data_YBE
# 
_chem_comp.id                                    YBE 
_chem_comp.name                                  "tert-butyl [(1R,4s)-4-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(2S)-6-oxopiperidin-2-yl]-1H-benzimidazol-1-yl}cyclohexyl]carbamate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C28 H37 N5 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-23 
_chem_comp.pdbx_modified_date                    2024-01-19 
_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                        507.624 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YBE 
_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        8FVS 
_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 
YBE C13 C1  C 0 1 N N N N N N 7.749  -16.285 -16.155 -4.874 4.029  1.077  C13 YBE 1  
YBE C17 C2  C 0 1 N N N N N N 6.225  -12.248 -15.039 -0.197 2.147  0.288  C17 YBE 2  
YBE C20 C3  C 0 1 N N N N N N 6.607  -10.864 -12.636 2.572  3.032  0.650  C20 YBE 3  
YBE C22 C4  C 0 1 N N N N N N 7.948  -9.064  -11.205 4.483  1.593  0.186  C22 YBE 4  
YBE C24 C5  C 0 1 N N N N N N 9.110  -8.301  -9.149  6.432  0.321  -0.342 C24 YBE 5  
YBE C26 C6  C 0 1 N N N N N N 10.409 -9.061  -9.421  6.975  -1.101 -0.184 C26 YBE 6  
YBE C01 C7  C 0 1 N N N N N N 8.339  -12.653 -22.565 0.198  -4.990 -2.110 C01 YBE 7  
YBE C02 C8  C 0 1 Y N N N N N 7.384  -11.470 -22.691 -0.591 -5.378 -0.886 C02 YBE 8  
YBE C03 C9  C 0 1 Y N N N N N 6.581  -10.919 -21.704 -1.128 -4.534 0.044  C03 YBE 9  
YBE C04 C10 C 0 1 Y N N N N N 6.460  -11.385 -20.252 -1.069 -3.051 0.080  C04 YBE 10 
YBE C05 C11 C 0 1 Y N N N N N 6.165  -12.704 -19.966 -2.234 -2.309 -0.051 C05 YBE 11 
YBE C06 C12 C 0 1 Y N N N N N 6.073  -13.074 -18.603 -2.170 -0.915 -0.016 C06 YBE 12 
YBE C08 C13 C 0 1 Y N N N N N 5.830  -14.100 -16.690 -2.526 1.230  -0.019 C08 YBE 13 
YBE C09 C14 C 0 1 N N S N N N 5.612  -15.182 -15.667 -3.239 2.555  -0.083 C09 YBE 14 
YBE C11 C15 C 0 1 N N N N N N 5.571  -17.563 -16.737 -5.403 3.067  -1.149 C11 YBE 15 
YBE C12 C16 C 0 1 N N N N N N 7.136  -17.542 -16.564 -5.989 3.692  0.084  C12 YBE 16 
YBE C14 C17 C 0 1 N N N N N N 6.952  -15.579 -15.180 -3.977 2.796  1.235  C14 YBE 17 
YBE C18 C18 C 0 1 N N N N N N 7.678  -11.842 -14.775 0.517  2.007  1.633  C18 YBE 18 
YBE C19 C19 C 0 1 N N N N N N 7.894  -11.175 -13.408 1.549  3.127  1.783  C19 YBE 19 
YBE C25 C20 C 0 1 N N N N N N 8.801  -8.349  -7.653  7.363  1.304  0.372  C25 YBE 20 
YBE C27 C21 C 0 1 N N N N N N 9.188  -6.830  -9.576  6.358  0.677  -1.828 C27 YBE 21 
YBE C29 C22 C 0 1 N N N N N N 5.342  -10.512 -13.433 1.858  3.173  -0.696 C29 YBE 22 
YBE C30 C23 C 0 1 N N N N N N 5.263  -11.068 -14.869 0.827  2.052  -0.845 C30 YBE 23 
YBE C31 C24 C 0 1 Y N N N N N 6.266  -12.160 -17.594 -0.925 -0.283 0.151  C31 YBE 24 
YBE C32 C25 C 0 1 Y N N N N N 6.571  -10.805 -17.892 0.230  -1.043 0.281  C32 YBE 25 
