data_Y40
# 
_chem_comp.id                                    Y40 
_chem_comp.name                                  "[(3aR,3bR,6aS,6bS)-5-(1H-benzotriazole-5-carbonyl)octahydrocyclobuta[1,2-c:3,4-c']dipyrrol-2(1H)-yl][4-(2-methoxyethoxy)quinolin-2-yl]methanone" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C28 H28 N6 O4" 
_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                        512.560 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y40 
_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        7G53 
_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 
Y40 N1  N1  N 0 1 N N N N N N -13.214 10.313 48.343 -0.970  -1.129 -0.545 N1  Y40 1  
Y40 C2  C1  C 0 1 N N N N N N -13.799 11.045 49.513 0.136   -2.066 -0.775 C2  Y40 2  
Y40 C3  C2  C 0 1 N N S N N N -12.691 11.984 50.045 1.424   -1.347 -0.335 C3  Y40 3  
Y40 C4  C3  C 0 1 N N R N N N -11.392 11.268 49.561 1.095   0.152  -0.537 C4  Y40 4  
Y40 C5  C4  C 0 1 N N N N N N -11.756 10.319 48.420 -0.436  0.230  -0.413 C5  Y40 5  
Y40 C6  C5  C 0 1 N N S N N N -12.309 13.196 49.177 1.486   -1.053 1.169  C6  Y40 6  
Y40 C7  C6  C 0 1 N N R N N N -10.915 12.568 48.906 1.825   0.410  0.792  C7  Y40 7  
Y40 C8  C7  C 0 1 N N N N N N -11.970 14.494 49.961 2.769   -1.562 1.849  C8  Y40 8  
Y40 N9  N2  N 0 1 N N N N N N -10.784 14.036 50.734 3.881   -0.788 1.285  N9  Y40 9  
Y40 C10 C8  C 0 1 N N N N N N -9.930  13.261 49.830 3.356   0.425  0.649  C10 Y40 10 
Y40 C15 C9  C 0 1 N N N N N N -13.890 9.655  47.403 -2.273  -1.465 -0.473 C15 Y40 11 
Y40 O16 O1  O 0 1 N N N N N N -15.095 9.674  47.445 -2.610  -2.625 -0.603 O16 Y40 12 
Y40 C17 C10 C 0 1 N N N N N N -10.527 14.313 52.042 5.182   -1.137 1.342  C17 Y40 13 
Y40 C18 C11 C 0 1 Y N N N N N -9.289  13.760 52.655 6.196   -0.324 0.641  C18 Y40 14 
Y40 O19 O2  O 0 1 N N N N N N -11.313 14.989 52.685 5.520   -2.121 1.971  O19 Y40 15 
Y40 C20 C12 C 0 1 Y N N N N N -9.316  12.409 53.023 6.132   1.076  0.701  C20 Y40 16 
Y40 C21 C13 C 0 1 Y N N N N N -8.203  11.835 53.598 7.062   1.838  0.058  C21 Y40 17 
Y40 C22 C14 C 0 1 Y N N N N N -8.117  14.549 52.787 7.213   -0.948 -0.069 C22 Y40 18 
Y40 C23 C15 C 0 1 Y N N N N N -6.980  13.948 53.385 8.170   -0.173 -0.730 C23 Y40 19 
Y40 C24 C16 C 0 1 Y N N N N N -7.033  12.585 53.757 8.086   1.231  -0.665 C24 Y40 20 
Y40 N25 N3  N 0 1 Y N N N N N -5.796  12.245 54.256 9.142   1.710  -1.399 N25 Y40 21 
Y40 N26 N4  N 0 1 Y N N N N N -5.029  13.416 54.168 9.830   0.591  -1.892 N26 Y40 22 
Y40 N27 N5  N 0 1 Y N N N N N -5.713  14.391 53.663 9.251   -0.483 -1.485 N27 Y40 23 
Y40 C28 C17 C 0 1 Y N N N N N -13.241 8.978  46.217 -3.297  -0.418 -0.236 C28 Y40 24 
