data_YN5 # _chem_comp.id YN5 _chem_comp.name "(6S)-1-(2,3-dihydro-1,4-benzodioxin-6-yl)-6-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}piperidin-2-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C32 H36 N4 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-10 _chem_comp.pdbx_modified_date 2024-02-02 _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 556.652 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YN5 _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 8FXO _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 YN5 C10 C1 C 0 1 Y N N N N N -11.440 3.018 -3.233 0.607 -0.088 -1.017 C10 YN5 1 YN5 C13 C2 C 0 1 Y N N N N N -10.899 4.982 -1.312 3.137 -0.298 0.121 C13 YN5 2 YN5 C15 C3 C 0 1 N N N N N N -10.605 0.340 -0.881 -0.405 -3.130 0.740 C15 YN5 3 YN5 C17 C4 C 0 1 N N N N N N -11.236 0.351 1.581 1.261 -2.286 2.399 C17 YN5 4 YN5 C20 C5 C 0 1 N N N N N N -9.201 0.593 -0.329 0.597 -4.187 0.271 C20 YN5 5 YN5 C22 C6 C 0 1 N N N N N N -10.926 -1.149 3.868 4.564 -3.864 2.356 C22 YN5 6 YN5 C24 C7 C 0 1 N N S N N N -11.393 -0.666 -3.605 -2.582 -1.828 -1.029 C24 YN5 7 YN5 C26 C8 C 0 1 N N N N N N -13.127 -2.004 -5.070 -4.579 -0.551 -1.711 C26 YN5 8 YN5 C28 C9 C 0 1 N N N N N N -10.599 -2.237 -5.238 -4.176 -2.799 -2.674 C28 YN5 9 YN5 C01 C10 C 0 1 N N N N N N -10.595 6.962 -5.379 5.588 0.304 -2.298 C01 YN5 10 YN5 C02 C11 C 0 1 Y N N N N N -11.200 7.537 -4.117 5.062 1.593 -1.720 C02 YN5 11 YN5 C03 C12 C 0 1 Y N N N N N -11.516 6.893 -2.929 3.882 1.772 -1.056 C03 YN5 12 YN5 C04 C13 C 0 1 Y N N N N N -12.052 7.873 -2.049 3.884 3.158 -0.734 C04 YN5 13 YN5 C05 C14 C 0 1 N N N N N N -12.568 7.708 -0.617 2.813 3.915 0.008 C05 YN5 14 YN5 C08 C15 C 0 1 Y N N N N N -11.342 5.375 -2.590 2.842 0.759 -0.744 C08 YN5 15 YN5 C09 C16 C 0 1 Y N N N N N -11.604 4.407 -3.560 1.581 0.866 -1.313 C09 YN5 16 YN5 C11 C17 C 0 1 Y N N N N N -11.026 2.629 -1.984 0.914 -1.147 -0.145 C11 YN5 17 YN5 C12 C18 C 0 1 Y N N N N N -10.748 3.619 -0.995 2.180 -1.242 0.417 C12 YN5 18 YN5 C16 C19 C 0 1 N N N N N N -11.737 0.486 0.143 -0.162 -2.816 2.217 C16 YN5 19 YN5 C18 C20 C 0 1 N N N N N N -10.140 -0.702 1.674 2.263 -3.343 1.930 C18 YN5 20 YN5 C19 C21 C 0 1 N N N N N N -8.890 -0.282 0.892 2.020 -3.656 0.452 C19 YN5 21 YN5 C23 C22 C 0 1 Y N N N N N -11.341 0.805 -3.190 -1.176 -1.321 -0.839 C23 YN5 22 YN5 C27 C23 C 0 1 N N N N N N -11.863 -2.378 -5.936 -4.923 -1.479 -2.840 C27 YN5 23 YN5 C29 C24 C 0 1 N N N N N N -10.465 -0.883 -4.730 -2.699 -2.490 -2.402 C29 YN5 24 YN5 C31 C25 C 0 1 Y N N N N N -13.922 -0.661 -2.947 -3.278 0.250 0.066 