data_Y3K
# 
_chem_comp.id                                    Y3K 
_chem_comp.name                                  "6-[(3aR,8aS)-6-{2-cyclopropyl-6-[(oxan-4-yl)methoxy]pyridine-4-carbonyl}octahydropyrrolo[3,4-d]azepine-2(1H)-carbonyl]-1-methyl-1,3-dihydro-2H-benzimidazol-2-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C32 H39 N5 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-09 
_chem_comp.pdbx_modified_date                    2024-12-13 
_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                        573.683 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y3K 
_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        7G7O 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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 
Y3K C10 C1  C 0 1 Y N N N N N -12.960 9.230  44.952 -1.290 -3.358 -0.342 C10 Y3K 1  
Y3K C11 C2  C 0 1 Y N N N N N -12.224 8.921  43.802 -0.107 -3.771 -0.920 C11 Y3K 2  
Y3K C13 C3  C 0 1 Y N N N N N -12.585 6.629  44.140 1.143  -2.470 0.521  C13 Y3K 3  
Y3K C16 C4  C 0 1 N N N N N N -11.576 5.038  42.603 3.500  -2.563 0.241  C16 Y3K 4  
Y3K C17 C5  C 0 1 N N N N N N -11.452 3.517  42.488 4.777  -1.967 0.837  C17 Y3K 5  
Y3K C18 C6  C 0 1 N N N N N N -10.832 3.170  41.098 6.000  -2.620 0.186  C18 Y3K 6  
Y3K C19 C7  C 0 1 N N N N N N -10.720 1.564  41.041 7.270  -1.962 0.731  C19 Y3K 7  
Y3K C21 C8  C 0 1 N N N N N N -10.312 1.449  43.429 6.129  0.115  1.096  C21 Y3K 8  
Y3K C22 C9  C 0 1 N N N N N N -10.556 2.978  43.608 4.812  -0.460 0.566  C22 Y3K 9  
Y3K C23 C10 C 0 1 N N N N N N -11.666 9.972  42.887 -0.144 -4.746 -2.069 C23 Y3K 10 
Y3K C24 C11 C 0 1 N N N N N N -10.371 9.637  42.182 -0.212 -6.236 -1.729 C24 Y3K 11 
Y3K C25 C12 C 0 1 N N N N N N -11.655 9.771  41.362 -1.442 -5.523 -2.295 C25 Y3K 12 
Y3K C27 C13 C 0 1 N N N N N N -13.888 12.648 50.941 -5.069 2.123  0.296  C27 Y3K 13 
Y3K C1  C14 C 0 1 N N N N N N -12.532 9.479  48.172 -3.632 -2.106 -0.795 C1  Y3K 14 
Y3K C2  C15 C 0 1 N N N N N N -12.196 11.003 47.853 -4.538 -1.108 -1.526 C2  Y3K 15 
Y3K C3  C16 C 0 1 N N S N N N -12.710 12.021 48.910 -4.401 0.306  -1.044 C3  Y3K 16 
Y3K C4  C17 C 0 1 N N R N N N -14.071 11.792 49.670 -5.506 0.633  0.047  C4  Y3K 17 
Y3K C5  C18 C 0 1 N N N N N N -14.483 10.385 50.139 -5.066 -0.036 1.345  C5  Y3K 18 
Y3K C6  C19 C 0 1 N N N N N N -15.025 9.542  48.991 -4.888 -1.530 1.292  C6  Y3K 19 
Y3K N7  N1  N 0 1 N N N N N N -13.971 9.181  47.942 -3.630 -1.874 0.654  N7  Y3K 20 