YBE C33 C26 C 0 1 Y N N N N N 6.660  -10.450 -19.228 0.161  -2.407 0.251  C33 YBE 26 
YBE C34 C27 C 0 1 Y N N N N N 5.896  -9.849  -22.287 -1.758 -5.411 0.970  C34 YBE 27 
YBE C35 C28 C 0 1 N N N N N N 4.867  -8.903  -21.632 -2.516 -5.021 2.213  C35 YBE 28 
YBE N07 N1  N 0 1 Y N N N N N 5.812  -14.276 -18.017 -3.103 0.067  -0.114 N07 YBE 29 
YBE N10 N2  N 0 1 N N N N N N 4.778  -16.336 -16.290 -4.177 2.544  -1.198 N10 YBE 30 
YBE N16 N3  N 0 1 Y N N N N N 6.106  -12.820 -16.409 -1.184 1.074  0.145  N16 YBE 31 
YBE N21 N4  N 0 1 N N N N N N 6.751  -9.783  -11.668 3.249  1.735  0.710  N21 YBE 32 
YBE N36 N5  N 0 1 Y N N N N N 6.296  -9.764  -23.566 -1.549 -6.617 0.531  N36 YBE 33 
YBE O15 O1  O 0 1 N N N N N N 5.031  -18.502 -17.223 -6.082 3.035  -2.155 O15 YBE 34 
YBE O23 O2  O 0 1 N N N N N N 8.029  -8.964  -9.792  5.105  0.400  0.242  O23 YBE 35 
YBE O28 O3  O 0 1 N N N N N N 8.738  -8.558  -11.938 5.034  2.542  -0.336 O28 YBE 36 
YBE O37 O4  O 0 1 Y N N N N N 7.202  -10.763 -23.784 -0.912 -6.619 -0.496 O37 YBE 37 
YBE H1  H1  H 0 1 N N N N N N 8.736  -16.498 -15.718 -4.286 4.865  0.698  H1  YBE 38 
YBE H2  H2  H 0 1 N N N N N N 7.871  -15.646 -17.042 -5.308 4.293  2.041  H2  YBE 39 
YBE H3  H3  H 0 1 N N N N N N 5.948  -13.023 -14.309 -0.701 3.112  0.243  H3  YBE 40 
YBE H4  H4  H 0 1 N N N N N N 6.365  -11.774 -12.067 3.307  3.831  0.756  H4  YBE 41 
YBE H5  H5  H 0 1 N N N N N N 11.245 -8.548  -8.924  7.028  -1.354 0.874  H5  YBE 42 
YBE H6  H6  H 0 1 N N N N N N 10.323 -10.086 -9.030  6.312  -1.801 -0.693 H6  YBE 43 
YBE H7  H7  H 0 1 N N N N N N 10.593 -9.096  -10.505 7.971  -1.160 -0.623 H7  YBE 44 
YBE H8  H8  H 0 1 N N N N N N 8.847  -12.819 -23.527 1.258  -4.945 -1.860 H8  YBE 45 
YBE H9  H9  H 0 1 N N N N N N 9.087  -12.439 -21.787 0.041  -5.731 -2.894 H9  YBE 46 
YBE H10 H10 H 0 1 N N N N N N 7.772  -13.554 -22.290 -0.134 -4.013 -2.462 H10 YBE 47 
YBE H11 H11 H 0 1 N N N N N N 6.010  -13.426 -20.754 -3.183 -2.807 -0.180 H11 YBE 48 
YBE H12 H12 H 0 1 N N N N N N 5.037  -14.762 -14.828 -2.510 3.350  -0.238 H12 YBE 49 
YBE H13 H13 H 0 1 N N N N N N 7.394  -18.297 -15.807 -6.688 2.995  0.546  H13 YBE 50 
YBE H14 H14 H 0 1 N N N N N N 7.579  -17.826 -17.530 -6.518 4.605  -0.190 H14 YBE 51 
YBE H15 H15 H 0 1 N N N N N N 6.822  -16.231 -14.303 -3.254 2.969  2.032  H15 YBE 52 
YBE H16 H16 H 0 1 N N N N N N 7.495  -14.670 -14.883 -4.589 1.927  1.475  H16 YBE 53 
YBE H17 H17 H 0 1 N N N N N N 8.305  -12.744 -14.824 -0.212 2.074  2.441  H17 YBE 54 
YBE H18 H18 H 0 1 N N N N N N 7.989  -11.136 -15.559 1.021  1.041  1.679  H18 YBE 55 
YBE H19 H19 H 0 1 N N N N N N 8.509  -11.848 -12.792 2.058  3.027  2.741  H19 YBE 56 
YBE H20 H20 H 0 1 N N N N N N 8.433  -10.230 -13.569 1.045  4.093  1.738  H20 YBE 57 
YBE H21 H21 H 0 1 N N N N N N 9.606  -7.848  -7.095  8.359  1.245  -0.067 H21 YBE 58 
YBE H22 H22 H 0 1 N N N N N N 7.847  -7.836  -7.459  6.976  2.317  0.260  H22 YBE 59 
