data_Y8Z # _chem_comp.id Y8Z _chem_comp.name "N-[(1R,3R)-3-{(2S)-2-benzyl-4-[2-(methylamino)-2-oxoethyl]-3-oxopiperazine-1-carbonyl}cyclopentyl]-4-chloro-3-(trifluoromethyl)benzamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C28 H30 Cl F3 N4 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-12 _chem_comp.pdbx_modified_date 2024-12-13 _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 579.010 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y8Z _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 7G5P _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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_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 Y8Z C10 C1 C 0 1 N N N N N N -14.724 10.514 47.329 -3.946 0.703 1.462 C10 Y8Z 1 Y8Z C11 C2 C 0 1 N N N N N N -14.007 10.230 48.683 -5.361 1.228 1.212 C11 Y8Z 2 Y8Z C13 C3 C 0 1 N N N N N N -13.266 12.679 48.460 -5.767 -0.911 0.043 C13 Y8Z 3 Y8Z C15 C4 C 0 1 N N N N N N -14.691 13.509 46.545 -3.944 -2.398 0.827 C15 Y8Z 4 Y8Z C16 C5 C 0 1 Y N N N N N -14.776 13.714 45.049 -2.511 -2.800 0.594 C16 Y8Z 5 Y8Z C17 C6 C 0 1 Y N N N N N -15.620 12.905 44.238 -1.499 -2.207 1.325 C17 Y8Z 6 Y8Z C18 C7 C 0 1 Y N N N N N -14.856 14.131 42.265 0.119 -3.538 0.166 C18 Y8Z 7 Y8Z C19 C8 C 0 1 Y N N N N N -14.042 14.922 43.072 -0.894 -4.135 -0.562 C19 Y8Z 8 Y8Z C20 C9 C 0 1 Y N N N N N -15.668 13.100 42.841 -0.184 -2.576 1.111 C20 Y8Z 9 Y8Z C21 C10 C 0 1 Y N N N N N -13.953 14.709 44.448 -2.209 -3.766 -0.348 C21 Y8Z 10 Y8Z C23 C11 C 0 1 N N N N N N -13.225 11.481 50.727 -7.662 0.329 0.827 C23 Y8Z 11 Y8Z C24 C12 C 0 1 N N N N N N -13.886 12.685 51.384 -8.220 1.071 -0.361 C24 Y8Z 12 Y8Z C27 C13 C 0 1 N N N N N N -15.830 14.364 51.257 -10.084 2.048 -1.589 C27 Y8Z 13 Y8Z C28 C14 C 0 1 N N N N N N -11.139 7.706 42.420 3.080 1.790 -0.082 C28 Y8Z 14 Y8Z C1 C15 C 0 1 N N N N N N -12.443 11.166 43.029 -0.489 1.791 -1.023 C1 Y8Z 15 Y8Z C2 C16 C 0 1 N N R N N N -11.338 10.159 42.585 0.696 2.286 -0.174 C2 Y8Z 16 Y8Z C3 C17 C 0 1 N N N N N N -10.118 10.658 43.347 0.202 2.333 1.287 C3 Y8Z 17 Y8Z C4 C18 C 0 1 N N N N N N -10.625 10.874 44.737 -0.975 1.327 1.322 C4 Y8Z 18 Y8Z C5 C19 C 0 1 N N S N N N -12.110 11.378 44.513 -1.661 1.555 -0.048 C5 Y8Z 19 Y8Z C6 C20 C 0 1 N N N N N N -13.059 10.590 45.411 -2.447 0.335 -0.454 C6 Y8Z 20 Y8Z O7 O1 O 0 1 N N N N N N -13.249 9.415 45.229 -2.115 -0.302 -1.431 O7 Y8Z 21 Y8Z N8 N1 N 0 1 N N N N N N -13.744 