Y40 N29 N6  N 0 1 Y N N N N N -12.653 9.781  45.339 -2.914  0.837  -0.097 N29 Y40 25 
Y40 C30 C18 C 0 1 Y N N N N N -12.761 7.095  44.807 -5.607  0.185  0.051  C30 Y40 26 
Y40 C31 C19 C 0 1 Y N N N N N -13.372 7.614  45.958 -4.646  -0.785 -0.170 C31 Y40 27 
Y40 C32 C20 C 0 1 Y N N N N N -12.120 7.928  43.920 -5.177  1.523  0.202  C32 Y40 28 
Y40 C33 C21 C 0 1 Y N N N N N -12.064 9.300  44.203 -3.793  1.816  0.117  C33 Y40 29 
Y40 C34 C22 C 0 1 Y N N N N N -11.420 10.152 43.262 -3.368  3.151  0.263  C34 Y40 30 
Y40 C35 C23 C 0 1 Y N N N N N -10.859 9.593  42.124 -4.285  4.131  0.482  C35 Y40 31 
Y40 C36 C24 C 0 1 Y N N N N N -10.899 8.200  41.867 -5.645  3.838  0.564  C36 Y40 32 
Y40 C37 C25 C 0 1 Y N N N N N -11.551 7.370  42.741 -6.094  2.560  0.428  C37 Y40 33 
Y40 O38 O3  O 0 1 N N N N N N -12.776 5.796  44.495 -6.921  -0.140 0.125  O38 Y40 34 
Y40 C39 C26 C 0 1 N N N N N N -13.046 5.009  45.667 -7.260  -1.518 -0.040 C39 Y40 35 
Y40 C40 C27 C 0 1 N N N N N N -13.420 3.630  45.185 -8.776  -1.688 0.074  C40 Y40 36 
Y40 O41 O4  O 0 1 N N N N N N -12.330 2.836  44.718 -9.414  -1.009 -1.009 O41 Y40 37 
Y40 C42 C28 C 0 1 N N N N N N -11.031 3.374  44.774 -10.840 -1.106 -0.996 C42 Y40 38 
Y40 H44 H1  H 0 1 N N N N N N -14.673 11.632 49.195 -0.009  -2.968 -0.181 H44 Y40 39 
Y40 H43 H2  H 0 1 N N N N N N -14.100 10.332 50.295 0.194   -2.322 -1.833 H43 Y40 40 
Y40 H12 H3  H 0 1 N N N N N N -12.731 12.181 51.127 2.339   -1.714 -0.802 H12 Y40 41 
Y40 H11 H4  H 0 1 N N N N N N -10.749 10.856 50.353 1.510   0.628  -1.426 H11 Y40 42 
Y40 H45 H5  H 0 1 N N N N N N -11.381 9.307  48.632 -0.838  0.863  -1.204 H45 Y40 43 
Y40 H46 H6  H 0 1 N N N N N N -11.326 10.678 47.474 -0.706  0.639  0.561  H46 Y40 44 
Y40 H14 H7  H 0 1 N N N N N N -12.932 13.345 48.282 0.562   -1.213 1.725  H14 Y40 45 
Y40 H13 H8  H 0 1 N N N N N N -10.623 12.496 47.848 1.402   1.188  1.427  H13 Y40 46 
Y40 H48 H9  H 0 1 N N N N N N -11.719 15.324 49.284 2.711   -1.400 2.925  H48 Y40 47 
Y40 H47 H10 H 0 1 N N N N N N -12.795 14.797 50.623 2.908   -2.622 1.638  H47 Y40 48 
Y40 H49 H11 H 0 1 N N N N N N -9.333  12.525 50.389 3.628   0.435  -0.406 H49 Y40 49 
Y40 H50 H12 H 0 1 N N N N N N -9.259  13.922 49.262 3.763   1.306  1.144  H50 Y40 50 
Y40 H51 H13 H 0 1 N N N N N N -10.205 11.819 52.857 5.341   1.553  1.259  H51 Y40 51 
Y40 H52 H14 H 0 1 N N N N N N -8.234  10.806 53.926 7.004   2.915  0.109  H52 Y40 52 
Y40 H53 H15 H 0 1 N N N N N N -8.092  15.573 52.444 7.265   -2.026 -0.111 H53 Y40 53 
Y40 H54 H16 H 0 1 N N N N N N -5.506  11.354 54.606 9.368   2.641  -1.549 H54 Y40 54 
