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 #