data_YID
# 
_chem_comp.id                                    YID 
_chem_comp.name                                  "(6S)-1-(3-tert-butylphenyl)-6-{(5P)-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                               "C34 H42 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-03 
_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                        554.722 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YID 
_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        8FXE 
_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 
YID C10 C1  C 0 1 Y N N N N N 18.898 25.527 -1.427 0.906  1.140  0.190  C10 YID 1  
YID C13 C2  C 0 1 Y N N N N N 21.538 25.928 -2.324 2.788  -0.860 0.604  C13 YID 2  
YID C15 C3  C 0 1 Y N N N N N 23.995 26.527 -1.956 4.955  -1.852 1.551  C15 YID 3  
YID C20 C4  C 0 1 N N N N N N 23.967 27.021 -0.509 5.467  -0.661 2.320  C20 YID 4  
YID C21 C5  C 0 1 Y N N N N N 20.466 26.325 -3.111 1.500  -1.026 1.094  C21 YID 5  
YID C24 C6  C 0 1 N N N N N N 17.036 23.510 0.141  0.635  4.213  0.170  C24 YID 6  
YID C26 C7  C 0 1 N N N N N N 15.766 23.938 2.270  2.363  3.571  -1.516 C26 YID 7  
YID C28 C8  C 0 1 N N N N N N 17.076 25.859 1.041  -0.052 3.123  -1.971 C28 YID 8  
YID C02 C9  C 0 1 N N N N N N 14.436 27.714 -4.478 -4.662 0.417  1.391  C02 YID 9  
YID C03 C10 C 0 1 N N N N N N 13.939 26.375 -5.102 -5.052 1.172  2.629  C03 YID 10 
YID C04 C11 C 0 1 N N N N N N 13.812 25.304 -4.104 -4.283 2.493  2.697  C04 YID 11 
YID C05 C12 C 0 1 N N N N N N 15.107 25.045 -3.509 -2.797 2.203  2.453  C05 YID 12 
YID C06 C13 C 0 1 N N S N N N 15.555 26.190 -2.690 -2.620 1.745  1.004  C06 YID 13 
YID C07 C14 C 0 1 Y N N N N N 17.018 26.036 -2.401 -1.211 1.247  0.808  C07 YID 14 
YID C09 C15 C 0 1 Y N N N N N 19.164 26.129 -2.625 0.549  -0.025 0.891  C09 YID 15 
YID C11 C16 C 0 1 Y N N N N N 19.992 25.099 -0.639 2.197  1.290  -0.301 C11 YID 16 
YID C12 C17 C 0 1 Y N N N N N 21.303 25.301 -1.093 3.130  0.300  -0.096 C12 YID 17 
YID C14 C18 C 0 1 Y N N N N N 22.993 26.123 -2.766 3.803  -1.921 0.820  C14 YID 18 
YID C18 C19 C 0 1 Y N N N N N 23.494 25.846 -4.057 3.807  -3.251 0.312  C18 YID 19 
YID C19 C20 C 0 1 N N N N N N 22.766 25.317 -5.269 2.760  -3.886 -0.566 C19 YID 20 
YID C23 C21 C 0 1 N N N N N N 16.698 24.969 -0.137 -0.356 3.242  -0.476 C23 YID 21 
YID C25 C22 C 0 1 N N N N N N 16.097 22.908 1.185  2.060  3.690  -0.021 C25 YID 22 
YID C27 C23 C 0 1 N N N N N N 16.342 25.358 2.314  1.373  2.600  -2.162 C27 YID 23 
YID C30 C24 C 0 1 N N N N N N 15.084 24.355 4.424  4.685  4.110  -1.774 C30 YID 24 
YID C32 C25 C 0 1 Y N N N N N 15.786 28.757 -2.644 -3.282 -0.133 -0.420 C32 YID 25 
YID C33 C26 C 0 1 Y N N N N N 15.187 29.063 -1.383 -2.966 -1.474 -0.243 C33 YID 26 
YID C34 C27 C 0 1 Y N N N N N 15.677 30.111 -0.603 -2.700 -2.270 -1.340 C34 YID 27 
YID C35 C28 C 0 1 N N N N N N 15.005 30.464 0.717  -2.357 -3.725 -1.149 C35 YID 28 
YID C36 C29 C 0 1 N N N N N N 13.485 30.605 0.530  -1.096 -3.843 -0.291 C36 YID 29 