Y3K C8  C20 C 0 1 N N N N N N -14.442 8.510  46.827 -2.493 -1.978 1.371  C8  Y3K 21 
Y3K C9  C21 C 0 1 Y N N N N N -13.541 8.173  45.682 -1.247 -2.448 0.721  C9  Y3K 22 
Y3K N12 N2  N 0 1 Y N N N N N -12.046 7.640  43.389 1.054  -3.325 -0.483 N12 Y3K 23 
Y3K C14 C22 C 0 1 Y N N N N N -13.356 6.826  45.309 0.001  -1.995 1.152  C14 Y3K 24 
Y3K O15 O1  O 0 1 N N N N N N -12.313 5.311  43.821 2.363  -2.039 0.929  O15 Y3K 25 
Y3K O20 O2  O 0 1 N N N N N N -9.820  1.169  42.106 7.225  -0.557 0.473  O20 Y3K 26 
Y3K O26 O3  O 0 1 N N N N N N -15.654 8.160  46.778 -2.491 -1.687 2.550  O26 Y3K 27 
Y3K N28 N3  N 0 1 N N N N N N -12.445 12.537 51.219 -3.599 2.139  0.153  N28 Y3K 28 
Y3K C29 C23 C 0 1 N N N N N N -11.663 12.103 50.009 -3.154 0.815  -0.362 C29 Y3K 29 
Y3K C30 C24 C 0 1 N N N N N N -11.862 12.605 52.541 -2.794 3.181  0.440  C30 Y3K 30 
Y3K C31 C25 C 0 1 Y N N N N N -10.350 12.414 52.767 -1.349 3.099  0.149  C31 Y3K 31 
Y3K C32 C26 C 0 1 Y N N N N N -9.830  11.098 52.646 -0.696 1.864  0.192  C32 Y3K 32 
Y3K C33 C27 C 0 1 Y N N N N N -8.448  10.780 52.946 0.652  1.784  -0.078 C33 Y3K 33 
Y3K C34 C28 C 0 1 Y N N N N N -7.605  11.845 53.362 1.367  2.932  -0.395 C34 Y3K 34 
Y3K C35 C29 C 0 1 Y N N N N N -8.126  13.220 53.455 0.720  4.172  -0.439 C35 Y3K 35 
Y3K C36 C30 C 0 1 Y N N N N N -9.516  13.514 53.167 -0.634 4.255  -0.174 C36 Y3K 36 
Y3K N37 N4  N 0 1 N N N N N N -7.031  14.064 53.877 1.686  5.117  -0.779 N37 Y3K 37 
Y3K C38 C31 C 0 1 N N N N N N -5.896  13.238 54.071 2.862  4.481  -0.933 C38 Y3K 38 
Y3K N39 N5  N 0 1 N N N N N N -6.237  11.878 53.752 2.700  3.164  -0.707 N39 Y3K 39 
Y3K O40 O4  O 0 1 N N N N N N -4.814  13.646 54.495 3.914  5.016  -1.232 O40 Y3K 40 
Y3K C41 C32 C 0 1 N N N N N N -7.181  15.428 54.581 1.459  6.555  -0.942 C41 Y3K 41 
Y3K O42 O5  O 0 1 N N N N N N -12.633 12.810 53.515 -3.258 4.189  0.937  O42 Y3K 42 
Y3K H53 H1  H 0 1 N N N N N N -13.080 10.254 45.273 -2.237 -3.728 -0.707 H53 Y3K 43 
Y3K H56 H2  H 0 1 N N N N N N -12.119 5.440  41.735 3.437  -2.305 -0.816 H56 Y3K 44 
Y3K H55 H3  H 0 1 N N N N N N -10.577 5.496  42.655 3.521  -3.648 0.349  H55 Y3K 45 
Y3K H57 H4  H 0 1 N N N N N N -12.450 3.060  42.563 4.796  -2.146 1.912  H57 Y3K 46 
Y3K H59 H5  H 0 1 N N N N N N -11.482 3.535  40.289 6.012  -3.685 0.421  H59 Y3K 47 
Y3K H58 H6  H 0 1 N N N N N N -9.835  3.625  41.001 5.954  -2.485 -0.894 H58 Y3K 48 
Y3K H60 H7  H 0 1 N N N N N N -11.710 1.110  41.194 7.336  -2.133 1.805  H60 Y3K 49 
Y3K H61 H8  H 0 1 N N N N N N -10.317 1.247  40.068 8.142  -2.394 0.239  H61 Y3K 50 