11.225 46.473 -3.517 -0.049 0.269 N8 Y8Z 22 Y8Z N9 N2 N 0 1 N N N N N N -11.659 8.795 43.032 1.822 1.356 -0.293 N9 Y8Z 23 Y8Z N12 N3 N 0 1 N N N N N N -13.401 11.489 49.251 -6.213 0.178 0.671 N12 Y8Z 24 Y8Z C14 C21 C 0 1 N N S N N N -13.485 12.594 46.916 -4.305 -1.234 -0.099 C14 Y8Z 25 Y8Z O22 O2 O 0 1 N N N N N N -12.935 13.801 48.955 -6.578 -1.677 -0.433 O22 Y8Z 26 Y8Z N25 N4 N 0 1 N N N N N N -15.083 13.164 50.788 -9.542 1.327 -0.435 N25 Y8Z 27 Y8Z O26 O3 O 0 1 N N N N N N -13.353 13.220 52.365 -7.481 1.437 -1.249 O26 Y8Z 28 Y8Z C29 C22 C 0 1 Y N N N N N -11.573 6.390 42.991 4.215 0.852 -0.203 C29 Y8Z 29 Y8Z C30 C23 C 0 1 Y N N N N N -12.674 6.311 43.906 3.988 -0.484 -0.535 C30 Y8Z 30 Y8Z C31 C24 C 0 1 Y N N N N N -12.283 3.905 43.940 6.344 -0.905 -0.429 C31 Y8Z 31 Y8Z C32 C25 C 0 1 Y N N N N N -11.202 4.035 43.018 6.576 0.421 -0.105 C32 Y8Z 32 Y8Z C33 C26 C 0 1 Y N N N N N -13.011 5.000 44.362 5.052 -1.355 -0.647 C33 Y8Z 33 Y8Z C34 C27 C 0 1 Y N N N N N -10.897 5.288 42.560 5.521 1.301 0.010 C34 Y8Z 34 Y8Z O35 O4 O 0 1 N N N N N N -10.349 7.789 41.449 3.280 2.954 0.208 O35 Y8Z 35 Y8Z C36 C28 C 0 1 N N N N N N -10.441 2.802 42.568 7.985 0.902 0.131 C36 Y8Z 36 Y8Z F37 F1 F 0 1 N N N N N N -9.640 2.283 43.487 7.966 2.266 0.442 F37 Y8Z 37 Y8Z F38 F2 F 0 1 N N N N N N -11.242 1.765 42.211 8.549 0.189 1.194 F38 Y8Z 38 Y8Z F39 F3 F 0 1 N N N N N N -9.689 2.968 41.474 8.747 0.698 -1.024 F39 Y8Z 39 Y8Z CL40 CL1 CL 0 0 N N N N N N -12.715 2.321 44.606 7.678 -2.007 -0.572 CL40 Y8Z 40 Y8Z H50 H1 H 0 1 N N N N N N -15.611 11.143 47.494 -3.268 1.539 1.632 H50 Y8Z 41 Y8Z H51 H2 H 0 1 N N N N N N -15.028 9.569 46.855 -3.945 0.045 2.331 H51 Y8Z 42 Y8Z H52 H3 H 0 1 N N N N N N -14.739 9.828 49.400 -5.783 1.583 2.152 H52 Y8Z 43 Y8Z H53 H4 H 0 1 N N N N N N -13.210 9.490 48.519 -5.317 2.055 0.504 H53 Y8Z 44 Y8Z H56 H5 H 0 1 N N N N N N -15.621 13.039 46.897 -4.598 -3.244 0.618 H56 Y8Z 45 Y8Z H55 H6 H 0 1 N N N N N N -14.566 14.486 47.035 -4.071 -2.088 1.865 H55 Y8Z 46 Y8Z H57 H7 H 0 1 N N N N N N -16.227 12.137 44.694 -1.735 -1.455 2.063 H57 Y8Z 47 Y8Z H58 H8 H 0 1 N N N N N N -14.875 14.296 41.198 1.146 -3.826 -0.002 H58 Y8Z 48 Y8Z H59 H9 H 0 1 N N N N N N -13.467 15.718 42.623 -0.657 -4.886 -1.300 H59 Y8Z 49 Y8Z H60 H10 H 0 1 N N N N N N -16.303 12.486 42.220 0.607 -2.112 1.681 H60 Y8Z 50 Y8Z H61 H11 H 0 1 N N N N N N -13.270 15.290 45.049 -3.000 -4.233 -0.916 H61 Y8Z 51 Y8Z H62 H12 H 0 1 N N N N N