YID C37 C30 C 0 1 N N N N N N 15.698 31.641 1.394  -3.518 -4.435 -0.450 C37 YID 30 
YID C38 C31 C 0 1 N N N N N N 15.262 29.285 1.663  -2.110 -4.373 -2.513 C38 YID 31 
YID C39 C32 C 0 1 Y N N N N N 16.740 30.867 -1.121 -2.749 -1.733 -2.614 C39 YID 32 
YID C40 C33 C 0 1 Y N N N N N 17.337 30.534 -2.349 -3.063 -0.398 -2.793 C40 YID 33 
YID C41 C34 C 0 1 Y N N N N N 16.875 29.483 -3.142 -3.329 0.403  -1.700 C41 YID 34 
YID N08 N1  N 0 1 Y N N N N N 17.983 26.389 -3.242 -0.757 0.107  1.239  N08 YID 35 
YID N17 N2  N 0 1 Y N N N N N 24.805 26.093 -4.042 4.891  -3.810 0.762  N17 YID 36 
YID N22 N3  N 0 1 Y N N N N N 17.543 25.465 -1.281 -0.230 1.925  0.154  N22 YID 37 
YID N31 N4  N 0 1 N N N N N N 15.284 27.603 -3.302 -3.557 0.674  0.689  N31 YID 38 
YID O01 O1  O 0 1 N N N N N N 14.253 28.792 -4.936 -5.387 -0.479 1.012  O01 YID 39 
YID O16 O2  O 0 1 Y N N N N N 25.083 26.538 -2.779 5.541  -3.052 1.443  O16 YID 40 
YID O29 O3  O 0 1 N N N N N N 15.541 23.362 3.551  3.694  3.083  -1.695 O29 YID 41 
YID H1  H1  H 0 1 N N N N N N 24.964 27.390 -0.228 5.081  -0.693 3.339  H1  YID 42 
YID H2  H2  H 0 1 N N N N N N 23.234 27.836 -0.414 6.556  -0.685 2.344  H2  YID 43 
YID H3  H3  H 0 1 N N N N N N 23.682 26.192 0.156  5.135  0.256  1.834  H3  YID 44 
YID H4  H4  H 0 1 N N N N N N 20.630 26.776 -4.078 1.236  -1.925 1.631  H4  YID 45 
YID H5  H5  H 0 1 N N N N N N 16.945 22.938 -0.794 0.541  5.193  -0.299 H5  YID 46 
YID H6  H6  H 0 1 N N N N N N 18.070 23.447 0.511  0.419  4.298  1.235  H6  YID 47 
YID H7  H7  H 0 1 N N N N N N 14.731 24.174 1.981  2.270  4.551  -1.985 H7  YID 48 
YID H8  H8  H 0 1 N N N N N N 18.163 25.815 1.202  -0.758 2.431  -2.431 H8  YID 49 
YID H9  H9  H 0 1 N N N N N N 16.778 26.897 0.829  -0.146 4.103  -2.440 H9  YID 50 
YID H10 H10 H 0 1 N N N N N N 12.956 26.545 -5.565 -6.122 1.377  2.605  H10 YID 51 
YID H11 H11 H 0 1 N N N N N N 14.657 26.057 -5.872 -4.819 0.571  3.508  H11 YID 52 
YID H12 H12 H 0 1 N N N N N N 13.104 25.614 -3.321 -4.654 3.174  1.932  H12 YID 53 
YID H13 H13 H 0 1 N N N N N N 13.443 24.390 -4.592 -4.411 2.942  3.682  H13 YID 54 
YID H14 H14 H 0 1 N N N N N N 15.037 24.152 -2.870 -2.214 3.107  2.624  H14 YID 55 
YID H15 H15 H 0 1 N N N N N N 15.841 24.867 -4.309 -2.462 1.415  3.128  H15 YID 56 
YID H16 H16 H 0 1 N N N N N N 15.019 26.149 -1.730 -2.801 2.587  0.336  H16 YID 57 
YID H17 H17 H 0 1 N N N N N N 19.818 24.617 0.312  2.467  2.184  -0.844 H17 YID 58 
YID H18 H18 H 0 1 N N N N N N 22.137 24.971 -0.491 4.135  0.422  -0.474 H18 YID 59 
YID H19 H19 H 0 1 N N N N N N 23.479 25.180 -6.095 1.998  -4.354 0.058  H19 YID 60 
YID H20 H20 H 0 1 N N N N N N 22.299 24.352 -5.024 2.298  -3.122 -1.191 H20 YID 61 
YID H21 H21 H 0 1 N N N N N N 21.988 26.034 -5.571 3.225  -4.641 -1.199 H21 YID 62 
YID H22 H22 H 0 1 N N N N N N 15.628 25.077 -0.370 -1.371 3.615  -0.340 H22 YID 63 
YID H23 H23 H 0 1 N N N N N N 15.166 22.589 0.693  2.766  4.382  0.439  H23 YID 64 
YID H24 H24 H 0 1 N N N N N N 16.583 22.037 1.649  2.154  2.711  0.447  H24 YID 65 
YID H25 H25 H 0 1 N N N N N N 17.058 25.400 3.148  1.589  2.516  -3.227 H25 YID 66 
