data_Y3F
# 
_chem_comp.id                                    Y3F 
_chem_comp.name                                  "[(3aR,3bR,6aS,6bS)-5-(1H-benzotriazole-5-carbonyl)octahydrocyclobuta[1,2-c:3,4-c']dipyrrol-2(1H)-yl](4-methoxynaphthalen-2-yl)methanone" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H25 N5 O3" 
_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                        467.519 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y3F 
_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        7G5N 
_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 
Y3F C10 C1  C 0 1 N N N N N N -10.248 12.838 49.434 2.550  -0.213 0.196  C10 Y3F 1  
Y3F C15 C2  C 0 1 N N N N N N -14.216 9.207  46.996 -3.154 -1.459 -1.343 C15 Y3F 2  
Y3F C17 C3  C 0 1 N N N N N N -10.708 13.991 51.666 4.391  -1.836 0.682  C17 Y3F 3  
Y3F C18 C4  C 0 1 Y N N N N N -9.434  13.475 52.281 5.405  -0.762 0.627  C18 Y3F 4  
Y3F C20 C5  C 0 1 Y N N N N N -9.433  12.128 52.643 6.594  -0.886 1.359  C20 Y3F 5  
Y3F C21 C6  C 0 1 Y N N N N N -8.312  11.545 53.222 7.537  0.097  1.317  C21 Y3F 6  
Y3F C22 C7  C 0 1 Y N N N N N -8.320  14.344 52.396 5.178  0.363  -0.156 C22 Y3F 7  
Y3F C23 C8  C 0 1 Y N N N N N -7.159  13.779 53.003 6.141  1.375  -0.203 C23 Y3F 8  
Y3F C24 C9  C 0 1 Y N N N N N -7.196  12.369 53.384 7.326  1.235  0.543  C24 Y3F 9  
Y3F C28 C10 C 0 1 Y N N N N N -13.471 8.664  45.808 -4.166 -0.610 -0.679 C28 Y3F 10 
Y3F N1  N1  N 0 1 N N N N N N -13.534 9.909  47.970 -1.856 -1.096 -1.328 N1  Y3F 11 
Y3F C2  C11 C 0 1 N N N N N N -14.184 10.573 49.113 -0.774 -1.787 -2.039 C2  Y3F 12 
Y3F C3  C12 C 0 1 N N S N N N -13.081 11.429 49.725 0.545  -1.333 -1.389 C3  Y3F 13 
Y3F C4  C13 C 0 1 N N R N N N -11.725 10.757 49.263 0.215  0.075  -0.835 C4  Y3F 14 
Y3F C5  C14 C 0 1 N N N N N N -12.123 9.670  48.262 -1.304 0.051  -0.600 C5  Y3F 15 
Y3F C6  C15 C 0 1 N N S N N N -12.662 12.702 48.966 0.705  -1.786 0.068  C6  Y3F 16 
Y3F C7  C16 C 0 1 N N R N N N -11.270 12.076 48.614 1.028  -0.311 0.412  C7  Y3F 17 
Y3F C8  C17 C 0 1 N N N N N N -12.400 13.885 49.880 2.016  -2.542 0.344  C8  Y3F 18 
Y3F N9  N2  N 0 1 N N N N N N -11.047 13.642 50.363 3.097  -1.555 0.429  N9  Y3F 19 
Y3F O16 O1  O 0 1 N N N N N N -15.459 9.041  46.968 -3.493 -2.484 -1.901 O16 Y3F 20 
Y3F O19 O2  O 0 1 N N N N N N -11.480 14.715 52.318 4.724  -2.973 0.956  O19 Y3F 21 
Y3F N25 N3  N 0 1 Y N N N N N -5.913  12.114 53.880 8.063  2.368  0.301  N25 Y3F 22 
Y3F N26 N4  N 0 1 Y N N N N N -5.182  13.242 53.819 7.308  3.160  -0.576 N26 Y3F 23 
Y3F N27 N5  N 0 1 Y N N N N N -5.838  14.221 53.344 6.206  2.559  -0.857 N27 Y3F 24 
Y3F C29 C18 C 0 1 Y N N N N N -13.628 7.276  45.510 -4.095 0.788  -0.808 C29 Y3F 25 
Y3F C30 C19 C 0 1 Y N N N N N -12.962 6.782  44.404 -5.016 1.591  -0.205 C30 Y3F 26 
Y3F C31 C20 C 0 1 Y N N N N N -12.782 9.516  44.968 -5.179 -1.199 0.059  C31 Y3F 27 
Y3F C32 C21 C 0 1 Y N N N N N -12.113 8.994  43.833 -6.138 -0.390 0.687  C32 Y3F 28 
Y3F C33 C22 C 0 1 Y N N N N N -12.214 7.624  43.524 -6.057 1.019  0.557  C33 Y3F 29 
Y3F C34 C23 C 0 1 Y N N N N N -11.565 7.102  42.383 -7.019 1.824  1.188  C34 Y3F 30 
