data_YRI
# 
_chem_comp.id                                    YRI 
_chem_comp.name                                  "(6S)-1-(3,4-dibromophenyl)-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                               "C30 H32 Br2 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-16 
_chem_comp.pdbx_modified_date                    2024-02-16 
_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                        656.408 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YRI 
_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        8G6T 
_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 
YRI C10  C1  C  0 1 Y N N N N N 0.590  -30.789 -14.982 1.832  -1.211 -0.100 C10  YRI 1  
YRI C13  C2  C  0 1 Y N N N N N 3.184  -30.700 -16.100 3.049  1.158  -0.886 C13  YRI 2  
YRI C15  C3  C  0 1 Y N N N N N 5.084  -31.475 -17.686 4.947  2.587  -1.851 C15  YRI 3  
YRI C20  C4  C  0 1 N N N N N N 4.337  -32.523 -18.506 5.943  1.504  -2.177 C20  YRI 4  
YRI C21  C5  C  0 1 Y N N N N N 2.052  -30.749 -16.923 1.897  0.738  -1.535 C21  YRI 5  
YRI C24  C6  C  0 1 N N N N N N -0.972 -32.115 -12.669 2.523  -4.081 0.796  C24  YRI 6  
YRI C26  C7  C  0 1 N N N N N N -2.140 -30.827 -10.760 3.599  -2.486 2.389  C26  YRI 7  
YRI C28  C8  C  0 1 N N N N N N -0.960 -29.566 -12.660 1.123  -2.818 2.437  C28  YRI 8  
YRI C02  C9  C  0 1 N N N N N N -4.114 -29.904 -18.187 -3.334 -2.801 -2.036 C02  YRI 9  
YRI C03  C10 C  0 1 N N N N N N -4.447 -31.400 -18.515 -3.220 -3.921 -3.030 C03  YRI 10 
YRI C04  C11 C  0 1 N N N N N N -3.459 -32.333 -17.969 -2.083 -4.863 -2.625 C04  YRI 11 
YRI C05  C12 C  0 1 N N N N N N -3.302 -32.233 -16.524 -0.839 -4.019 -2.323 C05  YRI 12 
YRI C06  C13 C  0 1 N N S N N N -2.920 -30.903 -16.030 -1.102 -3.193 -1.064 C06  YRI 13 
YRI C07  C14 C  0 1 Y N N N N N -1.405 -30.850 -15.876 0.017  -2.201 -0.876 C07  YRI 14 
YRI C09  C15 C  0 1 Y N N N N N 0.751  -30.786 -16.325 1.280  -0.452 -1.146 C09  YRI 15 
YRI C11  C16 C  0 1 Y N N N N N 1.736  -30.764 -14.146 2.982  -0.775 0.546  C11  YRI 16 
YRI C12  C17 C  0 1 Y N N N N N 3.006  -30.715 -14.719 3.586  0.399  0.157  C12  YRI 17 
YRI C14  C18 C  0 1 Y N N N N N 4.612  -30.682 -16.665 3.710  2.423  -1.297 C14  YRI 18 
YRI C18  C19 C  0 1 Y N N N N N 5.699  -29.893 -16.228 3.203  3.749  -1.207 C18  YRI 19 
YRI C19  C20 C  0 1 N N N N N N 5.736  -28.842 -15.128 1.861  4.169  -0.664 C19  YRI 20 
YRI C23  C21 C  0 1 N N N N N N -1.381 -30.835 -13.401 1.174  -3.394 1.020  C23  YRI 21 
YRI C25  C22 C  0 1 N N N N N N -1.466 -32.124 -11.226 3.650  -3.062 0.973  C25  YRI 22 
YRI C27  C23 C  0 1 N N N N N N -1.483 -29.520 -11.225 2.251  -1.799 2.613  C27  YRI 23 
YRI C30  C24 C  0 1 N N N N N N -3.408 -30.778 -8.797  5.143  -1.436 3.893  C30  YRI 24 
YRI C32  C25 C  0 1 Y N N N N N -2.978 -28.358 -16.499 -2.578 -1.381 -0.333 C32  YRI 25 