N -13.674 10.563 51.134 -7.873 0.890 1.737 H62 Y8Z 52 Y8Z H63 H13 H 0 1 N N N N N N -12.149 11.496 50.957 -8.125 -0.655 0.891 H63 Y8Z 53 Y8Z H65 H14 H 0 1 N N N N N N -16.717 14.515 50.624 -9.621 3.032 -1.653 H65 Y8Z 54 Y8Z H66 H15 H 0 1 N N N N N N -16.145 14.215 52.300 -9.873 1.487 -2.499 H66 Y8Z 55 Y8Z H67 H16 H 0 1 N N N N N N -15.180 15.249 51.193 -11.162 2.160 -1.473 H67 Y8Z 56 Y8Z H42 H17 H 0 1 N N N N N N -12.374 12.108 42.466 -0.762 2.547 -1.759 H42 Y8Z 57 Y8Z H41 H18 H 0 1 N N N N N N -13.448 10.737 42.903 -0.226 0.859 -1.523 H41 Y8Z 58 Y8Z H43 H19 H 0 1 N N N N N N -11.178 10.211 41.498 0.998 3.282 -0.498 H43 Y8Z 59 Y8Z H45 H20 H 0 1 N N N N N N -9.315 9.906 43.336 0.993 2.018 1.967 H45 Y8Z 60 Y8Z H44 H21 H 0 1 N N N N N N -9.745 11.599 42.916 -0.144 3.335 1.541 H44 Y8Z 61 Y8Z H47 H22 H 0 1 N N N N N N -10.610 9.936 45.311 -0.608 0.304 1.405 H47 Y8Z 62 Y8Z H46 H23 H 0 1 N N N N N N -10.026 11.634 45.261 -1.658 1.561 2.139 H46 Y8Z 63 Y8Z H48 H24 H 0 1 N N N N N N -12.167 12.449 44.757 -2.308 2.431 -0.010 H48 Y8Z 64 Y8Z H49 H25 H 0 1 N N N N N N -12.277 8.669 43.808 1.661 0.428 -0.525 H49 Y8Z 65 Y8Z H54 H26 H 0 1 N N N N N N -12.586 12.983 46.415 -4.091 -1.508 -1.132 H54 Y8Z 66 Y8Z H64 H27 H 0 1 N N N N N N -15.448 12.663 50.003 -10.133 1.034 0.276 H64 Y8Z 67 Y8Z H68 H28 H 0 1 N N N N N N -13.215 7.188 44.230 2.981 -0.836 -0.705 H68 Y8Z 68 Y8Z H69 H29 H 0 1 N N N N N N -13.840 4.864 45.041 4.877 -2.389 -0.904 H69 Y8Z 69 Y8Z H70 H30 H 0 1 N N N N N N -10.101 5.406 41.839 5.703 2.335 0.263 H70 Y8Z 70 # 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 Y8Z C1 C2 SING N N 1 Y8Z C1 C5 SING N N 2 Y8Z C2 C3 SING N N 3 Y8Z C2 N9 SING N N 4 Y8Z C3 C4 SING N N 5 Y8Z C4 C5 SING N N 6 Y8Z C5 C6 SING N N 7 Y8Z C6 O7 DOUB N N 8 Y8Z C6 N8 SING N N 9 Y8Z N8 C10 SING N N 10 Y8Z N8 C14 SING N N 11 Y8Z N9 C28 SING N N 12 Y8Z C10 C11 SING N N 13 Y8Z C11 N12 SING N N 14 Y8Z N12 C13 SING N N 15 Y8Z N12 C23 SING N N 16 Y8Z C13 C14 SING N N 17 Y8Z C13 O22 DOUB N N 18 Y8Z C14 C15 SING N N 19 Y8Z C15 C16 SING N N 20 Y8Z C16 C17 DOUB Y N 21 Y8Z C16 C21 SING Y N 22 Y8Z C17 C20 SING Y N 23 Y8Z C18 C19 SING Y N 24 Y8Z C18 C20 DOUB Y N 25 Y8Z C19 C21 DOUB Y N 26 Y8Z C23 C24 SING N N 27 Y8Z C24 N25 SING N N 28 Y8Z C24 O26 DOUB N N 29 Y8Z N25 C27 SING N N 30 Y8Z C28 C29 SING N N 31 Y8Z C28 O35 DOUB N N 32 Y8Z C29 C30 DOUB Y N 33 Y8Z C29 C34 SING Y N 34 Y8Z C30 C33 SING Y N 35 Y8Z C31 C32 SING Y N 36 Y8Z