Y3K H63 H9  H 0 1 N N N N N N -11.259 0.911  43.585 6.179  1.180  0.868  H63 Y3K 51 
Y3K H62 H10 H 0 1 N N N N N N -9.572  1.111  44.169 6.180  -0.028 2.175  H62 Y3K 52 
Y3K H65 H11 H 0 1 N N N N N N -9.590  3.503  43.582 4.742  -0.280 -0.507 H65 Y3K 53 
Y3K H64 H12 H 0 1 N N N N N N -11.044 3.155  44.578 3.975  0.022  1.072  H64 Y3K 54 
Y3K H66 H13 H 0 1 N N N N N N -11.773 11.013 43.225 0.430  -4.456 -2.949 H66 Y3K 55 
Y3K H67 H14 H 0 1 N N N N N N -9.582  10.399 42.094 0.316  -6.927 -2.386 H67 Y3K 56 
Y3K H68 H15 H 0 1 N N N N N N -9.911  8.648  42.322 -0.231 -6.511 -0.674 H68 Y3K 57 
Y3K H70 H16 H 0 1 N N N N N N -12.123 8.880  40.919 -2.270 -5.330 -1.613 H70 Y3K 58 
Y3K H69 H17 H 0 1 N N N N N N -11.794 10.631 40.690 -1.723 -5.745 -3.324 H69 Y3K 59 
Y3K H72 H18 H 0 1 N N N N N N -14.175 13.694 50.756 -5.527 2.778  -0.445 H72 Y3K 60 
Y3K H71 H19 H 0 1 N N N N N N -14.482 12.247 51.775 -5.353 2.437  1.301  H71 Y3K 61 
Y3K H46 H20 H 0 1 N N N N N N -11.924 8.834  47.520 -3.986 -3.118 -0.993 H46 Y3K 62 
Y3K H45 H21 H 0 1 N N N N N N -12.287 9.271  49.224 -2.615 -2.005 -1.173 H45 Y3K 63 
Y3K H47 H22 H 0 1 N N N N N N -11.103 11.105 47.784 -4.300 -1.137 -2.589 H47 Y3K 64 
Y3K H48 H23 H 0 1 N N N N N N -12.650 11.258 46.884 -5.575 -1.420 -1.397 H48 Y3K 65 
Y3K H44 H24 H 0 1 N N N N N N -12.768 13.005 48.422 -4.590 0.964  -1.893 H44 Y3K 66 
Y3K H43 H25 H 0 1 N N N N N N -14.885 12.220 49.066 -6.541 0.472  -0.254 H43 Y3K 67 
Y3K H50 H26 H 0 1 N N N N N N -13.604 9.881  50.567 -4.120 0.408  1.652  H50 Y3K 68 
Y3K H49 H27 H 0 1 N N N N N N -15.262 10.480 50.909 -5.806 0.191  2.112  H49 Y3K 69 
Y3K H51 H28 H 0 1 N N N N N N -15.434 8.610  49.408 -4.897 -1.928 2.306  H51 Y3K 70 
Y3K H52 H29 H 0 1 N N N N N N -15.829 10.106 48.496 -5.710 -1.969 0.727  H52 Y3K 71 
Y3K H54 H30 H 0 1 N N N N N N -13.772 6.005  45.874 0.077  -1.296 1.972  H54 Y3K 72 
Y3K H73 H31 H 0 1 N N N N N N -11.194 11.122 50.177 -2.862 0.157  0.457  H73 Y3K 73 
Y3K H74 H32 H 0 1 N N N N N N -10.888 12.842 49.758 -2.338 0.929  -1.076 H74 Y3K 74 
Y3K H75 H33 H 0 1 N N N N N N -10.488 10.306 52.319 -1.250 0.970  0.439  H75 Y3K 75 
Y3K H76 H34 H 0 1 N N N N N N -8.073  9.771  52.857 1.153  0.828  -0.044 H76 Y3K 76 
Y3K H77 H35 H 0 1 N N N N N N -9.908  14.517 53.250 -1.137 5.210  -0.212 H77 Y3K 77 
Y3K H78 H36 H 0 1 N N N N N N -5.620  11.092 53.796 3.397  2.491  -0.755 H78 Y3K 78 
Y3K H80 H37 H 0 1 N N N N N N -6.185  15.847 54.785 1.611  7.057  0.014  H80 Y3K 79 
