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 
# 
