data_YRI # _chem_comp.id YRI _chem_comp.name "(6S)-1-(3,4-dibromophenyl)-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 "C30 H32 Br2 N4 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-16 _chem_comp.pdbx_modified_date 2024-02-16 _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 656.408 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YRI _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 8G6T _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 YRI C10 C1 C 0 1 Y N N N N N 0.590 -30.789 -14.982 1.832 -1.211 -0.100 C10 YRI 1 YRI C13 C2 C 0 1 Y N N N N N 3.184 -30.700 -16.100 3.049 1.158 -0.886 C13 YRI 2 YRI C15 C3 C 0 1 Y N N N N N 5.084 -31.475 -17.686 4.947 2.587 -1.851 C15 YRI 3 YRI C20 C4 C 0 1 N N N N N N 4.337 -32.523 -18.506 5.943 1.504 -2.177 C20 YRI 4 YRI C21 C5 C 0 1 Y N N N N N 2.052 -30.749 -16.923 1.897 0.738 -1.535 C21 YRI 5 YRI C24 C6 C 0 1 N N N N N N -0.972 -32.115 -12.669 2.523 -4.081 0.796 C24 YRI 6 YRI C26 C7 C 0 1 N N N N N N -2.140 -30.827 -10.760 3.599 -2.486 2.389 C26 YRI 7 YRI C28 C8 C 0 1 N N N N N N -0.960 -29.566 -12.660 1.123 -2.818 2.437 C28 YRI 8 YRI C02 C9 C 0 1 N N N N N N -4.114 -29.904 -18.187 -3.334 -2.801 -2.036 C02 YRI 9 YRI C03 C10 C 0 1 N N N N N N -4.447 -31.400 -18.515 -3.220 -3.921 -3.030 C03 YRI 10 YRI C04 C11 C 0 1 N N N N N N -3.459 -32.333 -17.969 -2.083 -4.863 -2.625 C04 YRI 11 YRI C05 C12 C 0 1 N N N N N N -3.302 -32.233 -16.524 -0.839 -4.019 -2.323 C05 YRI 12 YRI C06 C13 C 0 1 N N S N N N -2.920 -30.903 -16.030 -1.102 -3.193 -1.064 C06 YRI 13 YRI C07 C14 C 0 1 Y N N N N N -1.405 -30.850 -15.876 0.017 -2.201 -0.876 C07 YRI 14 YRI C09 C15 C 0 1 Y N N N N N 0.751 -30.786 -16.325 1.280 -0.452 -1.146 C09 YRI 15 YRI C11 C16 C 0 1 Y N N N N N 1.736 -30.764 -14.146 2.982 -0.775 0.546 C11 YRI 16 YRI C12 C17 C 0 1 Y N N N N N 3.006 -30.715 -14.719 3.586 0.399 0.157 C12 YRI 17 YRI C14 C18 C 0 1 Y N N N N N 4.612 -30.682 -16.665 3.710 2.423 -1.297 C14 YRI 18 YRI C18 C19 C 0 1 Y N N N N N 5.699 -29.893 -16.228 3.203 3.749 -1.207 C18 YRI 19 YRI C19 C20 C 0 1 N N N N N N 5.736 -28.842 -15.128 1.861 4.169 -0.664 C19 YRI 20 YRI C23 C21 C 0 1 N N N N N N -1.381 -30.835 -13.401 1.174 -3.394 1.020 C23 YRI 21 YRI C25 C22 C 0 1 N N N N N N -1.466 -32.124 -11.226 3.650 -3.062 0.973 C25 YRI 22 YRI C27 C23 C 0 1 N N N N N N -1.483 -29.520 -11.225 2.251 -1.799 2.613 C27 YRI 23 YRI C30 C24 