YID H26 H26 H 0 1 N N N N N N 15.509 26.049 2.510  1.467  1.621  -1.693 H26 YID 67 
YID H27 H27 H 0 1 N N N N N N 14.907 23.917 5.418  5.667  3.658  -1.909 H27 YID 68 
YID H28 H28 H 0 1 N N N N N N 15.840 25.150 4.503  4.465  4.762  -2.619 H28 YID 69 
YID H29 H29 H 0 1 N N N N N N 14.145 24.779 4.038  4.677  4.694  -0.853 H29 YID 70 
YID H30 H30 H 0 1 N N N N N N 14.349 28.479 -1.031 -2.928 -1.894 0.751  H30 YID 71 
YID H31 H31 H 0 1 N N N N N N 13.019 30.860 1.493  -1.272 -3.381 0.680  H31 YID 72 
YID H32 H32 H 0 1 N N N N N N 13.278 31.402 -0.200 -0.848 -4.895 -0.153 H32 YID 73 
YID H33 H33 H 0 1 N N N N N N 13.071 29.654 0.162  -0.269 -3.337 -0.790 H33 YID 74 
YID H34 H34 H 0 1 N N N N N N 15.190 31.870 2.342  -4.417 -4.350 -1.061 H34 YID 75 
YID H35 H35 H 0 1 N N N N N N 16.748 31.382 1.594  -3.270 -5.487 -0.312 H35 YID 76 
YID H36 H36 H 0 1 N N N N N N 15.656 32.520 0.734  -3.694 -3.972 0.522  H36 YID 77 
YID H37 H37 H 0 1 N N N N N N 14.795 29.488 2.638  -1.283 -3.868 -3.011 H37 YID 78 
YID H38 H38 H 0 1 N N N N N N 14.830 28.369 1.233  -1.862 -5.426 -2.374 H38 YID 79 
YID H39 H39 H 0 1 N N N N N N 16.346 29.151 1.796  -3.009 -4.289 -3.124 H39 YID 80 
YID H40 H40 H 0 1 N N N N N N 17.105 31.719 -0.567 -2.540 -2.357 -3.470 H40 YID 81 
YID H41 H41 H 0 1 N N N N N N 18.183 31.112 -2.691 -3.100 0.018  -3.789 H41 YID 82 
YID H42 H42 H 0 1 N N N N N N 17.333 29.242 -4.090 -3.575 1.445  -1.841 H42 YID 83 
# 
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 
YID C19 C18 SING N N 1  
YID C03 C02 SING N N 2  
YID C03 C04 SING N N 3  
YID O01 C02 DOUB N N 4  
YID C02 N31 SING N N 5  
YID C04 C05 SING N N 6  
YID C18 N17 DOUB Y N 7  
YID C18 C14 SING Y N 8  
YID N17 O16 SING Y N 9  
YID C05 C06 SING N N 10 
YID N31 C06 SING N N 11 
YID N31 C32 SING N N 12 
YID N08 C09 SING Y N 13 
YID N08 C07 DOUB Y N 14 
YID C41 C32 DOUB Y N 15 
YID C41 C40 SING Y N 16 
YID C21 C09 DOUB Y N 17 
YID C21 C13 SING Y N 18 
YID O16 C15 SING Y N 19 
YID C14 C13 SING N N 20 
YID C14 C15 DOUB Y N 21 
YID C06 C07 SING N N 22 
YID C32 C33 SING Y N 23 
YID C09 C10 SING Y N 24 
YID C07 N22 SING Y N 25 
YID C40 C39 DOUB Y N 26 
YID C13 C12 DOUB Y N 27 
YID C15 C20 SING N N 28 
YID C10 N22 SING Y N 29 
YID C10 C11 DOUB Y N 30 
YID C33 C34 DOUB Y N 31 
YID N22 C23 SING N N 32 
YID C39 C34 SING Y N 33 
YID C12 C11 SING Y N 34 
YID C34 C35 SING N N 35 
YID C23 C24 SING N N 36 
YID C23 C28 SING N N 37 
YID C24 C25 SING N N 38 
YID C36 C35 SING N N 39 
YID C35 C37 SING N N 40 
YID C35 C38 SING N N 41 
YID C28 C27 SING N N 42 
YID C25 C26 SING N N 43 
YID C26 C27 SING N N 44 
YID C26 O29 SING N N 45 
YID O29 C30 SING N N 46 
YID C20 H1  SING N N 47 
YID C20 H2  SING N N 48 
YID C20 H3  SING N N 49 
YID C21 H4  SING N N 50 
YID C24 H5  SING N N 51 
YID C24 H6  SING N N 52 
YID C26 H7  SING N N 53 
YID C28 H8  SING N N 54 
YID C28 H9  SING N N 55 
YID C03 H10 SING N N 56 
YID C03 H11 SING N N 57 
YID C04 H12 SING N N 58 
YID C04 H13 SING N N 59 
YID C05 H14 SING N N 60 
YID C05 H15 SING N N 61 
YID C06 H16 SING N N 62 