C31 C33 DOUB Y N 37 Y8Z C31 CL40 SING N N 38 Y8Z C32 C34 DOUB Y N 39 Y8Z C32 C36 SING N N 40 Y8Z C36 F37 SING N N 41 Y8Z C36 F38 SING N N 42 Y8Z C36 F39 SING N N 43 Y8Z C10 H50 SING N N 44 Y8Z C10 H51 SING N N 45 Y8Z C11 H52 SING N N 46 Y8Z C11 H53 SING N N 47 Y8Z C15 H56 SING N N 48 Y8Z C15 H55 SING N N 49 Y8Z C17 H57 SING N N 50 Y8Z C18 H58 SING N N 51 Y8Z C19 H59 SING N N 52 Y8Z C20 H60 SING N N 53 Y8Z C21 H61 SING N N 54 Y8Z C23 H62 SING N N 55 Y8Z C23 H63 SING N N 56 Y8Z C27 H65 SING N N 57 Y8Z C27 H66 SING N N 58 Y8Z C27 H67 SING N N 59 Y8Z C1 H42 SING N N 60 Y8Z C1 H41 SING N N 61 Y8Z C2 H43 SING N N 62 Y8Z C3 H45 SING N N 63 Y8Z C3 H44 SING N N 64 Y8Z C4 H47 SING N N 65 Y8Z C4 H46 SING N N 66 Y8Z C5 H48 SING N N 67 Y8Z N9 H49 SING N N 68 Y8Z C14 H54 SING N N 69 Y8Z N25 H64 SING N N 70 Y8Z C30 H68 SING N N 71 Y8Z C33 H69 SING N N 72 Y8Z C34 H70 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 Y8Z SMILES ACDLabs 12.01 "O=C(C1CCC(NC(=O)c2ccc(Cl)c(c2)C(F)(F)F)C1)N1CCN(CC(=O)NC)C(=O)C1Cc1ccccc1" Y8Z InChI InChI 1.06 "InChI=1S/C28H30ClF3N4O4/c1-33-24(37)16-35-11-12-36(23(27(35)40)13-17-5-3-2-4-6-17)26(39)19-7-9-20(14-19)34-25(38)18-8-10-22(29)21(15-18)28(30,31)32/h2-6,8,10,15,19-20,23H,7,9,11-14,16H2,1H3,(H,33,37)(H,34,38)/t19-,20-,23?/m1/s1" Y8Z InChIKey InChI 1.06 VYTGFXCOUVGDEC-VJOPYQGCSA-N Y8Z SMILES_CANONICAL CACTVS 3.385 "CNC(=O)CN1CCN([C@@H](Cc2ccccc2)C1=O)C(=O)[C@H]3CC[C@H](C3)NC(=O)c4ccc(Cl)c(c4)C(F)(F)F" Y8Z SMILES CACTVS 3.385 "CNC(=O)CN1CCN([CH](Cc2ccccc2)C1=O)C(=O)[CH]3CC[CH](C3)NC(=O)c4ccc(Cl)c(c4)C(F)(F)F" Y8Z SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNC(=O)CN1CCN([C@H](C1=O)Cc2ccccc2)C(=O)[C@H]3CC[C@H](C3)NC(=O)c4ccc(c(c4)C(F)(F)F)Cl" Y8Z SMILES "OpenEye OEToolkits" 2.0.7 "CNC(=O)CN1CCN(C(C1=O)Cc2ccccc2)C(=O)C3CCC(C3)NC(=O)c4ccc(c(c4)C(F)(F)F)Cl" # 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 Y8Z "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(1R,3R)-3-{(2S)-2-benzyl-4-[2-(methylamino)-2-oxoethyl]-3-oxopiperazine-1-carbonyl}cyclopentyl]-4-chloro-3-(trifluoromethyl)benzamide" Y8Z "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "4-chloranyl-~{N}-[(1~{R},3~{S})-3-[(2~{S})-4-[2-(methylamino)-2-oxidanylidene-ethyl]-3-oxidanylidene-2-(phenylmethyl)piperazin-1-yl]carbonylcyclopentyl]-3-(trifluoromethyl)benzamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y8Z "Create component" 2023-06-12 RCSB Y8Z "Initial release" 2024-12-18 RCSB #