C 0 1 N N N N N N -3.408 -30.778 -8.797 5.143 -1.436 3.893 C30 YRI 24 YRI C32 C25 C 0 1 Y N N N N N -2.978 -28.358 -16.499 -2.578 -1.381 -0.333 C32 YRI 25 YRI C33 C26 C 0 1 Y N N N N N -3.488 -27.850 -15.320 -2.714 -1.574 1.035 C33 YRI 26 YRI C34 C27 C 0 1 Y N N N N N -3.149 -26.570 -14.926 -2.918 -0.490 1.867 C34 YRI 27 YRI C35 C28 C 0 1 Y N N N N N -2.315 -25.830 -15.729 -2.986 0.786 1.339 C35 YRI 28 YRI C36 C29 C 0 1 Y N N N N N -1.831 -26.355 -16.903 -2.851 0.982 -0.025 C36 YRI 29 YRI C38 C30 C 0 1 Y N N N N N -2.153 -27.619 -17.316 -2.647 -0.099 -0.862 C38 YRI 30 YRI N08 N1 N 0 1 Y N N N N N -0.508 -30.823 -16.869 0.174 -1.114 -1.574 N08 YRI 31 YRI N17 N2 N 0 1 Y N N N N N 6.758 -30.223 -16.983 4.129 4.527 -1.685 N17 YRI 32 YRI N22 N3 N 0 1 Y N N N N N -0.747 -30.825 -14.720 1.010 -2.311 0.047 N22 YRI 33 YRI N31 N4 N 0 1 N N N N N N -3.335 -29.686 -16.903 -2.366 -2.477 -1.178 N31 YRI 34 YRI O01 O1 O 0 1 N N N N N N -4.439 -28.985 -18.870 -4.360 -2.154 -2.016 O01 YRI 35 YRI O16 O2 O 0 1 Y N N N N N 6.352 -31.180 -17.847 5.102 3.905 -2.041 O16 YRI 36 YRI O29 O3 O 0 1 N N N N N N -2.128 -30.831 -9.353 4.652 -1.534 2.554 O29 YRI 37 YRI BR37 BR1 BR 0 0 N N N N N N -0.665 -25.318 -18.023 -2.946 2.728 -0.744 BR37 YRI 38 YRI BR39 BR2 BR 0 0 N N N N N N -1.822 -24.032 -15.212 -3.266 2.267 2.482 BR39 YRI 39 YRI H1 H1 H 0 1 N N N N N N 5.024 -32.977 -19.235 5.775 1.150 -3.194 H1 YRI 40 YRI H2 H2 H 0 1 N N N N N N 3.947 -33.303 -17.836 6.954 1.902 -2.093 H2 YRI 41 YRI H3 H3 H 0 1 N N N N N N 3.501 -32.045 -19.038 5.820 0.675 -1.480 H3 YRI 42 YRI H4 H4 H 0 1 N N N N N N 2.159 -30.759 -17.998 1.480 1.329 -2.338 H4 YRI 43 YRI H5 H5 H 0 1 N N N N N N -1.400 -32.980 -13.197 2.644 -4.886 1.520 H5 YRI 44 YRI H6 H6 H 0 1 N N N N N N 0.125 -32.191 -12.670 2.558 -4.491 -0.213 H6 YRI 45 YRI H7 H7 H 0 1 N N N N N N -3.179 -30.834 -11.122 3.721 -3.291 3.114 H7 YRI 46 YRI H8 H8 H 0 1 N N N N N N 0.139 -29.521 -12.636 0.163 -2.329 2.596 H8 YRI 47 YRI H9 H9 H 0 1 N N N N N N -1.351 -28.694 -13.205 1.245 -3.624 3.161 H9 YRI 48 YRI H10 H10 H 0 1 N N N N N N -5.432 -31.642 -18.090 -4.157 -4.476 -3.059 H10 YRI 49 YRI H11 H11 H 0 1 N N N N N N -4.479 -31.522 -19.608 -3.014 -3.509 -4.018 H11 YRI 50 YRI H12 H12 H 0 1 N N N N N N -3.775 -33.358 -18.215 -2.371 -5.424 -1.736 H12 YRI 51 YRI H13 H13 H 0 1 N N N N N N -2.487 -32.126 -18.440 -1.870 -5.552 -3.442 H13 YRI 52 