567 -2.028 -2.956 -0.373 H2 A1EMG 41 A1EMG H3 H3 H 0 1 N N N N N N 49.327 13.325 181.106 -2.740 -1.838 -1.562 H3 A1EMG 42 A1EMG H4 H4 H 0 1 N N N N N N 56.679 10.085 180.827 -9.590 -1.264 0.285 H4 A1EMG 43 A1EMG H5 H5 H 0 1 N N N N N N 50.683 11.331 181.891 -3.189 -0.624 2.432 H5 A1EMG 44 A1EMG H6 H6 H 0 1 N N N N N N 52.429 11.549 181.529 -2.320 -2.165 2.231 H6 A1EMG 45 A1EMG H7 H7 H 0 1 N N N N N N 51.256 13.340 185.006 0.942 -2.930 -0.167 H7 A1EMG 46 A1EMG H8 H8 H 0 1 N N N N N N 53.904 21.526 184.531 7.046 2.161 2.755 H8 A1EMG 47 A1EMG H9 H9 H 0 1 N N N N N N 59.692 11.823 180.490 -11.414 -0.237 0.339 H9 A1EMG 48 A1EMG H10 H10 H 0 1 N N N N N N 58.406 10.774 181.176 -12.172 0.433 -1.126 H10 A1EMG 49 A1EMG H11 H11 H 0 1 N N N N N N 58.752 10.735 179.414 -10.930 -0.835 -1.266 H11 A1EMG 50 A1EMG H12 H12 H 0 1 N N N N N N 52.892 19.380 185.193 5.998 0.016 2.182 H12 A1EMG 51 A1EMG H13 H13 H 0 1 N N N N N N 56.315 18.394 187.482 6.947 0.609 -1.943 H13 A1EMG 52 A1EMG H14 H14 H 0 1 N N N N N N 54.356 9.403 180.366 -7.375 -1.852 1.184 H14 A1EMG 53 A1EMG H15 H15 H 0 1 N N N N N N 52.071 10.114 179.819 -4.671 0.582 1.667 H15 A1EMG 54 A1EMG H16 H16 H 0 1 N N N N N N 52.415 10.241 178.060 -5.279 -1.036 2.090 H16 A1EMG 55 A1EMG H17 H17 H 0 1 N N N N N N 50.584 13.157 183.177 -0.692 -0.391 2.685 H17 A1EMG 56 A1EMG H18 H18 H 0 1 N N N N N N 52.360 12.916 183.297 -1.357 0.599 1.362 H18 A1EMG 57 A1EMG H19 H19 H 0 1 N N N N N N 51.227 15.599 180.596 -1.092 -0.116 -0.994 H19 A1EMG 58 A1EMG H20 H20 H 0 1 N N N N N N 49.990 15.382 181.881 -0.236 -1.627 -1.387 H20 A1EMG 59 A1EMG H21 H21 H 0 1 N N N N N N 52.097 13.516 187.359 2.894 -4.251 -0.872 H21 A1EMG 60 A1EMG H22 H22 H 0 1 N N N N N N 53.561 15.281 189.171 5.756 -4.022 -1.201 H22 A1EMG 61 A1EMG H23 H23 H 0 1 N N N N N N 56.399 22.951 184.878 8.429 4.388 1.495 H23 A1EMG 62 A1EMG H24 H24 H 0 1 N N N N N N 58.471 22.661 186.188 9.111 4.980 -0.896 H24 A1EMG 63 A1EMG H26 H26 H 0 1 N N N N N N 53.030 17.167 184.159 3.466 0.436 0.582 H26 A1EMG 64 A1EMG H27 H27 H 0 1 N N N N N N 53.643 13.080 178.329 -5.919 2.026 0.169 H27 A1EMG 65 A1EMG H28 H28 H 0 1 N N N N N N 55.765 15.916 177.985 -6.735 3.953 0.179 H28 A1EMG 66 A1EMG H29 H29 H 0 1 N N N N N N 54.655 14.624 177.413 -6.253 3.347 -1.424 H29 A1EMG 67 A1EMG H30 H30 H 0 1 N N N N N N 54.510 15.258 179.088 -7.370 4.727 -1.293 H30 A1EMG 68 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A1EMG O09 C08 DOUB N N 1 A1EMG C39 O38 SING N N 2 A1EMG O38 C37 SING N N 3 A1EMG C36 C37 DOUB Y N 4 A1EMG C36 C06 SING Y N 5 A1EMG C08 C07 SING N N 6 A1EMG C08 N10 SING N N 7 A1EMG C07 C06 SING N N 8 A1EMG C37 C03 SING Y N 9 A1EMG C06 C05 DOUB Y N 10 A1EMG C03 O02 SING N N 11 A1EMG C03 C04 