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 #