YRI C33  C26 C  0 1 Y N N N N N -3.488 -27.850 -15.320 -2.714 -1.574 1.035  C33  YRI 26 
YRI C34  C27 C  0 1 Y N N N N N -3.149 -26.570 -14.926 -2.918 -0.490 1.867  C34  YRI 27 
YRI C35  C28 C  0 1 Y N N N N N -2.315 -25.830 -15.729 -2.986 0.786  1.339  C35  YRI 28 
YRI C36  C29 C  0 1 Y N N N N N -1.831 -26.355 -16.903 -2.851 0.982  -0.025 C36  YRI 29 
YRI C38  C30 C  0 1 Y N N N N N -2.153 -27.619 -17.316 -2.647 -0.099 -0.862 C38  YRI 30 
YRI N08  N1  N  0 1 Y N N N N N -0.508 -30.823 -16.869 0.174  -1.114 -1.574 N08  YRI 31 
YRI N17  N2  N  0 1 Y N N N N N 6.758  -30.223 -16.983 4.129  4.527  -1.685 N17  YRI 32 
YRI N22  N3  N  0 1 Y N N N N N -0.747 -30.825 -14.720 1.010  -2.311 0.047  N22  YRI 33 
YRI N31  N4  N  0 1 N N N N N N -3.335 -29.686 -16.903 -2.366 -2.477 -1.178 N31  YRI 34 
YRI O01  O1  O  0 1 N N N N N N -4.439 -28.985 -18.870 -4.360 -2.154 -2.016 O01  YRI 35 
YRI O16  O2  O  0 1 Y N N N N N 6.352  -31.180 -17.847 5.102  3.905  -2.041 O16  YRI 36 
YRI O29  O3  O  0 1 N N N N N N -2.128 -30.831 -9.353  4.652  -1.534 2.554  O29  YRI 37 
YRI BR37 BR1 BR 0 0 N N N N N N -0.665 -25.318 -18.023 -2.946 2.728  -0.744 BR37 YRI 38 
YRI BR39 BR2 BR 0 0 N N N N N N -1.822 -24.032 -15.212 -3.266 2.267  2.482  BR39 YRI 39 
YRI H1   H1  H  0 1 N N N N N N 5.024  -32.977 -19.235 5.775  1.150  -3.194 H1   YRI 40 
YRI H2   H2  H  0 1 N N N N N N 3.947  -33.303 -17.836 6.954  1.902  -2.093 H2   YRI 41 
YRI H3   H3  H  0 1 N N N N N N 3.501  -32.045 -19.038 5.820  0.675  -1.480 H3   YRI 42 
YRI H4   H4  H  0 1 N N N N N N 2.159  -30.759 -17.998 1.480  1.329  -2.338 H4   YRI 43 
YRI H5   H5  H  0 1 N N N N N N -1.400 -32.980 -13.197 2.644  -4.886 1.520  H5   YRI 44 
YRI H6   H6  H  0 1 N N N N N N 0.125  -32.191 -12.670 2.558  -4.491 -0.213 H6   YRI 45 
YRI H7   H7  H  0 1 N N N N N N -3.179 -30.834 -11.122 3.721  -3.291 3.114  H7   YRI 46 
YRI H8   H8  H  0 1 N N N N N N 0.139  -29.521 -12.636 0.163  -2.329 2.596  H8   YRI 47 
YRI H9   H9  H  0 1 N N N N N N -1.351 -28.694 -13.205 1.245  -3.624 3.161  H9   YRI 48 
YRI H10  H10 H  0 1 N N N N N N -5.432 -31.642 -18.090 -4.157 -4.476 -3.059 H10  YRI 49 
YRI H11  H11 H  0 1 N N N N N N -4.479 -31.522 -19.608 -3.014 -3.509 -4.018 H11  YRI 50 
YRI H12  H12 H  0 1 N N N N N N -3.775 -33.358 -18.215 -2.371 -5.424 -1.736 H12  YRI 51 
YRI H13  H13 H  0 1 N N N N N N -2.487 -32.126 -18.440 -1.870 -5.552 -3.442 H13  YRI 52 
YRI H14  H14 H  0 1 N N N N N N -4.259 -32.508 -16.057 0.016  -4.675 -2.159 H14  YRI 53 
YRI H15  H15 H  0 1 N N N N N N -2.525 -32.948 -16.215 -0.636 -3.353 -3.162 H15  YRI 54 
YRI H16  H16 H  0 1 N N N N N N -3.364 -30.761 -15.034 -1.143 -3.856 -0.199 H16  YRI 55 
YRI H17  H17 H  0 1 N N N N N N 1.625  -30.783 -13.072 3.402  -1.357 1.353  H17  YRI 56 
YRI H18  H18 H  0 1 N N N N N N 3.873  -30.688 -14.076 4.484  0.732  0.657  H18  YRI 57 