YBE H23 H23 H 0 1 N N N N N N 8.727  -9.397  -7.328  7.416  1.051  1.431  H23 YBE 60 
YBE H24 H24 H 0 1 N N N N N N 10.031 -6.343  -9.064  7.354  0.618  -2.266 H24 YBE 61 
YBE H25 H25 H 0 1 N N N N N N 9.337  -6.772  -10.664 5.694  -0.023 -2.336 H25 YBE 62 
YBE H26 H26 H 0 1 N N N N N N 8.252  -6.320  -9.306  5.971  1.690  -1.940 H26 YBE 63 
YBE H27 H27 H 0 1 N N N N N N 5.279  -9.416  -13.494 1.354  4.138  -0.741 H27 YBE 64 
YBE H28 H28 H 0 1 N N N N N N 4.476  -10.899 -12.876 2.587  3.105  -1.503 H28 YBE 65 
YBE H29 H29 H 0 1 N N N N N N 5.534  -10.274 -15.580 1.330  1.087  -0.800 H29 YBE 66 
YBE H30 H30 H 0 1 N N N N N N 4.236  -11.406 -15.071 0.318  2.152  -1.804 H30 YBE 67 
YBE H31 H31 H 0 1 N N N N N N 6.727  -10.080 -17.107 1.185  -0.554 0.409  H31 YBE 68 
YBE H32 H32 H 0 1 N N N N N N 6.889  -9.427  -19.487 1.062  -2.992 0.356  H32 YBE 69 
YBE H33 H33 H 0 1 N N N N N N 4.524  -8.165  -22.372 -3.568 -4.878 1.967  H33 YBE 70 
YBE H34 H34 H 0 1 N N N N N N 4.008  -9.488  -21.273 -2.421 -5.809 2.960  H34 YBE 71 
YBE H35 H35 H 0 1 N N N N N N 5.336  -8.382  -20.784 -2.107 -4.092 2.611  H35 YBE 72 
YBE H36 H36 H 0 1 N N N N N N 3.785  -16.279 -16.392 -3.892 2.131  -2.028 H36 YBE 73 
YBE H37 H37 H 0 1 N N N N N N 5.895  -9.480  -11.250 2.809  0.977  1.127  H37 YBE 74 
# 
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 
YBE O37 N36 SING Y N 1  
YBE O37 C02 SING Y N 2  
YBE N36 C34 DOUB Y N 3  
YBE C02 C01 SING N N 4  
YBE C02 C03 DOUB Y N 5  
YBE C34 C03 SING Y N 6  
YBE C34 C35 SING N N 7  
YBE C03 C04 SING N N 8  
YBE C04 C05 DOUB Y N 9  
YBE C04 C33 SING Y N 10 
YBE C05 C06 SING Y N 11 
YBE C33 C32 DOUB Y N 12 
YBE C06 N07 SING Y N 13 
YBE C06 C31 DOUB Y N 14 
YBE N07 C08 DOUB Y N 15 
YBE C32 C31 SING Y N 16 
YBE C31 N16 SING Y N 17 
YBE O15 C11 DOUB N N 18 
YBE C11 C12 SING N N 19 
YBE C11 N10 SING N N 20 
YBE C08 N16 SING Y N 21 
YBE C08 C09 SING N N 22 
YBE C12 C13 SING N N 23 
YBE N16 C17 SING N N 24 
YBE N10 C09 SING N N 25 
YBE C13 C14 SING N N 26 
YBE C09 C14 SING N N 27 
YBE C17 C30 SING N N 28 
YBE C17 C18 SING N N 29 
YBE C30 C29 SING N N 30 
YBE C18 C19 SING N N 31 
YBE C29 C20 SING N N 32 
YBE C19 C20 SING N N 33 
YBE C20 N21 SING N N 34 
YBE O28 C22 DOUB N N 35 
YBE N21 C22 SING N N 36 
YBE C22 O23 SING N N 37 
YBE O23 C24 SING N N 38 
YBE C27 C24 SING N N 39 
YBE C26 C24 SING N N 40 
YBE C24 C25 SING N N 41 
YBE C13 H1  SING N N 42 
YBE C13 H2  SING N N 43 
YBE C17 H3  SING N N 44 
YBE C20 H4  SING N N 45 
YBE C26 H5  SING N N 46 
YBE C26 H6  SING N N 47 
YBE C26 H7  SING N N 48 
YBE C01 H8  SING N N 49 
YBE C01 H9  SING N N 50 
YBE C01 H10 SING N N 51 
YBE C05 H11 SING N N 52 
YBE C09 H12 SING N N 53 
YBE C12 H13 SING N N 54 
YBE C12 H14 SING N N 55 
YBE C14 H15 SING N N 56 
YBE C14 H16 SING N N 57 
YBE C18 H17 SING N N 58 
YBE C18 H18 SING N N 59 
YBE C19 H19 SING N N 60 