C31 YN5 25 YN5 C32 C26 C 0 1 Y N N N N N -14.137 -1.426 -1.799 -2.922 1.543 -0.293 C32 YN5 26 YN5 C33 C27 C 0 1 Y N N N N N -15.144 -1.014 -0.861 -2.694 2.497 0.686 C33 YN5 27 YN5 C34 C28 C 0 1 Y N N N N N -15.865 0.115 -1.093 -2.824 2.157 2.028 C34 YN5 28 YN5 C35 C29 C 0 1 Y N N N N N -15.637 0.902 -2.269 -3.179 0.864 2.383 C35 YN5 29 YN5 C36 C30 C 0 1 Y N N N N N -14.654 0.501 -3.194 -3.405 -0.086 1.407 C36 YN5 30 YN5 C38 C31 C 0 1 N N N N N N -17.009 -0.172 1.045 -1.893 4.263 2.626 C38 YN5 31 YN5 C39 C32 C 0 1 N N N N N N -15.810 -1.061 1.374 -2.486 4.782 1.309 C39 YN5 32 YN5 N06 N1 N 0 1 Y N N N N N -12.035 9.039 -2.714 4.995 3.641 -1.207 N06 YN5 33 YN5 N14 N2 N 0 1 Y N N N N N -10.962 1.251 -1.990 -0.235 -1.910 -0.053 N14 YN5 34 YN5 N25 N3 N 0 1 N N N N N N -12.868 -1.100 -3.877 -3.514 -0.712 -0.924 N25 YN5 35 YN5 N41 N4 N 0 1 Y N N N N N -11.618 1.866 -3.960 -0.687 -0.253 -1.399 N41 YN5 36 YN5 O07 O1 O 0 1 Y N N N N N -11.502 8.813 -3.959 5.661 2.791 -1.751 O07 YN5 37 YN5 O21 O2 O 0 1 N N N N N N -9.810 -0.906 3.036 3.593 -2.847 2.099 O21 YN5 38 YN5 O30 O3 O 0 1 N N N N N N -14.211 -2.383 -5.335 -5.308 0.396 -1.504 O30 YN5 39 YN5 O37 O4 O 0 1 N N N N N N -16.880 0.564 -0.169 -2.608 3.082 3.004 O37 YN5 40 YN5 O40 O5 O 0 1 N N N N N N -15.354 -1.792 0.286 -2.342 3.759 0.318 O40 YN5 41 YN5 H1 H1 H 0 1 N N N N N N -10.673 5.733 -0.569 4.121 -0.374 0.560 H1 YN5 42 YN5 H2 H2 H 0 1 N N N N N N -10.632 -0.692 -1.261 -1.419 -3.508 0.610 H2 YN5 43 YN5 H3 H3 H 0 1 N N N N N N -10.836 1.319 1.916 1.388 -1.378 1.809 H3 YN5 44 YN5 H4 H4 H 0 1 N N N N N N -12.075 0.057 2.229 1.434 -2.062 3.451 H4 YN5 45 YN5 H5 H5 H 0 1 N N N N N N -8.466 0.374 -1.118 0.470 -5.095 0.860 H5 YN5 46 YN5 H6 H6 H 0 1 N N N N N N -9.121 1.650 -0.036 0.423 -4.410 -0.782 H6 YN5 47 YN5 H7 H7 H 0 1 N N N N N N -10.587 -1.296 4.904 5.546 -3.406 2.472 H7 YN5 48 YN5 H8 H8 H 0 1 N N N N N N -11.610 -0.288 3.825 4.300 -4.396 3.270 H8 YN5 49 YN5 H9 H9 H 0 1 N N N N N N -11.451 -2.052 3.523 4.585 -4.564 1.521 H9 YN5 50 YN5 H10 H10 H 0 1 N N N N N N -11.036 -1.260 -2.751 -2.808 -2.561 -0.254 H10 YN5 51 YN5 H11 H11 H 0 1 N N N N N N -10.564 -2.947 -4.398 -4.595 -3.357 -1.836 H11 YN5 52 YN5 H12 H12 H 0 1 N N N N N N -9.773 -2.450 -5.932 -4.266 -3.387 -3.587 H12 YN5 53 YN5 H13 H13 H 0 1 N N N N N N -10.455 7.765 -6.118 6.558 0.483 -2.762 H13 YN5 54 YN5 H14 H14 H 0 1 N N N N N N -9.622 6.506 -5.144 5.696 -0.433 -1.502 H14 YN5 55 YN5 H15 H15 H 0 1 N N N N N N -11.268 6.197 -5.793 4.890 -0.070 -3.047 H15 YN5 56 YN5 H16 H16 H 0 1 N N N N N N -12.913 8.681 -0.237 3.025 