YRI H19  H19 H  0 1 N N N N N N 6.748  -28.415 -15.062 1.946  4.363  0.405  H19  YRI 58 
YRI H20  H20 H  0 1 N N N N N N 5.015  -28.044 -15.359 1.531  5.076  -1.172 H20  YRI 59 
YRI H21  H21 H  0 1 N N N N N N 5.471  -29.308 -14.167 1.136  3.374  -0.833 H21  YRI 60 
YRI H22  H22 H  0 1 N N N N N N -2.475 -30.829 -13.517 0.371  -4.120 0.894  H22  YRI 61 
YRI H23  H23 H  0 1 N N N N N N -2.193 -32.943 -11.120 4.610  -3.551 0.814  H23  YRI 62 
YRI H24  H24 H  0 1 N N N N N N -0.602 -32.313 -10.571 3.528  -2.256 0.249  H24  YRI 63 
YRI H25  H25 H  0 1 N N N N N N -0.638 -29.300 -10.556 2.215  -1.388 3.622  H25  YRI 64 
YRI H26  H26 H  0 1 N N N N N N -2.228 -28.714 -11.154 2.129  -0.993 1.889  H26  YRI 65 
YRI H27  H27 H  0 1 N N N N N N -3.332 -30.784 -7.700  5.940  -0.693 3.934  H27  YRI 66 
YRI H28  H28 H  0 1 N N N N N N -3.912 -29.857 -9.125  4.332  -1.137 4.557  H28  YRI 67 
YRI H29  H29 H  0 1 N N N N N N -3.988 -31.651 -9.129  5.533  -2.404 4.208  H29  YRI 68 
YRI H30  H30 H  0 1 N N N N N N -4.148 -28.450 -14.710 -2.662 -2.570 1.449  H30  YRI 69 
YRI H31  H31 H  0 1 N N N N N N -3.532 -26.159 -14.004 -3.024 -0.640 2.932  H31  YRI 70 
YRI H32  H32 H  0 1 N N N N N N -1.775 -28.020 -18.245 -2.542 0.054  -1.926 H32  YRI 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 
YRI O01  C02  DOUB N N 1  
YRI C03  C02  SING N N 2  
YRI C03  C04  SING N N 3  
YRI C20  C15  SING N N 4  
YRI C02  N31  SING N N 5  
YRI BR37 C36  SING N N 6  
YRI C04  C05  SING N N 7  
YRI O16  C15  SING Y N 8  
YRI O16  N17  SING Y N 9  
YRI C15  C14  DOUB Y N 10 
YRI C38  C36  DOUB Y N 11 
YRI C38  C32  SING Y N 12 
YRI N17  C18  DOUB Y N 13 
YRI C21  C09  DOUB Y N 14 
YRI C21  C13  SING Y N 15 
YRI N31  C32  SING N N 16 
YRI N31  C06  SING N N 17 
YRI C36  C35  SING Y N 18 
YRI N08  C09  SING Y N 19 
YRI N08  C07  DOUB Y N 20 
YRI C14  C18  SING Y N 21 
YRI C14  C13  SING N N 22 
YRI C05  C06  SING N N 23 
YRI C32  C33  DOUB Y N 24 
YRI C09  C10  SING Y N 25 
YRI C18  C19  SING N N 26 
YRI C13  C12  DOUB Y N 27 
YRI C06  C07  SING N N 28 
YRI C07  N22  SING Y N 29 
YRI C35  BR39 SING N N 30 
YRI C35  C34  DOUB Y N 31 
YRI C33  C34  SING Y N 32 
YRI C10  N22  SING Y N 33 
YRI C10  C11  DOUB Y N 34 
YRI N22  C23  SING N N 35 
YRI C12  C11  SING Y N 36 
YRI C23  C24  SING N N 37 
YRI C23  C28  SING N N 38 
YRI C24  C25  SING N N 39 
YRI C28  C27  SING N N 40 
YRI C25  C26  SING N N 41 
YRI C27  C26  SING N N 42 
YRI C26  O29  SING N N 43 
YRI O29  C30  SING N N 44 
YRI C20  H1   SING N N 45 
YRI C20  H2   SING N N 46 
YRI C20  H3   SING N N 47 
YRI C21  H4   SING N N 48 
YRI C24  H5   SING N N 49 
YRI C24  H6   SING N N 50 
YRI C26  H7   SING N N 51 
YRI C28  H8   SING N N 52 
YRI C28  H9   SING N N 53 
YRI C03  H10  SING N N 54 
YRI C03  H11  SING N N 55 
YRI C04  H12  SING N N 56 