Y40 H55 H17 H 0 1 N N N N N N -13.929 6.974  46.626 -4.935  -1.818 -0.290 H55 Y40 55 
Y40 H56 H18 H 0 1 N N N N N N -11.369 11.217 43.432 -2.318  3.395  0.202  H56 Y40 56 
Y40 H57 H19 H 0 1 N N N N N N -10.375 10.241 41.409 -3.954  5.153  0.594  H57 Y40 57 
Y40 H58 H20 H 0 1 N N N N N N -10.419 7.795  40.988 -6.352  4.636  0.739  H58 Y40 58 
Y40 H59 H21 H 0 1 N N N N N N -11.632 6.312  42.539 -7.151  2.346  0.490  H59 Y40 59 
Y40 H61 H22 H 0 1 N N N N N N -12.151 4.958  46.304 -6.929  -1.858 -1.021 H61 Y40 60 
Y40 H60 H23 H 0 1 N N N N N N -13.877 5.450  46.237 -6.768  -2.108 0.734  H60 Y40 61 
Y40 H62 H24 H 0 1 N N N N N N -13.898 3.096  46.019 -9.026  -2.748 0.037  H62 Y40 62 
Y40 H63 H25 H 0 1 N N N N N N -14.139 3.741  44.360 -9.118  -1.266 1.019  H63 Y40 63 
Y40 H64 H26 H 0 1 N N N N N N -10.312 2.641  44.379 -11.249 -0.566 -1.850 H64 Y40 64 
Y40 H66 H27 H 0 1 N N N N N N -10.988 4.292  44.169 -11.134 -2.155 -1.056 H66 Y40 65 
Y40 H65 H28 H 0 1 N N N N N N -10.777 3.611  45.818 -11.226 -0.673 -0.073 H65 Y40 66 
# 
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 
Y40 N1  C2  SING N N 1  
Y40 N1  C5  SING N N 2  
Y40 N1  C15 SING N N 3  
Y40 C2  C3  SING N N 4  
Y40 C3  C4  SING N N 5  
Y40 C3  C6  SING N N 6  
Y40 C4  C5  SING N N 7  
Y40 C4  C7  SING N N 8  
Y40 C6  C7  SING N N 9  
Y40 C6  C8  SING N N 10 
Y40 C7  C10 SING N N 11 
Y40 C8  N9  SING N N 12 
Y40 N9  C10 SING N N 13 
Y40 N9  C17 SING N N 14 
Y40 C15 O16 DOUB N N 15 
Y40 C15 C28 SING N N 16 
Y40 C17 C18 SING N N 17 
Y40 C17 O19 DOUB N N 18 
Y40 C18 C20 DOUB Y N 19 
Y40 C18 C22 SING Y N 20 
Y40 C20 C21 SING Y N 21 
Y40 C21 C24 DOUB Y N 22 
Y40 C22 C23 DOUB Y N 23 
Y40 C23 C24 SING Y N 24 
Y40 C23 N27 SING Y N 25 
Y40 C24 N25 SING Y N 26 
Y40 N25 N26 SING Y N 27 
Y40 N26 N27 DOUB Y N 28 
Y40 C28 N29 DOUB Y N 29 
Y40 C28 C31 SING Y N 30 
Y40 N29 C33 SING Y N 31 
Y40 C30 C32 SING Y N 32 
Y40 C30 C31 DOUB Y N 33 
Y40 C30 O38 SING N N 34 
Y40 C32 C33 DOUB Y N 35 
Y40 C32 C37 SING Y N 36 
Y40 C33 C34 SING Y N 37 
Y40 C34 C35 DOUB Y N 38 
Y40 C35 C36 SING Y N 39 
Y40 C36 C37 DOUB Y N 40 
Y40 O38 C39 SING N N 41 
Y40 C39 C40 SING N N 42 
Y40 C40 O41 SING N N 43 
Y40 O41 C42 SING N N 44 
Y40 C2  H44 SING N N 45 
Y40 C2  H43 SING N N 46 
Y40 C3  H12 SING N N 47 
Y40 C4  H11 SING N N 48 
Y40 C5  H45 SING N N 49 
Y40 C5  H46 SING N N 50 
Y40 C6  H14 SING N N 51 
Y40 C7  H13 SING N N 52 
Y40 C8  H48 SING N N 53 
Y40 C8  H47 SING N N 54 
Y40 C10 H49 SING N N 55 
Y40 C10 H50 SING N N 56 
Y40 C20 H51 SING N N 57 
Y40 C21 H52 SING N N 58 
Y40 C22 H53 SING N N 59 
Y40 N25 H54 SING N N 60 
Y40 C31 H55 SING N N 61 
Y40 C34 H56 SING N N 62 
