data_YN5
# 
_chem_comp.id                                    YN5 
_chem_comp.name                                  "(6S)-1-(2,3-dihydro-1,4-benzodioxin-6-yl)-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                               "C32 H36 N4 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-10 
_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                        556.652 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YN5 
_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        8FXO 
_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 
YN5 C10 C1  C 0 1 Y N N N N N -11.440 3.018  -3.233 0.607  -0.088 -1.017 C10 YN5 1  
YN5 C13 C2  C 0 1 Y N N N N N -10.899 4.982  -1.312 3.137  -0.298 0.121  C13 YN5 2  
YN5 C15 C3  C 0 1 N N N N N N -10.605 0.340  -0.881 -0.405 -3.130 0.740  C15 YN5 3  
YN5 C17 C4  C 0 1 N N N N N N -11.236 0.351  1.581  1.261  -2.286 2.399  C17 YN5 4  
YN5 C20 C5  C 0 1 N N N N N N -9.201  0.593  -0.329 0.597  -4.187 0.271  C20 YN5 5  
YN5 C22 C6  C 0 1 N N N N N N -10.926 -1.149 3.868  4.564  -3.864 2.356  C22 YN5 6  
YN5 C24 C7  C 0 1 N N S N N N -11.393 -0.666 -3.605 -2.582 -1.828 -1.029 C24 YN5 7  
YN5 C26 C8  C 0 1 N N N N N N -13.127 -2.004 -5.070 -4.579 -0.551 -1.711 C26 YN5 8  
YN5 C28 C9  C 0 1 N N N N N N -10.599 -2.237 -5.238 -4.176 -2.799 -2.674 C28 YN5 9  
YN5 C01 C10 C 0 1 N N N N N N -10.595 6.962  -5.379 5.588  0.304  -2.298 C01 YN5 10 
YN5 C02 C11 C 0 1 Y N N N N N -11.200 7.537  -4.117 5.062  1.593  -1.720 C02 YN5 11 
YN5 C03 C12 C 0 1 Y N N N N N -11.516 6.893  -2.929 3.882  1.772  -1.056 C03 YN5 12 
YN5 C04 C13 C 0 1 Y N N N N N -12.052 7.873  -2.049 3.884  3.158  -0.734 C04 YN5 13 
YN5 C05 C14 C 0 1 N N N N N N -12.568 7.708  -0.617 2.813  3.915  0.008  C05 YN5 14 
YN5 C08 C15 C 0 1 Y N N N N N -11.342 5.375  -2.590 2.842  0.759  -0.744 C08 YN5 15 
YN5 C09 C16 C 0 1 Y N N N N N -11.604 4.407  -3.560 1.581  0.866  -1.313 C09 YN5 16 
YN5 C11 C17 C 0 1 Y N N N N N -11.026 2.629  -1.984 0.914  -1.147 -0.145 C11 YN5 17 
YN5 C12 C18 C 0 1 Y N N N N N -10.748 3.619  -0.995 2.180  -1.242 0.417  C12 YN5 18 
YN5 C16 C19 C 0 1 N N N N N N -11.737 0.486  0.143  -0.162 -2.816 2.217  C16 YN5 19 
YN5 C18 C20 C 0 1 N N N N N N -10.140 -0.702 1.674  2.263  -3.343 1.930  C18 YN5 20 
YN5 C19 C21 C 0 1 N N N N N N -8.890  -0.282 0.892  2.020  -3.656 0.452  C19 YN5 21 
YN5 C23 C22 C 0 1 Y N N N N N -11.341 0.805  -3.190 -1.176 -1.321 -0.839 C23 YN5 22 
YN5 C27 C23 C 0 1 N N N N N N -11.863 -2.378 -5.936 -4.923 -1.479 -2.840 C27 YN5 23 
YN5 C29 C24 C 0 1 N N N N N N -10.465 -0.883 -4.730 -2.699 -2.490 -2.402 C29 YN5 24 
YN5 C31 C25 C 0 1 Y N N N N N -13.922 -0.661 -2.947 -3.278 0.250  0.066  C31 YN5 25 
YN5 C32 C26 C 0 1 Y N N N N N -14.137 -1.426 -1.799 -2.922 1.543  -0.293 C32 YN5 26 
YN5 C33 C27 C 0 1 Y N N N N N -15.144 -1.014 -0.861 -2.694 2.497  0.686  C33 YN5 27 
YN5 C34 C28 C 0 1 Y N N N N N -15.865 0.115  -1.093 -2.824 2.157  2.028  C34 YN5 28 
