data_YBE # _chem_comp.id YBE _chem_comp.name "tert-butyl [(1R,4s)-4-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(2S)-6-oxopiperidin-2-yl]-1H-benzimidazol-1-yl}cyclohexyl]carbamate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C28 H37 N5 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-01-23 _chem_comp.pdbx_modified_date 2024-01-19 _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 507.624 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YBE _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 8FVS _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 YBE C13 C1 C 0 1 N N N N N N 7.749 -16.285 -16.155 -4.874 4.029 1.077 C13 YBE 1 YBE C17 C2 C 0 1 N N N N N N 6.225 -12.248 -15.039 -0.197 2.147 0.288 C17 YBE 2 YBE C20 C3 C 0 1 N N N N N N 6.607 -10.864 -12.636 2.572 3.032 0.650 C20 YBE 3 YBE C22 C4 C 0 1 N N N N N N 7.948 -9.064 -11.205 4.483 1.593 0.186 C22 YBE 4 YBE C24 C5 C 0 1 N N N N N N 9.110 -8.301 -9.149 6.432 0.321 -0.342 C24 YBE 5 YBE C26 C6 C 0 1 N N N N N N 10.409 -9.061 -9.421 6.975 -1.101 -0.184 C26 YBE 6 YBE C01 C7 C 0 1 N N N N N N 8.339 -12.653 -22.565 0.198 -4.990 -2.110 C01 YBE 7 YBE C02 C8 C 0 1 Y N N N N N 7.384 -11.470 -22.691 -0.591 -5.378 -0.886 C02 YBE 8 YBE C03 C9 C 0 1 Y N N N N N 6.581 -10.919 -21.704 -1.128 -4.534 0.044 C03 YBE 9 YBE C04 C10 C 0 1 Y N N N N N 6.460 -11.385 -20.252 -1.069 -3.051 0.080 C04 YBE 10 YBE C05 C11 C 0 1 Y N N N N N 6.165 -12.704 -19.966 -2.234 -2.309 -0.051 C05 YBE 11 YBE C06 C12 C 0 1 Y N N N N N 6.073 -13.074 -18.603 -2.170 -0.915 -0.016 C06 YBE 12 YBE C08 C13 C 0 1 Y N N N N N 5.830 -14.100 -16.690 -2.526 1.230 -0.019 C08 YBE 13 YBE C09 C14 C 0 1 N N S N N N 5.612 -15.182 -15.667 -3.239 2.555 -0.083 C09 YBE 14 YBE C11 C15 C 0 1 N N N N N N 5.571 -17.563 -16.737 -5.403 3.067 -1.149 C11 YBE 15 YBE C12 C16 C 0 1 N N N N N N 7.136 -17.542 -16.564 -5.989 3.692 0.084 C12 YBE 16 YBE C14 C17 C 0 1 N N N N N N 6.952 -15.579 -15.180 -3.977 2.796 1.235 C14 YBE 17 YBE C18 C18 C 0 1 N N N N N N 7.678 -11.842 -14.775 0.517 2.007 1.633 C18 YBE 18 YBE C19 C19 C 0 1 N N N N N N 7.894 -11.175 -13.408 1.549 3.127 1.783 C19 YBE 19 YBE C25 C20 C 0 1 N N N N N N 8.801 -8.349 -7.653 7.363 1.304 0.372 C25 YBE 20 YBE C27 C21 C 0 1 N N N N N N 9.188 -6.830 -9.576 6.358 0.677 -1.828 C27 YBE 21 YBE C29 C22 C 0 1 N N N N N N 5.342 -10.512 -13.433 1.858 3.173 -0.696 C29 YBE 22 YBE C30 C23 C 0 1 N N N N N N 5.263 -11.068 -14.869 0.827 2.052 -0.845 C30 YBE 23 YBE C31 C24 C 0 1 Y N