YRI C04  H13  SING N N 57 
YRI C05  H14  SING N N 58 
YRI C05  H15  SING N N 59 
YRI C06  H16  SING N N 60 
YRI C11  H17  SING N N 61 
YRI C12  H18  SING N N 62 
YRI C19  H19  SING N N 63 
YRI C19  H20  SING N N 64 
YRI C19  H21  SING N N 65 
YRI C23  H22  SING N N 66 
YRI C25  H23  SING N N 67 
YRI C25  H24  SING N N 68 
YRI C27  H25  SING N N 69 
YRI C27  H26  SING N N 70 
YRI C30  H27  SING N N 71 
YRI C30  H28  SING N N 72 
YRI C30  H29  SING N N 73 
YRI C33  H30  SING N N 74 
YRI C34  H31  SING N N 75 
YRI C38  H32  SING N N 76 
# 
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 
YRI SMILES           ACDLabs              12.01 "Cc1noc(C)c1c1cc2nc(C3CCCC(=O)N3c3ccc(Br)c(Br)c3)n(C3CCC(OC)CC3)c2cc1"                                                                                                                                                 
YRI InChI            InChI                1.06  "InChI=1S/C30H32Br2N4O3/c1-17-29(18(2)39-34-17)19-7-14-26-25(15-19)33-30(36(26)20-8-11-22(38-3)12-9-20)27-5-4-6-28(37)35(27)21-10-13-23(31)24(32)16-21/h7,10,13-16,20,22,27H,4-6,8-9,11-12H2,1-3H3/t20-,22+,27-/m0/s1" 
YRI InChIKey         InChI                1.06  FMIALMAOMCXKFR-ZIHSNCGMSA-N                                                                                                                                                                                            
YRI SMILES_CANONICAL CACTVS               3.385 "CO[C@@H]1CC[C@@H](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[C@@H]5CCCC(=O)N5c6ccc(Br)c(Br)c6"                                                                                                                                  
YRI SMILES           CACTVS               3.385 "CO[CH]1CC[CH](CC1)n2c(nc3cc(ccc23)c4c(C)onc4C)[CH]5CCCC(=O)N5c6ccc(Br)c(Br)c6"                                                                                                                                        
YRI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)[C@@H]5CCCC(=O)N5c6ccc(c(c6)Br)Br"                                                                                                                                          
YRI SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)C5CCCC(=O)N5c6ccc(c(c6)Br)Br"                                                                                                                                               
# 
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 
YRI "SYSTEMATIC NAME" ACDLabs              12.01 "(6S)-1-(3,4-dibromophenyl)-6-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}piperidin-2-one" 
YRI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(6~{S})-1-[3,4-bis(bromanyl)phenyl]-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 
YRI "Create component" 2023-02-16 RCSB 
YRI "Initial release"  2024-02-21 RCSB 
# 