YN5 C35 C29 C 0 1 Y N N N N N -15.637 0.902  -2.269 -3.179 0.864  2.383  C35 YN5 29 
YN5 C36 C30 C 0 1 Y N N N N N -14.654 0.501  -3.194 -3.405 -0.086 1.407  C36 YN5 30 
YN5 C38 C31 C 0 1 N N N N N N -17.009 -0.172 1.045  -1.893 4.263  2.626  C38 YN5 31 
YN5 C39 C32 C 0 1 N N N N N N -15.810 -1.061 1.374  -2.486 4.782  1.309  C39 YN5 32 
YN5 N06 N1  N 0 1 Y N N N N N -12.035 9.039  -2.714 4.995  3.641  -1.207 N06 YN5 33 
YN5 N14 N2  N 0 1 Y N N N N N -10.962 1.251  -1.990 -0.235 -1.910 -0.053 N14 YN5 34 
YN5 N25 N3  N 0 1 N N N N N N -12.868 -1.100 -3.877 -3.514 -0.712 -0.924 N25 YN5 35 
YN5 N41 N4  N 0 1 Y N N N N N -11.618 1.866  -3.960 -0.687 -0.253 -1.399 N41 YN5 36 
YN5 O07 O1  O 0 1 Y N N N N N -11.502 8.813  -3.959 5.661  2.791  -1.751 O07 YN5 37 
YN5 O21 O2  O 0 1 N N N N N N -9.810  -0.906 3.036  3.593  -2.847 2.099  O21 YN5 38 
YN5 O30 O3  O 0 1 N N N N N N -14.211 -2.383 -5.335 -5.308 0.396  -1.504 O30 YN5 39 
YN5 O37 O4  O 0 1 N N N N N N -16.880 0.564  -0.169 -2.608 3.082  3.004  O37 YN5 40 
YN5 O40 O5  O 0 1 N N N N N N -15.354 -1.792 0.286  -2.342 3.759  0.318  O40 YN5 41 
YN5 H1  H1  H 0 1 N N N N N N -10.673 5.733  -0.569 4.121  -0.374 0.560  H1  YN5 42 
YN5 H2  H2  H 0 1 N N N N N N -10.632 -0.692 -1.261 -1.419 -3.508 0.610  H2  YN5 43 
YN5 H3  H3  H 0 1 N N N N N N -10.836 1.319  1.916  1.388  -1.378 1.809  H3  YN5 44 
YN5 H4  H4  H 0 1 N N N N N N -12.075 0.057  2.229  1.434  -2.062 3.451  H4  YN5 45 
YN5 H5  H5  H 0 1 N N N N N N -8.466  0.374  -1.118 0.470  -5.095 0.860  H5  YN5 46 
YN5 H6  H6  H 0 1 N N N N N N -9.121  1.650  -0.036 0.423  -4.410 -0.782 H6  YN5 47 
YN5 H7  H7  H 0 1 N N N N N N -10.587 -1.296 4.904  5.546  -3.406 2.472  H7  YN5 48 
YN5 H8  H8  H 0 1 N N N N N N -11.610 -0.288 3.825  4.300  -4.396 3.270  H8  YN5 49 
YN5 H9  H9  H 0 1 N N N N N N -11.451 -2.052 3.523  4.585  -4.564 1.521  H9  YN5 50 
YN5 H10 H10 H 0 1 N N N N N N -11.036 -1.260 -2.751 -2.808 -2.561 -0.254 H10 YN5 51 
YN5 H11 H11 H 0 1 N N N N N N -10.564 -2.947 -4.398 -4.595 -3.357 -1.836 H11 YN5 52 
YN5 H12 H12 H 0 1 N N N N N N -9.773  -2.450 -5.932 -4.266 -3.387 -3.587 H12 YN5 53 
YN5 H13 H13 H 0 1 N N N N N N -10.455 7.765  -6.118 6.558  0.483  -2.762 H13 YN5 54 
YN5 H14 H14 H 0 1 N N N N N N -9.622  6.506  -5.144 5.696  -0.433 -1.502 H14 YN5 55 
YN5 H15 H15 H 0 1 N N N N N N -11.268 6.197  -5.793 4.890  -0.070 -3.047 H15 YN5 56 
YN5 H16 H16 H 0 1 N N N N N N -12.913 8.681  -0.237 3.025  3.890  1.077  H16 YN5 57 
YN5 H17 H17 H 0 1 N N N N N N -13.405 6.994  -0.609 2.796  4.950  -0.335 H17 YN5 58 
YN5 H18 H18 H 0 1 N N N N N N -11.757 7.330  0.024  1.844  3.454  -0.181 H18 YN5 59 
YN5 H19 H19 H 0 1 N N N N N N -11.927 4.700  -4.548 1.355  1.683  -1.982 H19 YN5 60 
YN5 H20 H20 H 0 1 N N N N N N -10.423 3.324  -0.008 2.414  -2.056 1.087  H20 YN5 61 
YN5 H21 H21 H 0 1 N N N N N N -12.200 1.476  0.021  -0.876 -2.063 2.551  H21 YN5 62 