N N N N 6.266 -12.160 -17.594 -0.925 -0.283 0.151 C31 YBE 24 YBE C32 C25 C 0 1 Y N N N N N 6.571 -10.805 -17.892 0.230 -1.043 0.281 C32 YBE 25 YBE C33 C26 C 0 1 Y N N N N N 6.660 -10.450 -19.228 0.161 -2.407 0.251 C33 YBE 26 YBE C34 C27 C 0 1 Y N N N N N 5.896 -9.849 -22.287 -1.758 -5.411 0.970 C34 YBE 27 YBE C35 C28 C 0 1 N N N N N N 4.867 -8.903 -21.632 -2.516 -5.021 2.213 C35 YBE 28 YBE N07 N1 N 0 1 Y N N N N N 5.812 -14.276 -18.017 -3.103 0.067 -0.114 N07 YBE 29 YBE N10 N2 N 0 1 N N N N N N 4.778 -16.336 -16.290 -4.177 2.544 -1.198 N10 YBE 30 YBE N16 N3 N 0 1 Y N N N N N 6.106 -12.820 -16.409 -1.184 1.074 0.145 N16 YBE 31 YBE N21 N4 N 0 1 N N N N N N 6.751 -9.783 -11.668 3.249 1.735 0.710 N21 YBE 32 YBE N36 N5 N 0 1 Y N N N N N 6.296 -9.764 -23.566 -1.549 -6.617 0.531 N36 YBE 33 YBE O15 O1 O 0 1 N N N N N N 5.031 -18.502 -17.223 -6.082 3.035 -2.155 O15 YBE 34 YBE O23 O2 O 0 1 N N N N N N 8.029 -8.964 -9.792 5.105 0.400 0.242 O23 YBE 35 YBE O28 O3 O 0 1 N N N N N N 8.738 -8.558 -11.938 5.034 2.542 -0.336 O28 YBE 36 YBE O37 O4 O 0 1 Y N N N N N 7.202 -10.763 -23.784 -0.912 -6.619 -0.496 O37 YBE 37 YBE H1 H1 H 0 1 N N N N N N 8.736 -16.498 -15.718 -4.286 4.865 0.698 H1 YBE 38 YBE H2 H2 H 0 1 N N N N N N 7.871 -15.646 -17.042 -5.308 4.293 2.041 H2 YBE 39 YBE H3 H3 H 0 1 N N N N N N 5.948 -13.023 -14.309 -0.701 3.112 0.243 H3 YBE 40 YBE H4 H4 H 0 1 N N N N N N 6.365 -11.774 -12.067 3.307 3.831 0.756 H4 YBE 41 YBE H5 H5 H 0 1 N N N N N N 11.245 -8.548 -8.924 7.028 -1.354 0.874 H5 YBE 42 YBE H6 H6 H 0 1 N N N N N N 10.323 -10.086 -9.030 6.312 -1.801 -0.693 H6 YBE 43 YBE H7 H7 H 0 1 N N N N N N 10.593 -9.096 -10.505 7.971 -1.160 -0.623 H7 YBE 44 YBE H8 H8 H 0 1 N N N N N N 8.847 -12.819 -23.527 1.258 -4.945 -1.860 H8 YBE 45 YBE H9 H9 H 0 1 N N N N N N 9.087 -12.439 -21.787 0.041 -5.731 -2.894 H9 YBE 46 YBE H10 H10 H 0 1 N N N N N N 7.772 -13.554 -22.290 -0.134 -4.013 -2.462 H10 YBE 47 YBE H11 H11 H 0 1 N N N N N N 6.010 -13.426 -20.754 -3.183 -2.807 -0.180 H11 YBE 48 YBE H12 H12 H 0 1 N N N N N N 5.037 -14.762 -14.828 -2.510 3.350 -0.238 H12 YBE 49 YBE H13 H13 H 0 1 N N N N N N 7.394 -18.297 -15.807 -6.688 2.995 0.546 H13 YBE 50 YBE H14 H14 H 0 1 N N N N N N 7.579 -17.826 -17.530 -6.518 4.605 -0.190 H14 YBE 51 YBE H15 H15 H 0 1 N N N N N N 6.822 -16.231 -14.303 -3.254 2.969 2.032 H15 YBE 52 YBE H16 H16 H 0 1 N N N N N N 7.495 -14.670 -14.883 -4.589 1.927 1.475 H16 YBE 53 YBE H17 H17 H 0 1 N N N N N N 8.305 -12.744 -14.824 -0.212 2.074 