data_YD8 # _chem_comp.id YD8 _chem_comp.name "1-[2,4-dimethyl-5-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-pyrrol-3-yl]ethanone" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H25 N5 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-04-06 _chem_comp.pdbx_modified_date 2022-03-25 _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 351.445 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YD8 _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 7EHY _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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.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 YD8 C1 C1 C 0 1 Y N N 28.461 30.724 41.908 -1.865 -0.359 -0.304 C1 YD8 1 YD8 C11 C2 C 0 1 N N N 32.424 30.205 43.071 -5.842 -1.822 0.361 C11 YD8 2 YD8 C12 C3 C 0 1 N N N 31.080 30.928 43.221 -4.477 -1.172 0.597 C12 YD8 3 YD8 C13 C4 C 0 1 N N N 34.734 30.897 42.914 -8.225 -1.393 0.293 C13 YD8 4 YD8 C15 C5 C 0 1 Y N N 25.171 30.582 40.656 1.531 0.665 0.004 C15 YD8 5 YD8 C17 C6 C 0 1 Y N N 23.790 30.025 40.673 2.992 0.487 0.060 C17 YD8 6 YD8 C18 C7 C 0 1 Y N N 22.597 30.573 39.985 3.654 -0.695 -0.056 C18 YD8 7 YD8 C19 C8 C 0 1 Y N N 21.599 29.534 40.405 5.039 -0.408 0.055 C19 YD8 8 YD8 C2 C9 C 0 1 Y N N 27.191 30.770 41.334 -0.596 0.212 -0.165 C2 YD8 9 YD8 C20 C10 C 0 1 Y N N 22.278 28.560 41.295 5.153 0.960 0.237 C20 YD8 10 YD8 C22 C11 C 0 1 N N N 21.655 27.364 41.956 6.441 1.723 0.405 C22 YD8 11 YD8 C23 C12 C 0 1 N N N 20.138 29.465 40.150 6.138 -1.374 -0.010 C23 YD8 12 YD8 C24 C13 C 0 1 N N N 19.473 30.809 40.147 6.828 -1.644 -1.322 C24 YD8 13 YD8 C26 C14 C 0 1 N N N 22.519 31.806 39.102 3.034 -2.053 -0.264 C26 YD8 14 YD8 C3 C15 C 0 1 Y N N 26.892 31.715 40.232 -0.478 1.602 0.014 C3 YD8 15 YD8 C4 C16 C 0 1 Y N N 27.914 32.537 39.811 -1.614 2.396 0.051 C4 YD8 16 YD8 C5 C17 C 0 1 Y N N 29.164 32.469 40.413 -2.860 1.823 -0.087 C5 YD8 17 YD8 C6 C18 C 0 1 Y N N 29.452 31.581 41.442 -2.987 0.447 -0.270 C6 YD8 18 YD8 C8 C19 C 0 1 N N N 31.767 32.302 41.177 -5.306 0.905 -0.331 C8 YD8 19 YD8 C9 C20 C 0 1 N N N 33.044 32.308 42.004 -6.671 0.254 -0.567 C9 YD8 20 YD8 N10 N1 N 0 1 N N N 33.428 30.912 42.245 -6.891 -0.795 0.438 N10 YD8 21 YD8 N14 N2 N 0 1 Y N N 25.608 31.559 39.856 0.878 1.864 0.119 N14 YD8 22 YD8 N16 N3 N 0 1 Y N N 26.049 30.095 41.559 0.658 -0.302 -0.162 N16 YD8 23 YD8 N21 N4 N 0 1 Y N N 23.573 28.908 41.381 3.918 1.490 0.233 N21 YD8 24 YD8 N7 N5 N 0 1 N N N 30.755 31.591 41.957 -4.257 -0.122 -0.408 N7 YD8 25 YD8 O25 O1 O 0 1 N N N 19.499 28.439 40.069 6.494 -1.957 0.993 O25 YD8 26 YD8 H1 H1 H 0 1 N N N 28.673 30.029 42.707 -1.967 -1.426 -0.442 H1 YD8 27 YD8 H2 H2 H 0 1 N N N 32.234 29.224 42.611 -5.859 -2.286 -0.625 H2 YD8 28 YD8 H3 H3 H 0 1 N N N 32.848 30.063 44.076 -6.020 -2.581 1.123 H3 YD8 29 YD8 H4 H4 H 0 1 N N N 31.151 31.677 44.023 -4.451 -0.732 1.594 H4 YD8 30 YD8 H5 H5 H 0 1 N N N 30.294 30.199 43.468 -3.695 -1.926 0.512 H5 YD8 31 YD8 H6 H6 H 0 1 N N N 35.038 29.857 43.103 -8.319 -1.834 -0.700 H6 YD8 32 YD8 H7 H7 H 0 1 N N N 35.481 31.386 42.271 -8.361 -2.166 1.049 H7 YD8 33 YD8 H8 H8 H 0 1 N N N 34.663 31.437 43.870 -8.984 -0.622 0.421 H8 YD8 34 YD8 H9 H9 H 0 1 N N N 21.729 26.494 41.287 6.806 2.040 -0.572 H9 YD8 35 YD8 H10 H10 H 0 1 N N N 22.183 27.149 42.897 6.265 2.600 1.029 H10 YD8 36 YD8 H11 H11 H 0 1 N N N 20.596 27.573 42.169 7.184 1.082 