Y3F C35 C24 C 0 1 Y N N N N N -10.841 7.910  41.544 -8.012 1.244  1.917  C35 Y3F 31 
Y3F C36 C25 C 0 1 Y N N N N N -10.750 9.305  41.836 -8.089 -0.141 2.049  C36 Y3F 32 
Y3F C37 C26 C 0 1 Y N N N N N -11.364 9.860  42.956 -7.181 -0.954 1.444  C37 Y3F 33 
Y3F O38 O3  O 0 1 N N N N N N -12.983 5.480  44.006 -4.933 2.940  -0.338 O38 Y3F 34 
Y3F C39 C27 C 0 1 N N N N N N -13.551 4.527  44.924 -3.854 3.449  -1.124 C39 Y3F 35 
Y3F H1  H1  H 0 1 N N N N N N -9.595  12.144 49.983 2.763  0.104  -0.825 H1  Y3F 36 
Y3F H2  H2  H 0 1 N N N N N N -9.636  13.484 48.788 2.983  0.494  0.904  H2  Y3F 37 
Y3F H3  H3  H 0 1 N N N N N N -10.316 11.530 52.471 6.763  -1.767 1.961  H3  Y3F 38 
Y3F H4  H4  H 0 1 N N N N N N -8.304  10.510 53.530 8.449  -0.007 1.885  H4  Y3F 39 
Y3F H5  H5  H 0 1 N N N N N N -8.348  15.366 52.047 4.264  0.455  -0.723 H5  Y3F 40 
Y3F H6  H6  H 0 1 N N N N N N -15.022 11.200 48.775 -0.889 -2.866 -1.934 H6  Y3F 41 
Y3F H7  H7  H 0 1 N N N N N N -14.550 9.831  49.838 -0.784 -1.511 -3.093 H7  Y3F 42 
Y3F H8  H8  H 0 1 N N N N N N -13.157 11.559 50.815 1.425  -1.413 -2.027 H8  Y3F 43 
Y3F H9  H9  H 0 1 N N N N N N -11.092 10.411 50.093 0.578  0.924  -1.414 H9  Y3F 44 
Y3F H10 H10 H 0 1 N N N N N N -11.985 8.672  48.703 -1.750 0.973  -0.972 H10 Y3F 45 
Y3F H11 H11 H 0 1 N N N N N N -11.521 9.752  47.345 -1.510 -0.055 0.465  H11 Y3F 46 
Y3F H12 H12 H 0 1 N N N N N N -13.283 12.930 48.087 -0.185 -2.208 0.534  H12 Y3F 47 
Y3F H13 H13 H 0 1 N N N N N N -11.058 12.014 47.536 0.667  0.076  1.365  H13 Y3F 48 
Y3F H14 H14 H 0 1 N N N N N N -12.456 14.832 49.324 1.938  -3.085 1.286  H14 Y3F 49 
Y3F H15 H15 H 0 1 N N N N N N -13.118 13.906 50.713 2.217  -3.240 -0.468 H15 Y3F 50 
Y3F H16 H16 H 0 1 N N N N N N -5.590  11.233 54.225 8.937  2.579  0.666  H16 Y3F 51 
Y3F H17 H17 H 0 1 N N N N N N -14.244 6.637  46.125 -3.300 1.230  -1.390 H17 Y3F 52 
Y3F H18 H18 H 0 1 N N N N N N -12.753 10.576 45.175 -5.231 -2.274 0.150  H18 Y3F 53 
Y3F H19 H19 H 0 1 N N N N N N -11.640 6.046  42.167 -6.971 2.899  1.096  H19 Y3F 54 
Y3F H20 H20 H 0 1 N N N N N N -10.348 7.498  40.676 -8.750 1.866  2.401  H20 Y3F 55 
Y3F H21 H21 H 0 1 N N N N N N -10.190 9.946  41.171 -8.887 -0.576 2.634  H21 Y3F 56 
Y3F H22 H22 H 0 1 N N N N N N -11.281 10.917 43.163 -7.256 -2.026 1.551  H22 Y3F 57 
Y3F H23 H23 H 0 1 N N N N N N -13.506 3.520  44.483 -3.904 4.538  -1.149 H23 Y3F 58 
Y3F H24 H24 H 0 1 N N N N N N -12.982 4.540  45.865 -2.906 3.139  -0.683 H24 Y3F 59 
Y3F H25 H25 H 0 1 N N N N N N -14.599 4.792  45.126 -3.928 3.059  -2.139 H25 Y3F 60 
# 
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 
Y3F N1  C2  SING N N 1  
Y3F N1  C5  SING N N 2  
Y3F N1  C15 SING N N 3  
Y3F C2  C3  SING N N 4  
Y3F C3  C4  SING N N 5  
Y3F C3  C6  SING N N 6  
Y3F C4  C5  SING N N 7  
Y3F C4  C7  SING N N 8  
Y3F C6  C7  SING N N 9  
Y3F C6  C8  SING N N 10 
Y3F C7  C10 SING N N 11 
Y3F C8  N9  SING N N 12 
Y3F N9  C10 SING N N 13 
Y3F N9  C17 SING N N 14 
Y3F C15 O16 DOUB N N 15 
Y3F C15 C28 SING N N 16 
Y3F C17 C18 SING N N 17 
Y3F C17 O19 DOUB N N 18 
Y3F C18 C20 DOUB Y N 19 
Y3F C18 C22 SING Y N 20 
Y3F C20 C21 SING Y N 21 