YN5 H22 H22 H 0 1 N N N N N N -12.488 -0.295 -0.045 -0.289 -3.724 2.807  H22 YN5 63 
YN5 H23 H23 H 0 1 N N N N N N -10.520 -1.638 1.238  2.136  -4.251 2.520  H23 YN5 64 
YN5 H24 H24 H 0 1 N N N N N N -8.373  -1.190 0.548  2.734  -4.409 0.118  H24 YN5 65 
YN5 H25 H25 H 0 1 N N N N N N -8.230  0.283  1.567  2.147  -2.748 -0.137 H25 YN5 66 
YN5 H26 H26 H 0 1 N N N N N N -11.844 -1.722 -6.819 -5.997 -1.668 -2.839 H26 YN5 67 
YN5 H27 H27 H 0 1 N N N N N N -11.964 -3.425 -6.259 -4.639 -1.019 -3.786 H27 YN5 68 
YN5 H28 H28 H 0 1 N N N N N N -9.433  -0.725 -4.385 -2.320 -1.814 -3.168 H28 YN5 69 
YN5 H29 H29 H 0 1 N N N N N N -10.696 -0.169 -5.534 -2.124 -3.417 -2.411 H29 YN5 70 
YN5 H30 H30 H 0 1 N N N N N N -13.553 -2.317 -1.618 -2.822 1.805  -1.336 H30 YN5 71 
YN5 H31 H31 H 0 1 N N N N N N -16.216 1.797  -2.445 -3.277 0.600  3.426  H31 YN5 72 
YN5 H32 H32 H 0 1 N N N N N N -14.469 1.085  -4.083 -3.682 -1.092 1.687  H32 YN5 73 
YN5 H33 H33 H 0 1 N N N N N N -17.143 0.544  1.869  -0.839 4.025  2.485  H33 YN5 74 
YN5 H34 H34 H 0 1 N N N N N N -17.900 -0.812 0.967  -1.998 5.022  3.401  H34 YN5 75 
YN5 H35 H35 H 0 1 N N N N N N -16.103 -1.763 2.168  -3.542 5.014  1.448  H35 YN5 76 
YN5 H36 H36 H 0 1 N N N N N N -14.990 -0.422 1.734  -1.952 5.679  0.994  H36 YN5 77 
# 
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 
YN5 C27 C28 SING N N 1  
YN5 C27 C26 SING N N 2  
YN5 C01 C02 SING N N 3  
YN5 O30 C26 DOUB N N 4  
YN5 C28 C29 SING N N 5  
YN5 C26 N25 SING N N 6  
YN5 C29 C24 SING N N 7  
YN5 C02 O07 SING Y N 8  
YN5 C02 C03 DOUB Y N 9  
YN5 N41 C10 SING Y N 10 
YN5 N41 C23 DOUB Y N 11 
YN5 O07 N06 SING Y N 12 
YN5 N25 C24 SING N N 13 
YN5 N25 C31 SING N N 14 
YN5 C24 C23 SING N N 15 
YN5 C09 C10 DOUB Y N 16 
YN5 C09 C08 SING Y N 17 
YN5 C10 C11 SING Y N 18 
YN5 C36 C31 DOUB Y N 19 
YN5 C36 C35 SING Y N 20 
YN5 C23 N14 SING Y N 21 
YN5 C31 C32 SING Y N 22 
YN5 C03 C08 SING N N 23 
YN5 C03 C04 SING Y N 24 
YN5 N06 C04 DOUB Y N 25 
YN5 C08 C13 DOUB Y N 26 
YN5 C35 C34 DOUB Y N 27 
YN5 C04 C05 SING N N 28 
YN5 N14 C11 SING Y N 29 
YN5 N14 C15 SING N N 30 
YN5 C11 C12 DOUB Y N 31 
YN5 C32 C33 DOUB Y N 32 
YN5 C13 C12 SING Y N 33 
YN5 C34 C33 SING Y N 34 
YN5 C34 O37 SING N N 35 
YN5 C15 C20 SING N N 36 
YN5 C15 C16 SING N N 37 
YN5 C33 O40 SING N N 38 
YN5 C20 C19 SING N N 39 
YN5 O37 C38 SING N N 40 
YN5 C16 C17 SING N N 41 
YN5 O40 C39 SING N N 42 
YN5 C19 C18 SING N N 43 
YN5 C38 C39 SING N N 44 
YN5 C17 C18 SING N N 45 
YN5 C18 O21 SING N N 46 
YN5 O21 C22 SING N N 47 
YN5 C13 H1  SING N N 48 
YN5 C15 H2  SING N N 49 
YN5 C17 H3  SING N N 50 
YN5 C17 H4  SING N N 51 
YN5 C20 H5  SING N N 52 
YN5 C20 H6  SING N N 53 
YN5 C22 H7  SING N N 54 
YN5 C22 H8  SING N N 55 
YN5 C22 H9  SING N N 56 
YN5 C24 H10 SING N N 57 
YN5 C28 H11 SING N N 58 
YN5 C28 H12 SING N N 59 
YN5 C01 H13 SING N N 60 
YN5 C01 H14 SING N N 61 
YN5 C01 H15 SING N N 62 
YN5 C05 H16 SING N N 63 
YN5 C05 H17 SING N N 64 
YN5 C05 H18 SING N N 65 
