data_YW5 # _chem_comp.id YW5 _chem_comp.name "2-[(R)-(1H-benzimidazol-2-yl)(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-2,3-dihydro-1H-isoindol-1-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C34 H31 F N4 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-27 _chem_comp.pdbx_modified_date 2024-03-08 _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 530.635 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YW5 _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 8GB4 _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 YW5 C11 C1 C 0 1 Y N N N N N -9.708 41.560 62.206 3.548 -0.296 -0.115 C11 YW5 1 YW5 C15 C2 C 0 1 Y N N N N N -8.110 41.415 60.094 1.175 0.343 -0.516 C15 YW5 2 YW5 C01 C3 C 0 1 N N N N N N -17.039 43.665 66.173 10.271 -1.589 0.820 C01 YW5 3 YW5 C03 C4 C 0 1 N N N N N N -15.958 43.426 64.054 9.824 0.776 1.076 C03 YW5 4 YW5 C04 C5 C 0 1 N N N N N N -14.610 43.478 63.393 8.316 0.527 1.144 C04 YW5 5 YW5 C05 C6 C 0 1 N N N N N N -13.351 43.204 64.313 7.732 0.567 -0.271 C05 YW5 6 YW5 C06 C7 C 0 1 N N N N N N -13.684 42.280 65.521 8.439 -0.481 -1.135 C06 YW5 7 YW5 C07 C8 C 0 1 N N N N N N -15.071 42.320 66.062 9.944 -0.203 -1.138 C07 YW5 8 YW5 C08 C9 C 0 1 Y N N N N N -12.089 42.614 63.565 6.257 0.262 -0.216 C08 YW5 9 YW5 C09 C10 C 0 1 Y N N N N N -11.774 41.236 63.569 5.344 1.195 -0.675 C09 YW5 10 YW5 C10 C11 C 0 1 Y N N N N N -10.631 40.728 62.899 3.992 0.922 -0.627 C10 YW5 11 YW5 C12 C12 C 0 1 Y N N N N N -10.046 42.936 62.211 4.472 -1.231 0.345 C12 YW5 12 YW5 C13 C13 C 0 1 Y N N N N N -11.186 43.451 62.874 5.822 -0.948 0.292 C13 YW5 13 YW5 C14 C14 C 0 1 Y N N N N N -8.427 41.026 61.422 2.095 -0.592 -0.055 C14 YW5 14 YW5 C16 C15 C 0 1 Y N N N N N -6.982 40.950 59.363 -0.189 0.062 -0.451 C16 YW5 15 YW5 C17 C16 C 0 1 Y N N N N N -6.111 40.038 59.949 -0.615 -1.160 0.076 C17 YW5 16 YW5 C18 C17 C 0 1 N N N N N N -4.966 39.710 58.915 -2.122 -1.153 0.004 C18 YW5 17 YW5 C20 C18 C 0 1 N N R N N N -4.344 40.402 56.440 -3.868 0.586 -0.852 C20 YW5 18 YW5 C21 C19 C 0 1 Y N N N N N -3.169 41.490 56.465 -4.831 -0.534 -0.552 C21 YW5 19 YW5 C23 C20 C 0 1 Y N N N N N -1.444 42.812 57.108 -6.631 -1.813 -0.578 C23 YW5 20 YW5 C24 C21 C 0 1 Y N N N N N -1.724 43.169 55.773 -5.675 -2.345 0.305 C24 YW5 21 YW5 C26 C22 C 0 1 Y N N N N N -0.959 44.186 55.117 -5.963 -3.521 1.001 C26 YW5 22 YW5 C27 C23 C 0 1 Y N N N N N 0.054 44.820 55.803 -7.166 -4.143 0.820 C27 YW5 23 YW5 C28 C24 C 0 1 Y N N N N N 0.347 44.463 57.167 -8.109 -3.618 -0.051 C28 YW5 24 YW5 C29 C25 C 0 1 Y N N N N N -0.382 43.483 57.811 -7.846 -2.460 -0.752 C29 YW5 25 YW5 C30 C26 C 0 1 Y N N N N N -3.713 38.916 56.233 -4.185 1.770 0.025 C30 YW5 26 YW5 C31 C27 C 0 1 Y N N N N N -2.322 38.757 56.132 -4.803 2.882 -0.513 C31 YW5 27 YW5 C32 C28 C 0 1 Y N N N N N -1.748 37.484 55.955 -5.094 3.970 0.293 C32 YW5 28 YW5 C34 C29 C 0 1 Y N N N N N -2.546 36.332 55.864 -4.765 3.941 1.638 C34 YW5 29 YW5 C35 C30 C 0 1 Y N N N N N -3.943 36.478 55.960 -4.147 2.828 2.174 C35 YW5 30 YW5 C36 C31 C 0 1 Y N N N N N -4.530 37.749 56.139 -3.862 1.740 1.369 C36 YW5 31 YW5 C37 C32 C 0 1 N N N N N N -6.440 41.237 57.915 -1.381 0.835 -0.850 C37 YW5 32 YW5 C39 C33 C 0 1 Y N N N N N -6.375 39.599 61.283 0.300 -2.084 0.529 C39 YW5 33 YW5 C40 C34 C 0 1 Y N N N N N -7.510 40.082 61.997 1.653 -1.810 0.462 C40 YW5 34 YW5 F33 F1 F 0 1 N N N N N N -0.426 37.374 55.868 -5.699 5.058 -0.232 F33 YW5 35 YW5 N02 N1 N 0 1 N N N N N N -15.702 43.598 65.539 10.454 -0.252 0.239 N02 YW5 36 YW5 N19 N2 N 0 1 N N N N N N -5.265 40.498 57.652 -2.499 0.135 -0.589 N19 YW5 37 YW5 N22 N3 N 0 1 Y N N N N N -2.366 41.759 57.503 -6.067 -0.668 -1.105 N22 YW5 38 YW5 N25 N4 N 0 1 Y N N N N N -2.806 42.331 55.368 -4.601 -1.515 0.270 N25 YW5 39 YW5 O38 O1 O 0 1 N N N N N N -6.932 41.990 57.085 -1.356 1.945 -1.345 O38 YW5 40 YW5 H1 H1 H 0 1 N N N N N N -8.772 42.113 59.604 1.516 1.286 -0.917 H1 YW5 41 YW5 H2 H2 H 0 1 N N N N N N -16.924 43.791 67.260 9.206 -1.808 0.901 H2 YW5 42 YW5 H3 H3 H 0 1 N N N N N N -17.597 44.519 65.762 10.747 -2.332 0.180 H3 YW5 43 YW5 H4 H4 H 0 1 N N N N N N -17.589 42.735 65.968 10.724 -1.619 1.811 H4 YW5 44 YW5 H5 H5 H 0 1 N N N N N N -16.599 44.238 63.680 10.011 1.760 0.644 H5 YW5 45 YW5 H6 H6 H 0 1 N N N N N N -16.442 42.458 63.859 10.245 0.735 2.080 H6 YW5 46 YW5 H7 H7 H 0 1 N N N N N N -14.604 42.727 62.590 8.128 -0.450 1.588 H7 YW5 47 YW5 H8 H8 H 0 1 N N N N N N -14.492 44.481 62.958 7.846 1.300 1.753 H8 YW5 48 YW5 H9 H9 H 0 1 N N N N N N -13.046 44.176 64.728 7.885 1.556 -0.701 H9 YW5 49 YW5 H10 H10 H 0 1 N N N N N N -13.483 41.245 65.208 8.253 -1.475 -0.727 H10 YW5 50 YW5 H11 H11 H 0 1 N N N N N N -13.004 42.553 66.341 8.058 -0.429 -2.155 H11 YW5 51 YW5 H12 H12 H 0 1 N N N N N N -15.640 41.445 65.714 10.452 -0.956 -1.740 H12 YW5 52 YW5 H13 H13 H 0 1 N N N N N N -15.050 42.329 67.162 10.130 0.785 -1.558 H13 YW5 53 YW5 H14 H14 H 0 1 N N N N N N -12.421 40.551 64.097 5.690 2.138 -1.071 H14 YW5 54 YW5 H15 H15 H 0 1 N N N N N N -10.454 39.663 62.916 3.280 1.650 -0.985 H15 YW5 55 YW5 H16 H16 H 0 1 N N N N N N -9.403 43.625 61.684 4.133 -2.176 0.743 H16 YW5 56 YW5 H17 H17 H 0 1 N N N N N N -11.370 44.515 62.851 6.539 -1.672 0.649 H17 YW5 57 YW5 H18 H18 H 0 1 N N N N N N -4.955 38.633 58.694 -2.472 -1.971 -0.625 H18 YW5 58 YW5 H19 H19 H 0 1 N N N N N N -3.990 40.010 59.325 -2.545 -1.243 1.005 H19 YW5 59 YW5 H20 H20 H 0 1 N N N N N N -4.949 40.611 55.545 -3.961 0.874 -1.899 H20 YW5 60 YW5 H21 H21 H 0 1 N N N N N N -1.174 44.454 54.093 -5.235 -3.939 1.681 H21 YW5 61 YW5 H22 H22 H 0 1 N N N N N N 0.632 45.590 55.314 -7.384 -5.053 1.360 H22 YW5 62 YW5 H23 H23 H 0 1 N N N N N N 1.145 44.967 57.692 -9.056 -4.121 -0.183 H23 YW5 63 YW5 H24 H24 H 0 1 N N N N N N -0.157 43.222 58.835 -8.584 -2.056 -1.430 H24 YW5 64 YW5 H25 H25 H 0 1 N N N N N N -1.682 39.625 56.191 -5.059 2.903 -1.562 H25 YW5 65 YW5 H26 H26 H 0 1 N N N N N N -2.099 35.359 55.724 -4.991 4.789 2.267 H26 YW5 66 YW5 H27 H27 H 0 1 N N N N N N -4.575 35.604 55.896 -3.890 2.805 3.223 H27 YW5 67 YW5 H28 H28 H 0 1 N N N N N N -5.604 37.839 56.205 -3.379 0.870 1.789 H28 YW5 68 YW5 H29 H29 H 0 1 N N N N N N -5.707 38.894 61.755 -0.040 -3.025 0.935 H29 YW5 69 YW5 H30 H30 H 0 1 N N N N N N -7.686 39.727 63.002 2.369 -2.536 0.819 H30 YW5 70 YW5 H32 H32 H 0 1 N N N N N N -2.396 41.312 58.397 -6.476 -0.071 -1.751 H32 YW5 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 YW5 C26 C24 DOUB Y N 1 YW5 C26 C27 SING Y N 2 YW5 N25 C24 SING Y N 3 YW5 N25 C21 DOUB Y N 4 YW5 C24 C23 SING Y N 5 YW5 C27 C28 DOUB Y N 6 YW5 C34 C32 DOUB Y N 7 YW5 C34 C35 SING Y N 8 YW5 F33 C32 SING N N 9 YW5 C32 C31 SING Y N 10 YW5 C35 C36 DOUB Y N 11 YW5 C31 C30 DOUB Y N 12 YW5 C36 C30 SING Y N 13 YW5 C30 C20 SING N N 14 YW5 C20 C21 SING N N 15 YW5 C20 N19 SING N N 16 YW5 C21 N22 SING Y N 17 YW5 O38 C37 DOUB N N 18 YW5 C23 N22 SING Y N 19 YW5 C23 C29 DOUB Y N 20 YW5 C28 C29 SING Y N 21 YW5 N19 C37 SING N N 22 YW5 N19 C18 SING N N 23 YW5 C37 C16 SING N N 24 YW5 C18 C17 SING N N 25 YW5 C16 C17 DOUB Y N 26 YW5 C16 C15 SING Y N 27 YW5 C17 C39 SING Y N 28 YW5 C15 C14 DOUB Y N 29 YW5 C39 C40 DOUB Y N 30 YW5 C14 C40 SING Y N 31 YW5 C14 C11 SING N N 32 YW5 C11 C12 DOUB Y N 33 YW5 C11 C10 SING Y N 34 YW5 C12 C13 SING