YBE C19 H20 SING N N 61 
YBE C25 H21 SING N N 62 
YBE C25 H22 SING N N 63 
YBE C25 H23 SING N N 64 
YBE C27 H24 SING N N 65 
YBE C27 H25 SING N N 66 
YBE C27 H26 SING N N 67 
YBE C29 H27 SING N N 68 
YBE C29 H28 SING N N 69 
YBE C30 H29 SING N N 70 
YBE C30 H30 SING N N 71 
YBE C32 H31 SING N N 72 
YBE C33 H32 SING N N 73 
YBE C35 H33 SING N N 74 
YBE C35 H34 SING N N 75 
YBE C35 H35 SING N N 76 
YBE N10 H36 SING N N 77 
YBE N21 H37 SING N N 78 
# 
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 
YBE SMILES           ACDLabs              12.01 "Cc1noc(C)c1c1cc2nc(C3CCCC(=O)N3)n(C3CCC(NC(=O)OC(C)(C)C)CC3)c2cc1"                                                                                                                                                 
YBE InChI            InChI                1.06  "InChI=1S/C28H37N5O4/c1-16-25(17(2)37-32-16)18-9-14-23-22(15-18)31-26(21-7-6-8-24(34)30-21)33(23)20-12-10-19(11-13-20)29-27(35)36-28(3,4)5/h9,14-15,19-21H,6-8,10-13H2,1-5H3,(H,29,35)(H,30,34)/t19-,20+,21-/m0/s1" 
YBE InChIKey         InChI                1.06  RZFKUAQHDVKWMN-HBMCJLEFSA-N                                                                                                                                                                                         
YBE SMILES_CANONICAL CACTVS               3.385 "Cc1onc(C)c1c2ccc3n([C@H]4CC[C@H](CC4)NC(=O)OC(C)(C)C)c(nc3c2)[C@@H]5CCCC(=O)N5"                                                                                                                                    
YBE SMILES           CACTVS               3.385 "Cc1onc(C)c1c2ccc3n([CH]4CC[CH](CC4)NC(=O)OC(C)(C)C)c(nc3c2)[CH]5CCCC(=O)N5"                                                                                                                                        
YBE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)NC(=O)OC(C)(C)C)[C@@H]5CCCC(=O)N5"                                                                                                                                          
YBE SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)NC(=O)OC(C)(C)C)C5CCCC(=O)N5"                                                                                                                                               
# 
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 
YBE "SYSTEMATIC NAME" ACDLabs              12.01 "tert-butyl [(1R,4s)-4-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(2S)-6-oxopiperidin-2-yl]-1H-benzimidazol-1-yl}cyclohexyl]carbamate"     
YBE "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{tert}-butyl ~{N}-[4-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(2~{S})-6-oxidanylidenepiperidin-2-yl]benzimidazol-1-yl]cyclohexyl]carbamate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YBE "Create component" 2023-01-23 RCSB 
YBE "Initial release"  2024-01-24 RCSB 
# 