2.441 H17 YBE 54 YBE H18 H18 H 0 1 N N N N N N 7.989 -11.136 -15.559 1.021 1.041 1.679 H18 YBE 55 YBE H19 H19 H 0 1 N N N N N N 8.509 -11.848 -12.792 2.058 3.027 2.741 H19 YBE 56 YBE H20 H20 H 0 1 N N N N N N 8.433 -10.230 -13.569 1.045 4.093 1.738 H20 YBE 57 YBE H21 H21 H 0 1 N N N N N N 9.606 -7.848 -7.095 8.359 1.245 -0.067 H21 YBE 58 YBE H22 H22 H 0 1 N N N N N N 7.847 -7.836 -7.459 6.976 2.317 0.260 H22 YBE 59 YBE H23 H23 H 0 1 N N N N N N 8.727 -9.397 -7.328 7.416 1.051 1.431 H23 YBE 60 YBE H24 H24 H 0 1 N N N N N N 10.031 -6.343 -9.064 7.354 0.618 -2.266 H24 YBE 61 YBE H25 H25 H 0 1 N N N N N N 9.337 -6.772 -10.664 5.694 -0.023 -2.336 H25 YBE 62 YBE H26 H26 H 0 1 N N N N N N 8.252 -6.320 -9.306 5.971 1.690 -1.940 H26 YBE 63 YBE H27 H27 H 0 1 N N N N N N 5.279 -9.416 -13.494 1.354 4.138 -0.741 H27 YBE 64 YBE H28 H28 H 0 1 N N N N N N 4.476 -10.899 -12.876 2.587 3.105 -1.503 H28 YBE 65 YBE H29 H29 H 0 1 N N N N N N 5.534 -10.274 -15.580 1.330 1.087 -0.800 H29 YBE 66 YBE H30 H30 H 0 1 N N N N N N 4.236 -11.406 -15.071 0.318 2.152 -1.804 H30 YBE 67 YBE H31 H31 H 0 1 N N N N N N 6.727 -10.080 -17.107 1.185 -0.554 0.409 H31 YBE 68 YBE H32 H32 H 0 1 N N N N N N 6.889 -9.427 -19.487 1.062 -2.992 0.356 H32 YBE 69 YBE H33 H33 H 0 1 N N N N N N 4.524 -8.165 -22.372 -3.568 -4.878 1.967 H33 YBE 70 YBE H34 H34 H 0 1 N N N N N N 4.008 -9.488 -21.273 -2.421 -5.809 2.960 H34 YBE 71 YBE H35 H35 H 0 1 N N N N N N 5.336 -8.382 -20.784 -2.107 -4.092 2.611 H35 YBE 72 YBE H36 H36 H 0 1 N N N N N N 3.785 -16.279 -16.392 -3.892 2.131 -2.028 H36 YBE 73 YBE H37 H37 H 0 1 N N N N N N 5.895 -9.480 -11.250 2.809 0.977 1.127 H37 YBE 74 # 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 YBE O37 N36 SING Y N 1 YBE O37 C02 SING Y N 2 YBE N36 C34 DOUB Y N 3 YBE C02 C01 SING N N 4 YBE C02 C03 DOUB Y N 5 YBE C34 C03 SING Y N 6 YBE C34 C35 SING N N 7 YBE C03 C04 SING N N 8 YBE C04 C05 DOUB Y N 9 YBE C04 C33 SING Y N 10 YBE C05 C06 SING Y N 11 YBE C33 C32 DOUB Y N 12 YBE C06 N07 SING Y N 13 YBE C06 C31 DOUB Y N 14 YBE N07 C08 DOUB Y N 15 YBE C32 C31 SING Y N 16 YBE C31 N16 SING Y N 17 YBE O15 C11 DOUB N N 18 YBE C11 C12 SING N N 19 YBE C11 N10 SING N N 20 YBE C08 N16 SING Y N 21 YBE C08 C09 SING N N 22 YBE C12 C13 SING N N 23 YBE N16 C17 SING N N 24 YBE N10 C09 SING N N 25 YBE C13 C14 SING N N 26 YBE C09 C14 SING N N 27 YBE C17 C30 SING N N 28 YBE C17 C18 SING N N 29 YBE C30 C29 SING N N 30 YBE C18 C19 SING N N 31 YBE C29 C20 SING N N 32 YBE C19 C20 SING N N 33 