DOUB Y N 12 A1EMG C05 C04 SING Y N 13 A1EMG O02 C01 SING N N 14 A1EMG N10 C15 SING N N 15 A1EMG N10 C11 SING N N 16 A1EMG C15 C14 SING N N 17 A1EMG C14 C13 SING N N 18 A1EMG C11 C12 SING N N 19 A1EMG C13 C12 SING N N 20 A1EMG C13 O16 SING N N 21 A1EMG O16 C17 SING N N 22 A1EMG C17 C35 DOUB Y N 23 A1EMG C17 C18 SING Y N 24 A1EMG C35 C34 SING Y N 25 A1EMG C27 C26 DOUB Y N 26 A1EMG C27 C28 SING Y N 27 A1EMG C18 C19 DOUB Y N 28 A1EMG N29 C28 SING Y N 29 A1EMG N29 C30 SING Y N 30 A1EMG C26 C25 SING Y N 31 A1EMG C28 C32 DOUB Y N 32 A1EMG C30 N31 DOUB Y N 33 A1EMG C34 N24 SING N N 34 A1EMG C34 C20 DOUB Y N 35 A1EMG C25 C33 DOUB Y N 36 A1EMG C25 N24 SING N N 37 A1EMG C32 N31 SING Y N 38 A1EMG C32 C33 SING Y N 39 A1EMG C19 C20 SING Y N 40 A1EMG N24 C22 SING N N 41 A1EMG C20 N21 SING N N 42 A1EMG C22 N21 SING N N 43 A1EMG C22 O23 DOUB N N 44 A1EMG C13 H1 SING N N 45 A1EMG C15 H2 SING N N 46 A1EMG C15 H3 SING N N 47 A1EMG C04 H4 SING N N 48 A1EMG C11 H5 SING N N 49 A1EMG C11 H6 SING N N 50 A1EMG C18 H7 SING N N 51 A1EMG C27 H8 SING N N 52 A1EMG C01 H9 SING N N 53 A1EMG C01 H10 SING N N 54 A1EMG C01 H11 SING N N 55 A1EMG C26 H12 SING N N 56 A1EMG C33 H13 SING N N 57 A1EMG C05 H14 SING N N 58 A1EMG C07 H15 SING N N 59 A1EMG C07 H16 SING N N 60 A1EMG C12 H17 SING N N 61 A1EMG C12 H18 SING N N 62 A1EMG C14 H19 SING N N 63 A1EMG C14 H20 SING N N 64 A1EMG C19 H21 SING N N 65 A1EMG N21 H22 SING N N 66 A1EMG N29 H23 SING N N 67 A1EMG C30 H24 SING N N 68 A1EMG C35 H26 SING N N 69 A1EMG C36 H27 SING N N 70 A1EMG C39 H28 SING N N 71 A1EMG C39 H29 SING N N 72 A1EMG C39 H30 SING N N 73 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor A1EMG InChI InChI 1.06 "InChI=1S/C29H29N5O5/c1-37-26-8-3-18(13-27(26)38-2)14-28(35)33-11-9-20(10-12-33)39-21-5-7-23-25(16-21)34(29(36)32-23)19-4-6-22-24(15-19)31-17-30-22/h3-8,13,15-17,20H,9-12,14H2,1-2H3,(H,30,31)(H,32,36)" A1EMG InChIKey InChI 1.06 VARRNOOVAYKSMS-UHFFFAOYSA-N A1EMG SMILES_CANONICAL CACTVS 3.385 "COc1ccc(CC(=O)N2CCC(CC2)Oc3ccc4NC(=O)N(c5ccc6[nH]cnc6c5)c4c3)cc1OC" A1EMG SMILES CACTVS 3.385 "COc1ccc(CC(=O)N2CCC(CC2)Oc3ccc4NC(=O)N(c5ccc6[nH]cnc6c5)c4c3)cc1OC" A1EMG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COc1ccc(cc1OC)CC(=O)N2CCC(CC2)Oc3ccc4c(c3)N(C(=O)N4)c5ccc6c(c5)nc[nH]6" A1EMG SMILES "OpenEye OEToolkits" 2.0.7 "COc1ccc(cc1OC)CC(=O)N2CCC(CC2)Oc3ccc4c(c3)N(C(=O)N4)c5ccc6c(c5)nc[nH]6" # _pdbx_chem_comp_identifier.comp_id A1EMG _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "3-(1~{H}-benzimidazol-5-yl)-5-[1-[2-(3,4-dimethoxyphenyl)ethanoyl]piperidin-4-yl]oxy-1~{H}-benzimidazol-2-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1EMG "Create component" 2025-02-27 PDBC A1EMG "Initial release" 2026-03-04 RCSB #