Y3K H79 H38 H 0 1 N N N N N N -7.742  16.116 53.931 2.160  6.953  -1.676 H79 Y3K 80 
Y3K H81 H39 H 0 1 N N N N N N -7.724  15.294 55.528 0.438  6.726  -1.283 H81 Y3K 81 
# 
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 
Y3K C1  C2  SING N N 1  
Y3K C1  N7  SING N N 2  
Y3K C2  C3  SING N N 3  
Y3K C3  C4  SING N N 4  
Y3K C3  C29 SING N N 5  
Y3K C4  C5  SING N N 6  
Y3K C4  C27 SING N N 7  
Y3K C5  C6  SING N N 8  
Y3K C6  N7  SING N N 9  
Y3K N7  C8  SING N N 10 
Y3K C8  C9  SING N N 11 
Y3K C8  O26 DOUB N N 12 
Y3K C9  C10 DOUB Y N 13 
Y3K C9  C14 SING Y N 14 
Y3K C10 C11 SING Y N 15 
Y3K C11 N12 DOUB Y N 16 
Y3K C11 C23 SING N N 17 
Y3K N12 C13 SING Y N 18 
Y3K C13 C14 DOUB Y N 19 
Y3K C13 O15 SING N N 20 
Y3K O15 C16 SING N N 21 
Y3K C16 C17 SING N N 22 
Y3K C17 C18 SING N N 23 
Y3K C17 C22 SING N N 24 
Y3K C18 C19 SING N N 25 
Y3K C19 O20 SING N N 26 
Y3K O20 C21 SING N N 27 
Y3K C21 C22 SING N N 28 
Y3K C23 C24 SING N N 29 
Y3K C23 C25 SING N N 30 
Y3K C24 C25 SING N N 31 
Y3K C27 N28 SING N N 32 
Y3K N28 C29 SING N N 33 
Y3K N28 C30 SING N N 34 
Y3K C30 C31 SING N N 35 
Y3K C30 O42 DOUB N N 36 
Y3K C31 C32 DOUB Y N 37 
Y3K C31 C36 SING Y N 38 
Y3K C32 C33 SING Y N 39 
Y3K C33 C34 DOUB Y N 40 
Y3K C34 C35 SING Y N 41 
Y3K C34 N39 SING N N 42 
Y3K C35 C36 DOUB Y N 43 
Y3K C35 N37 SING N N 44 
Y3K N37 C38 SING N N 45 
Y3K N37 C41 SING N N 46 
Y3K C38 N39 SING N N 47 
Y3K C38 O40 DOUB N N 48 
Y3K C10 H53 SING N N 49 
Y3K C16 H56 SING N N 50 
Y3K C16 H55 SING N N 51 
Y3K C17 H57 SING N N 52 
Y3K C18 H59 SING N N 53 
Y3K C18 H58 SING N N 54 
Y3K C19 H60 SING N N 55 
Y3K C19 H61 SING N N 56 
Y3K C21 H63 SING N N 57 
Y3K C21 H62 SING N N 58 
Y3K C22 H65 SING N N 59 
Y3K C22 H64 SING N N 60 
Y3K C23 H66 SING N N 61 
Y3K C24 H67 SING N N 62 
Y3K C24 H68 SING N N 63 
Y3K C25 H70 SING N N 64 
Y3K C25 H69 SING N N 65 
Y3K C27 H72 SING N N 66 
Y3K C27 H71 SING N N 67 
Y3K C1  H46 SING N N 68 
Y3K C1  H45 SING N N 69 
Y3K C2  H47 SING N N 70 
Y3K C2  H48 SING N N 71 
Y3K C3  H44 SING N N 72 
Y3K C4  H43 SING N N 73 
Y3K C5  H50 SING N N 74 
Y3K C5  H49 SING N N 75 
Y3K C6  H51 SING N N 76 
Y3K C6  H52 SING N N 77 
Y3K C14 H54 SING N N 78 
Y3K C29 H73 SING N N 79 
Y3K C29 H74 SING N N 80 
Y3K C32 H75 SING N N 81 
Y3K C33 H76 SING N N 82 
Y3K C36 H77 SING N N 83 
Y3K N39 H78 SING N N 84 
Y3K C41 H80 SING N N 85 
Y3K C41 H79 SING N N 86 
Y3K C41 H81 SING N N 87 
# 
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 