YBE C20 N21 SING N N 34 YBE O28 C22 DOUB N N 35 YBE N21 C22 SING N N 36 YBE C22 O23 SING N N 37 YBE O23 C24 SING N N 38 YBE C27 C24 SING N N 39 YBE C26 C24 SING N N 40 YBE C24 C25 SING N N 41 YBE C13 H1 SING N N 42 YBE C13 H2 SING N N 43 YBE C17 H3 SING N N 44 YBE C20 H4 SING N N 45 YBE C26 H5 SING N N 46 YBE C26 H6 SING N N 47 YBE C26 H7 SING N N 48 YBE C01 H8 SING N N 49 YBE C01 H9 SING N N 50 YBE C01 H10 SING N N 51 YBE C05 H11 SING N N 52 YBE C09 H12 SING N N 53 YBE C12 H13 SING N N 54 YBE C12 H14 SING N N 55 YBE C14 H15 SING N N 56 YBE C14 H16 SING N N 57 YBE C18 H17 SING N N 58 YBE C18 H18 SING N N 59 YBE C19 H19 SING N N 60 YBE C19 H20 SING N N 61 YBE C25 H21 SING N N 62 YBE C25 H22 SING N N 63 YBE C25 H23 SING N N 64 YBE C27 H24 SING N N 65 YBE C27 H25 SING N N 66 YBE C27 H26 SING N N 67 YBE C29 H27 SING N N 68 YBE C29 H28 SING N N 69 YBE C30 H29 SING N N 70 YBE C30 H30 SING N N 71 YBE C32 H31 SING N N 72 YBE C33 H32 SING N N 73 YBE C35 H33 SING N N 74 YBE C35 H34 SING N N 75 YBE C35 H35 SING N N 76 YBE N10 H36 SING N N 77 YBE N21 H37 SING N N 78 # 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 YBE SMILES ACDLabs 12.01 "Cc1noc(C)c1c1cc2nc(C3CCCC(=O)N3)n(C3CCC(NC(=O)OC(C)(C)C)CC3)c2cc1" YBE InChI InChI 1.06 "InChI=1S/C28H37N5O4/c1-16-25(17(2)37-32-16)18-9-14-23-22(15-18)31-26(21-7-6-8-24(34)30-21)33(23)20-12-10-19(11-13-20)29-27(35)36-28(3,4)5/h9,14-15,19-21H,6-8,10-13H2,1-5H3,(H,29,35)(H,30,34)/t19-,20+,21-/m0/s1" YBE InChIKey InChI 1.06 RZFKUAQHDVKWMN-HBMCJLEFSA-N YBE SMILES_CANONICAL CACTVS 3.385 "Cc1onc(C)c1c2ccc3n([C@H]4CC[C@H](CC4)NC(=O)OC(C)(C)C)c(nc3c2)[C@@H]5CCCC(=O)N5" YBE SMILES CACTVS 3.385 "Cc1onc(C)c1c2ccc3n([CH]4CC[CH](CC4)NC(=O)OC(C)(C)C)c(nc3c2)[CH]5CCCC(=O)N5" YBE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)NC(=O)OC(C)(C)C)[C@@H]5CCCC(=O)N5" YBE SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)NC(=O)OC(C)(C)C)C5CCCC(=O)N5" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier YBE "SYSTEMATIC NAME" ACDLabs 12.01 "tert-butyl [(1R,4s)-4-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(2S)-6-oxopiperidin-2-yl]-1H-benzimidazol-1-yl}cyclohexyl]carbamate" YBE "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{tert}-butyl ~{N}-[4-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(2~{S})-6-oxidanylidenepiperidin-2-yl]benzimidazol-1-yl]cyclohexyl]carbamate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YBE "Create component" 2023-01-23 RCSB YBE "Initial release" 2024-01-24 RCSB #