YRI H14 H14 H 0 1 N N N N N N -4.259 -32.508 -16.057 0.016 -4.675 -2.159 H14 YRI 53 YRI H15 H15 H 0 1 N N N N N N -2.525 -32.948 -16.215 -0.636 -3.353 -3.162 H15 YRI 54 YRI H16 H16 H 0 1 N N N N N N -3.364 -30.761 -15.034 -1.143 -3.856 -0.199 H16 YRI 55 YRI H17 H17 H 0 1 N N N N N N 1.625 -30.783 -13.072 3.402 -1.357 1.353 H17 YRI 56 YRI H18 H18 H 0 1 N N N N N N 3.873 -30.688 -14.076 4.484 0.732 0.657 H18 YRI 57 YRI H19 H19 H 0 1 N N N N N N 6.748 -28.415 -15.062 1.946 4.363 0.405 H19 YRI 58 YRI H20 H20 H 0 1 N N N N N N 5.015 -28.044 -15.359 1.531 5.076 -1.172 H20 YRI 59 YRI H21 H21 H 0 1 N N N N N N 5.471 -29.308 -14.167 1.136 3.374 -0.833 H21 YRI 60 YRI H22 H22 H 0 1 N N N N N N -2.475 -30.829 -13.517 0.371 -4.120 0.894 H22 YRI 61 YRI H23 H23 H 0 1 N N N N N N -2.193 -32.943 -11.120 4.610 -3.551 0.814 H23 YRI 62 YRI H24 H24 H 0 1 N N N N N N -0.602 -32.313 -10.571 3.528 -2.256 0.249 H24 YRI 63 YRI H25 H25 H 0 1 N N N N N N -0.638 -29.300 -10.556 2.215 -1.388 3.622 H25 YRI 64 YRI H26 H26 H 0 1 N N N N N N -2.228 -28.714 -11.154 2.129 -0.993 1.889 H26 YRI 65 YRI H27 H27 H 0 1 N N N N N N -3.332 -30.784 -7.700 5.940 -0.693 3.934 H27 YRI 66 YRI H28 H28 H 0 1 N N N N N N -3.912 -29.857 -9.125 4.332 -1.137 4.557 H28 YRI 67 YRI H29 H29 H 0 1 N N N N N N -3.988 -31.651 -9.129 5.533 -2.404 4.208 H29 YRI 68 YRI H30 H30 H 0 1 N N N N N N -4.148 -28.450 -14.710 -2.662 -2.570 1.449 H30 YRI 69 YRI H31 H31 H 0 1 N N N N N N -3.532 -26.159 -14.004 -3.024 -0.640 2.932 H31 YRI 70 YRI H32 H32 H 0 1 N N N N N N -1.775 -28.020 -18.245 -2.542 0.054 -1.926 H32 YRI 71 # 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 YRI O01 C02 DOUB N N 1 YRI C03 C02 SING N N 2 YRI C03 C04 SING N N 3 YRI C20 C15 SING N N 4 YRI C02 N31 SING N N 5 YRI BR37 C36 SING N N 6 YRI C04 C05 SING N N 7 YRI O16 C15 SING Y N 8 YRI O16 N17 SING Y N 9 YRI C15 C14 DOUB Y N 10 YRI C38 C36 DOUB Y N 11 YRI C38 C32 SING Y N 12 YRI N17 C18 DOUB Y N 13 YRI C21 C09 DOUB Y N 14 YRI C21 C13 SING Y N 15 YRI N31 C32 SING N N 16 YRI N31 C06 SING N N 17 YRI C36 C35 SING Y N 18 YRI N08 C09 SING Y N 19 YRI N08 C07 DOUB Y N 20 YRI C14 C18 SING Y N 21 YRI C14 C13 SING N N 22 YRI C05 C06 SING N N 23 YRI C32 C33 DOUB Y N 24 YRI C09 C10 SING Y N 25 YRI C18 C19 SING N N 26 YRI C13 C12 DOUB Y N 27 YRI C06 C07 SING N N 28 YRI C07 N22 SING Y N 29 YRI C35 BR39 SING N N 30 YRI C35 C34 DOUB Y N 31 YRI C33 C34 