Y3F C21 C24 DOUB Y N 22 
Y3F C22 C23 DOUB Y N 23 
Y3F C23 C24 SING Y N 24 
Y3F C23 N27 SING Y N 25 
Y3F C24 N25 SING Y N 26 
Y3F N25 N26 SING Y N 27 
Y3F N26 N27 DOUB Y N 28 
Y3F C28 C29 DOUB Y N 29 
Y3F C28 C31 SING Y N 30 
Y3F C29 C30 SING Y N 31 
Y3F C30 C33 DOUB Y N 32 
Y3F C30 O38 SING N N 33 
Y3F C31 C32 DOUB Y N 34 
Y3F C32 C33 SING Y N 35 
Y3F C32 C37 SING Y N 36 
Y3F C33 C34 SING Y N 37 
Y3F C34 C35 DOUB Y N 38 
Y3F C35 C36 SING Y N 39 
Y3F C36 C37 DOUB Y N 40 
Y3F O38 C39 SING N N 41 
Y3F C10 H1  SING N N 42 
Y3F C10 H2  SING N N 43 
Y3F C20 H3  SING N N 44 
Y3F C21 H4  SING N N 45 
Y3F C22 H5  SING N N 46 
Y3F C2  H6  SING N N 47 
Y3F C2  H7  SING N N 48 
Y3F C3  H8  SING N N 49 
Y3F C4  H9  SING N N 50 
Y3F C5  H10 SING N N 51 
Y3F C5  H11 SING N N 52 
Y3F C6  H12 SING N N 53 
Y3F C7  H13 SING N N 54 
Y3F C8  H14 SING N N 55 
Y3F C8  H15 SING N N 56 
Y3F N25 H16 SING N N 57 
Y3F C29 H17 SING N N 58 
Y3F C31 H18 SING N N 59 
Y3F C34 H19 SING N N 60 
Y3F C35 H20 SING N N 61 
Y3F C36 H21 SING N N 62 
Y3F C37 H22 SING N N 63 
Y3F C39 H23 SING N N 64 
Y3F C39 H24 SING N N 65 
Y3F C39 H25 SING N N 66 
# 
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 
Y3F SMILES           ACDLabs              12.01 "COc1cc(cc2ccccc21)C(=O)N1CC2C(C1)C1CN(CC21)C(=O)c1cc2nn[NH]c2cc1"                                                                                                                                 
Y3F InChI            InChI                1.06  "InChI=1S/C27H25N5O3/c1-35-25-10-17(8-15-4-2-3-5-18(15)25)27(34)32-13-21-19-11-31(12-20(19)22(21)14-32)26(33)16-6-7-23-24(9-16)29-30-28-23/h2-10,19-22H,11-14H2,1H3,(H,28,29,30)/t19-,20+,21+,22-" 
Y3F InChIKey         InChI                1.06  CJZJFGVPYXRIEF-ZDNVTZCJSA-N                                                                                                                                                                        
Y3F SMILES_CANONICAL CACTVS               3.385 "COc1cc(cc2ccccc12)C(=O)N3C[C@H]4[C@@H]5CN(C[C@@H]5[C@H]4C3)C(=O)c6ccc7[nH]nnc7c6"                                                                                                                 
Y3F SMILES           CACTVS               3.385 "COc1cc(cc2ccccc12)C(=O)N3C[CH]4[CH]5CN(C[CH]5[CH]4C3)C(=O)c6ccc7[nH]nnc7c6"                                                                                                                       
Y3F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COc1cc(cc2c1cccc2)C(=O)N3C[C@H]4[C@@H]5CN(C[C@@H]5[C@H]4C3)C(=O)c6ccc7c(c6)nn[nH]7"                                                                                                               
Y3F SMILES           "OpenEye OEToolkits" 2.0.7 "COc1cc(cc2c1cccc2)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 
Y3F "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-methoxynaphthalen-2-yl)methanone"      
Y3F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1~{H}-benzotriazol-5-yl-[(1~{R},2~{R},6~{S},7~{S})-9-(4-methoxynaphthalen-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 
Y3F "Create component" 2023-06-09 RCSB 
Y3F "Initial release"  2024-12-18 RCSB 
# 