YN5 C09 H19 SING N N 66 
YN5 C12 H20 SING N N 67 
YN5 C16 H21 SING N N 68 
YN5 C16 H22 SING N N 69 
YN5 C18 H23 SING N N 70 
YN5 C19 H24 SING N N 71 
YN5 C19 H25 SING N N 72 
YN5 C27 H26 SING N N 73 
YN5 C27 H27 SING N N 74 
YN5 C29 H28 SING N N 75 
YN5 C29 H29 SING N N 76 
YN5 C32 H30 SING N N 77 
YN5 C35 H31 SING N N 78 
YN5 C36 H32 SING N N 79 
YN5 C38 H33 SING N N 80 
YN5 C38 H34 SING N N 81 
YN5 C39 H35 SING N N 82 
YN5 C39 H36 SING N N 83 
# 
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 
YN5 SMILES           ACDLabs              12.01 "Cc1noc(C)c1c1cc2nc(C3CCCC(=O)N3c3ccc4OCCOc4c3)n(C3CCC(OC)CC3)c2cc1"                                                                                                                                                                     
YN5 InChI            InChI                1.06  "InChI=1S/C32H36N4O5/c1-19-31(20(2)41-34-19)21-7-13-26-25(17-21)33-32(36(26)22-8-11-24(38-3)12-9-22)27-5-4-6-30(37)35(27)23-10-14-28-29(18-23)40-16-15-39-28/h7,10,13-14,17-18,22,24,27H,4-6,8-9,11-12,15-16H2,1-3H3/t22-,24+,27-/m0/s1" 
YN5 InChIKey         InChI                1.06  ZVVSHSLAQZHUJM-LLGBQNBKSA-N                                                                                                                                                                                                              
YN5 SMILES_CANONICAL CACTVS               3.385 "CO[C@H]1CC[C@H](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[C@@H]5CCCC(=O)N5c6ccc7OCCOc7c6"                                                                                                                                                        
YN5 SMILES           CACTVS               3.385 "CO[CH]1CC[CH](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[CH]5CCCC(=O)N5c6ccc7OCCOc7c6"                                                                                                                                                            
YN5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)[C@@H]5CCCC(=O)N5c6ccc7c(c6)OCCO7"                                                                                                                                                            
YN5 SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)C5CCCC(=O)N5c6ccc7c(c6)OCCO7"                                                                                                                                                                 
# 
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 
YN5 "SYSTEMATIC NAME" ACDLabs              12.01 "(6S)-1-(2,3-dihydro-1,4-benzodioxin-6-yl)-6-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}piperidin-2-one" 
YN5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(6~{S})-1-(2,3-dihydro-1,4-benzodioxin-6-yl)-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 
YN5 "Create component" 2023-02-10 RCSB 
YN5 "Initial release"  2024-02-07 RCSB 
# 