0.880 H11 YD8 37 YD8 H12 H12 H 0 1 N N N 18.384 30.680 40.064 6.436 -0.971 -2.084 H12 YD8 38 YD8 H13 H13 H 0 1 N N N 19.709 31.337 41.083 7.900 -1.481 -1.210 H13 YD8 39 YD8 H14 H14 H 0 1 N N N 19.839 31.397 39.292 6.647 -2.677 -1.622 H14 YD8 40 YD8 H15 H15 H 0 1 N N N 22.270 32.683 39.717 2.829 -2.511 0.703 H15 YD8 41 YD8 H16 H16 H 0 1 N N N 23.490 31.967 38.610 2.102 -1.946 -0.820 H16 YD8 42 YD8 H17 H17 H 0 1 N N N 21.740 31.661 38.338 3.722 -2.684 -0.827 H17 YD8 43 YD8 H18 H18 H 0 1 N N N 27.742 33.239 39.008 -1.523 3.463 0.189 H18 YD8 44 YD8 H19 H19 H 0 1 N N N 29.943 33.133 40.067 -3.743 2.444 -0.057 H19 YD8 45 YD8 H20 H20 H 0 1 N N N 31.939 31.786 40.221 -5.128 1.663 -1.093 H20 YD8 46 YD8 H21 H21 H 0 1 N N N 31.438 33.334 40.983 -5.289 1.368 0.655 H21 YD8 47 YD8 H22 H22 H 0 1 N N N 33.843 32.827 41.455 -7.453 1.009 -0.481 H22 YD8 48 YD8 H23 H23 H 0 1 N N N 32.867 32.818 42.962 -6.698 -0.186 -1.564 H23 YD8 49 YD8 H25 H25 H 0 1 N N N 25.104 32.055 39.149 1.288 2.733 0.248 H25 YD8 50 YD8 H27 H27 H 0 1 N N N 24.270 28.409 41.896 3.712 2.432 0.338 H27 YD8 51 # # 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 YD8 C26 C18 SING N N 1 YD8 C4 C3 DOUB Y N 2 YD8 C4 C5 SING Y N 3 YD8 N14 C3 SING Y N 4 YD8 N14 C15 SING Y N 5 YD8 C18 C19 SING Y N 6 YD8 C18 C17 DOUB Y N 7 YD8 O25 C23 DOUB N N 8 YD8 C24 C23 SING N N 9 YD8 C23 C19 SING N N 10 YD8 C3 C2 SING Y N 11 YD8 C19 C20 DOUB Y N 12 YD8 C5 C6 DOUB Y N 13 YD8 C15 C17 SING N N 14 YD8 C15 N16 DOUB Y N 15 YD8 C17 N21 SING Y N 16 YD8 C8 N7 SING N N 17 YD8 C8 C9 SING N N 18 YD8 C20 N21 SING Y N 19 YD8 C20 C22 SING N N 20 YD8 C2 N16 SING Y N 21 YD8 C2 C1 DOUB Y N 22 YD8 C6 C1 SING Y N 23 YD8 C6 N7 SING N N 24 YD8 N7 C12 SING N N 25 YD8 C9 N10 SING N N 26 YD8 N10 C13 SING N N 27 YD8 N10 C11 SING N N 28 YD8 C11 C12 SING N N 29 YD8 C1 H1 SING N N 30 YD8 C11 H2 SING N N 31 YD8 C11 H3 SING N N 32 YD8 C12 H4 SING N N 33 YD8 C12 H5 SING N N 34 YD8 C13 H6 SING N N 35 YD8 C13 H7 SING N N 36 YD8 C13 H8 SING N N 37 YD8 C22 H9 SING N N 38 YD8 C22 H10 SING N N 39 YD8 C22 H11 SING N N 40 YD8 C24 H12 SING N N 41 YD8 C24 H13 SING N N 42 YD8 C24 H14 SING N N 43 YD8 C26 H15 SING N N 44 YD8 C26 H16 SING N N 45 YD8 C26 H17 SING N N 46 YD8 C4 H18 SING N N 47 YD8 C5 H19 SING N N 48 YD8 C8 H20 SING N N 49 YD8 C8 H21 SING N N 50 YD8 C9 H22 SING N N 51 YD8 C9 H23 SING N N 52 YD8 N14 H25 SING N N 53 YD8 N21 H27 SING N N 54 # # 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 YD8 InChI InChI 1.03 "InChI=1S/C20H25N5O/c1-12-18(14(3)26)13(2)21-19(12)20-22-16-6-5-15(11-17(16)23-20)25-9-7-24(4)8-10-25/h5-6,11,21H,7-10H2,1-4H3,(H,22,23)" YD8 InChIKey InChI 1.03 AESBJGGTJKBCMI-UHFFFAOYSA-N YD8 SMILES_CANONICAL CACTVS 3.385 "CN1CCN(CC1)c2ccc3[nH]c(nc3c2)c4[nH]c(C)c(C(C)=O)c4C" YD8 SMILES CACTVS 3.385 "CN1CCN(CC1)c2ccc3[nH]c(nc3c2)c4[nH]c(C)c(C(C)=O)c4C" YD8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c([nH]c1c2[nH]c3ccc(cc3n2)N4CCN(CC4)C)C)C(=O)C" YD8 SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c([nH]c1c2[nH]c3ccc(cc3n2)N4CCN(CC4)C)C)C(=O)C" # _pdbx_chem_comp_identifier.comp_id YD8 _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 "1-[2,4-dimethyl-5-[5-(4-methylpiperazin-1-yl)-1~{H}-benzimidazol-2-yl]-1~{H}-pyrrol-3-yl]ethanone" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YD8 "Create component" 2021-04-06 PDBJ YD8 "Initial release" 2022-03-30 RCSB ##