Y N 35 YW5 C13 C08 DOUB Y N 36 YW5 C10 C09 DOUB Y N 37 YW5 C04 C03 SING N N 38 YW5 C04 C05 SING N N 39 YW5 C08 C09 SING Y N 40 YW5 C08 C05 SING N N 41 YW5 C03 N02 SING N N 42 YW5 C05 C06 SING N N 43 YW5 C06 C07 SING N N 44 YW5 N02 C07 SING N N 45 YW5 N02 C01 SING N N 46 YW5 C15 H1 SING N N 47 YW5 C01 H2 SING N N 48 YW5 C01 H3 SING N N 49 YW5 C01 H4 SING N N 50 YW5 C03 H5 SING N N 51 YW5 C03 H6 SING N N 52 YW5 C04 H7 SING N N 53 YW5 C04 H8 SING N N 54 YW5 C05 H9 SING N N 55 YW5 C06 H10 SING N N 56 YW5 C06 H11 SING N N 57 YW5 C07 H12 SING N N 58 YW5 C07 H13 SING N N 59 YW5 C09 H14 SING N N 60 YW5 C10 H15 SING N N 61 YW5 C12 H16 SING N N 62 YW5 C13 H17 SING N N 63 YW5 C18 H18 SING N N 64 YW5 C18 H19 SING N N 65 YW5 C20 H20 SING N N 66 YW5 C26 H21 SING N N 67 YW5 C27 H22 SING N N 68 YW5 C28 H23 SING N N 69 YW5 C29 H24 SING N N 70 YW5 C31 H25 SING N N 71 YW5 C34 H26 SING N N 72 YW5 C35 H27 SING N N 73 YW5 C36 H28 SING N N 74 YW5 C39 H29 SING N N 75 YW5 C40 H30 SING N N 76 YW5 N22 H32 SING N N 77 # 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 YW5 SMILES ACDLabs 12.01 "CN1CCC(CC1)c1ccc(cc1)c1ccc2CN(C(c3cccc(F)c3)c3nc4ccccc4[NH]3)C(=O)c2c1" YW5 InChI InChI 1.06 "InChI=1S/C34H31FN4O/c1-38-17-15-24(16-18-38)22-9-11-23(12-10-22)25-13-14-27-21-39(34(40)29(27)20-25)32(26-5-4-6-28(35)19-26)33-36-30-7-2-3-8-31(30)37-33/h2-14,19-20,24,32H,15-18,21H2,1H3,(H,36,37)/t32-/m1/s1" YW5 InChIKey InChI 1.06 ZMKPSKAUYOLPIA-JGCGQSQUSA-N YW5 SMILES_CANONICAL CACTVS 3.385 "CN1CCC(CC1)c2ccc(cc2)c3ccc4CN([C@H](c5cccc(F)c5)c6[nH]c7ccccc7n6)C(=O)c4c3" YW5 SMILES CACTVS 3.385 "CN1CCC(CC1)c2ccc(cc2)c3ccc4CN([CH](c5cccc(F)c5)c6[nH]c7ccccc7n6)C(=O)c4c3" YW5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1CCC(CC1)c2ccc(cc2)c3ccc4c(c3)C(=O)N(C4)[C@H](c5cccc(c5)F)c6[nH]c7ccccc7n6" YW5 SMILES "OpenEye OEToolkits" 2.0.7 "CN1CCC(CC1)c2ccc(cc2)c3ccc4c(c3)C(=O)N(C4)C(c5cccc(c5)F)c6[nH]c7ccccc7n6" # 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 YW5 "SYSTEMATIC NAME" ACDLabs 12.01 "2-[(R)-(1H-benzimidazol-2-yl)(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-2,3-dihydro-1H-isoindol-1-one" YW5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[(~{R})-1~{H}-benzimidazol-2-yl-(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-3~{H}-isoindol-1-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 YW5 "Create component" 2023-02-27 RCSB YW5 "Initial release" 2024-03-13 RCSB #