YID C11 H17 SING N N 63 
YID C12 H18 SING N N 64 
YID C19 H19 SING N N 65 
YID C19 H20 SING N N 66 
YID C19 H21 SING N N 67 
YID C23 H22 SING N N 68 
YID C25 H23 SING N N 69 
YID C25 H24 SING N N 70 
YID C27 H25 SING N N 71 
YID C27 H26 SING N N 72 
YID C30 H27 SING N N 73 
YID C30 H28 SING N N 74 
YID C30 H29 SING N N 75 
YID C33 H30 SING N N 76 
YID C36 H31 SING N N 77 
YID C36 H32 SING N N 78 
YID C36 H33 SING N N 79 
YID C37 H34 SING N N 80 
YID C37 H35 SING N N 81 
YID C37 H36 SING N N 82 
YID C38 H37 SING N N 83 
YID C38 H38 SING N N 84 
YID C38 H39 SING N N 85 
YID C39 H40 SING N N 86 
YID C40 H41 SING N N 87 
YID C41 H42 SING N N 88 
# 
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 
YID SMILES           ACDLabs              12.01 "Cc1noc(C)c1c1cc2nc(C3CCCC(=O)N3c3cc(ccc3)C(C)(C)C)n(C3CCC(OC)CC3)c2cc1"                                                                                                                                                       
YID InChI            InChI                1.06  "InChI=1S/C34H42N4O3/c1-21-32(22(2)41-36-21)23-13-18-29-28(19-23)35-33(38(29)25-14-16-27(40-6)17-15-25)30-11-8-12-31(39)37(30)26-10-7-9-24(20-26)34(3,4)5/h7,9-10,13,18-20,25,27,30H,8,11-12,14-17H2,1-6H3/t25-,27+,30-/m0/s1" 
YID InChIKey         InChI                1.06  AITZELJGZIFAPE-NSROOHRNSA-N                                                                                                                                                                                                    
YID SMILES_CANONICAL CACTVS               3.385 "CO[C@@H]1CC[C@@H](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[C@@H]5CCCC(=O)N5c6cccc(c6)C(C)(C)C"                                                                                                                                        
YID SMILES           CACTVS               3.385 "CO[CH]1CC[CH](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[CH]5CCCC(=O)N5c6cccc(c6)C(C)(C)C"                                                                                                                                              
YID SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)[C@@H]5CCCC(=O)N5c6cccc(c6)C(C)(C)C"                                                                                                                                                
YID SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)C5CCCC(=O)N5c6cccc(c6)C(C)(C)C"                                                                                                                                                     
# 
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 
YID "SYSTEMATIC NAME" ACDLabs              12.01 "(6S)-1-(3-tert-butylphenyl)-6-{(5P)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}piperidin-2-one" 
YID "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(6~{S})-1-(3-~{tert}-butylphenyl)-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 
YID "Create component" 2023-02-03 RCSB 
YID "Initial release"  2024-02-07 RCSB 
# 