3.890 1.077 H16 YN5 57 YN5 H17 H17 H 0 1 N N N N N N -13.405 6.994 -0.609 2.796 4.950 -0.335 H17 YN5 58 YN5 H18 H18 H 0 1 N N N N N N -11.757 7.330 0.024 1.844 3.454 -0.181 H18 YN5 59 YN5 H19 H19 H 0 1 N N N N N N -11.927 4.700 -4.548 1.355 1.683 -1.982 H19 YN5 60 YN5 H20 H20 H 0 1 N N N N N N -10.423 3.324 -0.008 2.414 -2.056 1.087 H20 YN5 61 YN5 H21 H21 H 0 1 N N N N N N -12.200 1.476 0.021 -0.876 -2.063 2.551 H21 YN5 62 YN5 H22 H22 H 0 1 N N N N N N -12.488 -0.295 -0.045 -0.289 -3.724 2.807 H22 YN5 63 YN5 H23 H23 H 0 1 N N N N N N -10.520 -1.638 1.238 2.136 -4.251 2.520 H23 YN5 64 YN5 H24 H24 H 0 1 N N N N N N -8.373 -1.190 0.548 2.734 -4.409 0.118 H24 YN5 65 YN5 H25 H25 H 0 1 N N N N N N -8.230 0.283 1.567 2.147 -2.748 -0.137 H25 YN5 66 YN5 H26 H26 H 0 1 N N N N N N -11.844 -1.722 -6.819 -5.997 -1.668 -2.839 H26 YN5 67 YN5 H27 H27 H 0 1 N N N N N N -11.964 -3.425 -6.259 -4.639 -1.019 -3.786 H27 YN5 68 YN5 H28 H28 H 0 1 N N N N N N -9.433 -0.725 -4.385 -2.320 -1.814 -3.168 H28 YN5 69 YN5 H29 H29 H 0 1 N N N N N N -10.696 -0.169 -5.534 -2.124 -3.417 -2.411 H29 YN5 70 YN5 H30 H30 H 0 1 N N N N N N -13.553 -2.317 -1.618 -2.822 1.805 -1.336 H30 YN5 71 YN5 H31 H31 H 0 1 N N N N N N -16.216 1.797 -2.445 -3.277 0.600 3.426 H31 YN5 72 YN5 H32 H32 H 0 1 N N N N N N -14.469 1.085 -4.083 -3.682 -1.092 1.687 H32 YN5 73 YN5 H33 H33 H 0 1 N N N N N N -17.143 0.544 1.869 -0.839 4.025 2.485 H33 YN5 74 YN5 H34 H34 H 0 1 N N N N N N -17.900 -0.812 0.967 -1.998 5.022 3.401 H34 YN5 75 YN5 H35 H35 H 0 1 N N N N N N -16.103 -1.763 2.168 -3.542 5.014 1.448 H35 YN5 76 YN5 H36 H36 H 0 1 N N N N N N -14.990 -0.422 1.734 -1.952 5.679 0.994 H36 YN5 77 # 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 YN5 C27 C28 SING N N 1 YN5 C27 C26 SING N N 2 YN5 C01 C02 SING N N 3 YN5 O30 C26 DOUB N N 4 YN5 C28 C29 SING N N 5 YN5 C26 N25 SING N N 6 YN5 C29 C24 SING N N 7 YN5 C02 O07 SING Y N 8 YN5 C02 C03 DOUB Y N 9 YN5 N41 C10 SING Y N 10 YN5 N41 C23 DOUB Y N 11 YN5 O07 N06 SING Y N 12 YN5 N25 C24 SING N N 13 YN5 N25 C31 SING N N 14 YN5 C24 C23 SING N N 15 YN5 C09 C10 DOUB Y N 16 YN5 C09 C08 SING Y N 17 YN5 C10 C11 SING Y N 18 YN5 C36 C31 DOUB Y N 19 YN5 C36 C35 SING Y N 20 YN5 C23 N14 SING Y N 21 YN5 C31 C32 SING Y N 22 YN5 C03 C08 SING N N 23 YN5 C03 C04 SING Y N 24 YN5 N06 C04 DOUB Y N 25 YN5 C08 C13 DOUB Y N 26 YN5 C35 C34 DOUB Y N 27 YN5 C04 C05 SING N N 28 YN5 N14 C11 SING Y N 29 YN5 N14 C15 SING N N 30 YN5 C11 C12 DOUB Y N 31 YN5 C32 C33 DOUB Y N 32 YN5 C13 C12 SING Y N 33 YN5 C34 C33 SING Y N 34 YN5 C34 O37 SING N N 35 YN5 C15 C20 SING N N 