Y3K SMILES           ACDLabs              12.01 "O=C1Nc2ccc(cc2N1C)C(=O)N1CC2CCN(CCC2C1)C(=O)c1cc(OCC2CCOCC2)nc(c1)C1CC1"                                                                                                                                               
Y3K InChI            InChI                1.06  "InChI=1S/C32H39N5O5/c1-35-28-15-22(4-5-26(28)34-32(35)40)30(38)37-17-23-6-10-36(11-7-24(23)18-37)31(39)25-14-27(21-2-3-21)33-29(16-25)42-19-20-8-12-41-13-9-20/h4-5,14-16,20-21,23-24H,2-3,6-13,17-19H2,1H3,(H,34,40)" 
Y3K InChIKey         InChI                1.06  USOBLGWPXWJKIW-UHFFFAOYSA-N                                                                                                                                                                                             
Y3K SMILES_CANONICAL CACTVS               3.385 "CN1C(=O)Nc2ccc(cc12)C(=O)N3C[C@H]4CCN(CC[C@H]4C3)C(=O)c5cc(OCC6CCOCC6)nc(c5)C7CC7"                                                                                                                                     
Y3K SMILES           CACTVS               3.385 "CN1C(=O)Nc2ccc(cc12)C(=O)N3C[CH]4CCN(CC[CH]4C3)C(=O)c5cc(OCC6CCOCC6)nc(c5)C7CC7"                                                                                                                                       
Y3K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1c2cc(ccc2NC1=O)C(=O)N3C[C@H]4CCN(CC[C@H]4C3)C(=O)c5cc(nc(c5)OCC6CCOCC6)C7CC7"                                                                                                                                       
Y3K SMILES           "OpenEye OEToolkits" 2.0.7 "CN1c2cc(ccc2NC1=O)C(=O)N3CC4CCN(CCC4C3)C(=O)c5cc(nc(c5)OCC6CCOCC6)C7CC7"                                                                                                                                               
# 
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 
Y3K "SYSTEMATIC NAME" ACDLabs              12.01 "6-[(3aR,8aS)-6-{2-cyclopropyl-6-[(oxan-4-yl)methoxy]pyridine-4-carbonyl}octahydropyrrolo[3,4-d]azepine-2(1H)-carbonyl]-1-methyl-1,3-dihydro-2H-benzimidazol-2-one"                           
Y3K "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-[[(3~{a}~{R},8~{a}~{S})-6-[2-cyclopropyl-6-(oxan-4-ylmethoxy)pyridin-4-yl]carbonyl-1,3,3~{a},4,5,7,8,8~{a}-octahydropyrrolo[3,4-d]azepin-2-yl]carbonyl]-3-methyl-1~{H}-benzimidazol-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 
Y3K "Create component" 2023-06-09 RCSB 
Y3K "Initial release"  2024-12-18 RCSB 
# 