SING Y N 32 YRI C10 N22 SING Y N 33 YRI C10 C11 DOUB Y N 34 YRI N22 C23 SING N N 35 YRI C12 C11 SING Y N 36 YRI C23 C24 SING N N 37 YRI C23 C28 SING N N 38 YRI C24 C25 SING N N 39 YRI C28 C27 SING N N 40 YRI C25 C26 SING N N 41 YRI C27 C26 SING N N 42 YRI C26 O29 SING N N 43 YRI O29 C30 SING N N 44 YRI C20 H1 SING N N 45 YRI C20 H2 SING N N 46 YRI C20 H3 SING N N 47 YRI C21 H4 SING N N 48 YRI C24 H5 SING N N 49 YRI C24 H6 SING N N 50 YRI C26 H7 SING N N 51 YRI C28 H8 SING N N 52 YRI C28 H9 SING N N 53 YRI C03 H10 SING N N 54 YRI C03 H11 SING N N 55 YRI C04 H12 SING N N 56 YRI C04 H13 SING N N 57 YRI C05 H14 SING N N 58 YRI C05 H15 SING N N 59 YRI C06 H16 SING N N 60 YRI C11 H17 SING N N 61 YRI C12 H18 SING N N 62 YRI C19 H19 SING N N 63 YRI C19 H20 SING N N 64 YRI C19 H21 SING N N 65 YRI C23 H22 SING N N 66 YRI C25 H23 SING N N 67 YRI C25 H24 SING N N 68 YRI C27 H25 SING N N 69 YRI C27 H26 SING N N 70 YRI C30 H27 SING N N 71 YRI C30 H28 SING N N 72 YRI C30 H29 SING N N 73 YRI C33 H30 SING N N 74 YRI C34 H31 SING N N 75 YRI C38 H32 SING N N 76 # 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 YRI SMILES ACDLabs 12.01 "Cc1noc(C)c1c1cc2nc(C3CCCC(=O)N3c3ccc(Br)c(Br)c3)n(C3CCC(OC)CC3)c2cc1" YRI InChI InChI 1.06 "InChI=1S/C30H32Br2N4O3/c1-17-29(18(2)39-34-17)19-7-14-26-25(15-19)33-30(36(26)20-8-11-22(38-3)12-9-20)27-5-4-6-28(37)35(27)21-10-13-23(31)24(32)16-21/h7,10,13-16,20,22,27H,4-6,8-9,11-12H2,1-3H3/t20-,22+,27-/m0/s1" YRI InChIKey InChI 1.06 FMIALMAOMCXKFR-ZIHSNCGMSA-N YRI SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1CC[C@@H](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[C@@H]5CCCC(=O)N5c6ccc(Br)c(Br)c6" YRI SMILES CACTVS 3.385 "CO[CH]1CC[CH](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[CH]5CCCC(=O)N5c6ccc(Br)c(Br)c6" YRI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)[C@@H]5CCCC(=O)N5c6ccc(c(c6)Br)Br" YRI SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)C5CCCC(=O)N5c6ccc(c(c6)Br)Br" # 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 YRI "SYSTEMATIC NAME" ACDLabs 12.01 "(6S)-1-(3,4-dibromophenyl)-6-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}piperidin-2-one" YRI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(6~{S})-1-[3,4-bis(bromanyl)phenyl]-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 YRI "Create component" 2023-02-16 RCSB YRI "Initial release" 2024-02-21 RCSB #