36 YN5 C15 C16 SING N N 37 YN5 C33 O40 SING N N 38 YN5 C20 C19 SING N N 39 YN5 O37 C38 SING N N 40 YN5 C16 C17 SING N N 41 YN5 O40 C39 SING N N 42 YN5 C19 C18 SING N N 43 YN5 C38 C39 SING N N 44 YN5 C17 C18 SING N N 45 YN5 C18 O21 SING N N 46 YN5 O21 C22 SING N N 47 YN5 C13 H1 SING N N 48 YN5 C15 H2 SING N N 49 YN5 C17 H3 SING N N 50 YN5 C17 H4 SING N N 51 YN5 C20 H5 SING N N 52 YN5 C20 H6 SING N N 53 YN5 C22 H7 SING N N 54 YN5 C22 H8 SING N N 55 YN5 C22 H9 SING N N 56 YN5 C24 H10 SING N N 57 YN5 C28 H11 SING N N 58 YN5 C28 H12 SING N N 59 YN5 C01 H13 SING N N 60 YN5 C01 H14 SING N N 61 YN5 C01 H15 SING N N 62 YN5 C05 H16 SING N N 63 YN5 C05 H17 SING N N 64 YN5 C05 H18 SING N N 65 YN5 C09 H19 SING N N 66 YN5 C12 H20 SING N N 67 YN5 C16 H21 SING N N 68 YN5 C16 H22 SING N N 69 YN5 C18 H23 SING N N 70 YN5 C19 H24 SING N N 71 YN5 C19 H25 SING N N 72 YN5 C27 H26 SING N N 73 YN5 C27 H27 SING N N 74 YN5 C29 H28 SING N N 75 YN5 C29 H29 SING N N 76 YN5 C32 H30 SING N N 77 YN5 C35 H31 SING N N 78 YN5 C36 H32 SING N N 79 YN5 C38 H33 SING N N 80 YN5 C38 H34 SING N N 81 YN5 C39 H35 SING N N 82 YN5 C39 H36 SING N N 83 # 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 YN5 SMILES ACDLabs 12.01 "Cc1noc(C)c1c1cc2nc(C3CCCC(=O)N3c3ccc4OCCOc4c3)n(C3CCC(OC)CC3)c2cc1" YN5 InChI InChI 1.06 "InChI=1S/C32H36N4O5/c1-19-31(20(2)41-34-19)21-7-13-26-25(17-21)33-32(36(26)22-8-11-24(38-3)12-9-22)27-5-4-6-30(37)35(27)23-10-14-28-29(18-23)40-16-15-39-28/h7,10,13-14,17-18,22,24,27H,4-6,8-9,11-12,15-16H2,1-3H3/t22-,24+,27-/m0/s1" YN5 InChIKey InChI 1.06 ZVVSHSLAQZHUJM-LLGBQNBKSA-N YN5 SMILES_CANONICAL CACTVS 3.385 "CO[C@H]1CC[C@H](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[C@@H]5CCCC(=O)N5c6ccc7OCCOc7c6" YN5 SMILES CACTVS 3.385 "CO[CH]1CC[CH](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[CH]5CCCC(=O)N5c6ccc7OCCOc7c6" YN5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)[C@@H]5CCCC(=O)N5c6ccc7c(c6)OCCO7" YN5 SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)C5CCCC(=O)N5c6ccc7c(c6)OCCO7" # 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 YN5 "SYSTEMATIC NAME" ACDLabs 12.01 "(6S)-1-(2,3-dihydro-1,4-benzodioxin-6-yl)-6-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}piperidin-2-one" YN5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(6~{S})-1-(2,3-dihydro-1,4-benzodioxin-6-yl)-6-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-(4-methoxycyclohexyl)benzimidazol-2-yl]piperidin-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 YN5 "Create component" 2023-02-10 RCSB YN5 "Initial release" 2024-02-07 RCSB #