Y40 C35 H57 SING N N 63 
Y40 C36 H58 SING N N 64 
Y40 C37 H59 SING N N 65 
Y40 C39 H61 SING N N 66 
Y40 C39 H60 SING N N 67 
Y40 C40 H62 SING N N 68 
Y40 C40 H63 SING N N 69 
Y40 C42 H64 SING N N 70 
Y40 C42 H66 SING N N 71 
Y40 C42 H65 SING N N 72 
# 
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 
Y40 SMILES           ACDLabs              12.01 "COCCOc1cc(nc2ccccc12)C(=O)N1CC2C3CN(CC3C2C1)C(=O)c1cc2nn[NH]c2cc1"                                                                                                                                 
Y40 InChI            InChI                1.06  "InChI=1S/C28H28N6O4/c1-37-8-9-38-26-11-25(29-22-5-3-2-4-17(22)26)28(36)34-14-20-18-12-33(13-19(18)21(20)15-34)27(35)16-6-7-23-24(10-16)31-32-30-23/h2-7,10-11,18-21H,8-9,12-15H2,1H3,(H,30,31,32)" 
Y40 InChIKey         InChI                1.06  VIHUOEBIQGAKKA-UHFFFAOYSA-N                                                                                                                                                                         
Y40 SMILES_CANONICAL CACTVS               3.385 "COCCOc1cc(nc2ccccc12)C(=O)N3C[C@@H]4[C@H]5CN(C[C@H]5[C@@H]4C3)C(=O)c6ccc7[nH]nnc7c6"                                                                                                               
Y40 SMILES           CACTVS               3.385 "COCCOc1cc(nc2ccccc12)C(=O)N3C[CH]4[CH]5CN(C[CH]5[CH]4C3)C(=O)c6ccc7[nH]nnc7c6"                                                                                                                     
Y40 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COCCOc1cc(nc2c1cccc2)C(=O)N3C[C@H]4[C@@H]5CN(C[C@@H]5[C@H]4C3)C(=O)c6ccc7c(c6)nn[nH]7"                                                                                                             
Y40 SMILES           "OpenEye OEToolkits" 2.0.7 "COCCOc1cc(nc2c1cccc2)C(=O)N3CC4C5CN(CC5C4C3)C(=O)c6ccc7c(c6)nn[nH]7"                                                                                                                               
# 
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 
Y40 "SYSTEMATIC NAME" ACDLabs              12.01 "[(3aR,3bR,6aS,6bS)-5-(1H-benzotriazole-5-carbonyl)octahydrocyclobuta[1,2-c:3,4-c']dipyrrol-2(1H)-yl][4-(2-methoxyethoxy)quinolin-2-yl]methanone"      
Y40 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1~{H}-benzotriazol-5-yl-[(1~{R},2~{S},6~{R},7~{S})-9-[4-(2-methoxyethoxy)quinolin-2-yl]carbonyl-4,9-diazatricyclo[5.3.0.0^{2,6}]decan-4-yl]methanone" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y40 "Create component" 2023-06-09 RCSB 
Y40 "Initial release"  2024-12-18 RCSB 
# 
