data_YD3 # _chem_comp.id YD3 _chem_comp.name "8-[[(3R,4R)-3-[[1,1-bis(oxidanylidene)thian-4-yl]methoxy]piperidin-4-yl]amino]-3-methyl-5-(5-methylpyridin-3-yl)-1H-quinolin-2-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H34 N4 O4 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-07-11 _chem_comp.pdbx_modified_date 2015-08-07 _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 510.648 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YD3 _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 5A83 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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.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 YD3 O3 O3 O 0 1 N N N -24.486 42.823 12.014 -0.765 1.979 3.681 O3 YD3 1 YD3 C22 C22 C 0 1 N N N -25.276 43.694 11.655 -1.395 1.465 2.773 C22 YD3 2 YD3 N3 N3 N 0 1 N N N -26.514 43.750 12.200 -0.887 0.395 2.134 N3 YD3 3 YD3 C23 C23 C 0 1 N N N -24.979 44.719 10.678 -2.651 1.998 2.409 C23 YD3 4 YD3 C24 C24 C 0 1 N N N -23.660 44.673 9.950 -3.200 3.194 3.144 C24 YD3 5 YD3 C25 C25 C 0 1 N N N -25.908 45.685 10.393 -3.364 1.439 1.401 C25 YD3 6 YD3 C26 C26 C 0 1 Y N N -27.210 45.733 11.020 -2.834 0.315 0.719 C26 YD3 7 YD3 C6 C6 C 0 1 Y N N -28.166 46.722 10.759 -3.547 -0.294 -0.336 C6 YD3 8 YD3 C4 C4 C 0 1 Y N N -27.879 47.921 9.921 -4.868 0.237 -0.747 C4 YD3 9 YD3 C3 C3 C 0 1 Y N N -26.788 48.749 10.170 -5.861 0.478 0.202 C3 YD3 10 YD3 N N N 0 1 Y N N -26.496 49.838 9.448 -7.035 0.950 -0.163 N YD3 11 YD3 C2 C2 C 0 1 Y N N -27.308 50.139 8.427 -7.319 1.212 -1.425 C2 YD3 12 YD3 C5 C5 C 0 1 Y N N -28.699 48.277 8.854 -5.137 0.510 -2.092 C5 YD3 13 YD3 C1 C1 C 0 1 Y N N -28.427 49.397 8.084 -6.388 1.000 -2.424 C1 YD3 14 YD3 C C C 0 1 N N N -29.313 49.795 6.928 -6.729 1.304 -3.860 C YD3 15 YD3 C21 C21 C 0 1 Y N N -27.493 44.699 11.934 -1.585 -0.200 1.102 C21 YD3 16 YD3 C9 C9 C 0 1 Y N N -28.747 44.619 12.563 -1.062 -1.312 0.435 C9 YD3 17 YD3 C8 C8 C 0 1 Y N N -29.691 45.601 12.251 -1.775 -1.899 -0.598 C8 YD3 18 YD3 C7 C7 C 0 1 Y N N -29.411 46.631 11.373 -3.004 -1.394 -0.986 C7 YD3 19 YD3 N1 N1 N 0 1 N N N -29.012 43.582 13.455 0.179 -1.832 0.811 N1 YD3 20 YD3 C10 C10 C 0 1 N N R -30.301 43.253 14.049 0.728 -2.997 0.112 C10 YD3 21 YD3 C14 C14 C 0 1 N N R -31.008 42.175 13.237 2.254 -2.995 0.234 C14 YD3 22 YD3 C13 C13 C 0 1 N N N -32.351 41.805 13.869 2.816 -4.246 -0.445 C13 YD3 23 YD3 N2 N2 N 0 1 N N N -32.172 41.412 15.264 2.257 -5.444 0.193 N2 YD3 24 YD3 C12 C12 C 0 1 N N N -31.448 42.373 16.104 0.797 -5.492 0.047 C12 YD3 25 YD3 C11 C11 C 0 1 N N N -30.125 42.780 15.491 0.174 -4.278 0.741 C11 YD3 26 YD3 O O O 0 1 N N N -31.246 42.729 11.936 2.782 -1.829 -0.401 O YD3 27 YD3 C15 C15 C 0 1 N N N -31.449 41.765 10.898 3.999 -1.353 0.177 C15 YD3 28 YD3 C16 C16 C 0 1 N N N -31.345 42.506 9.588 4.470 -0.109 -0.578 C16 YD3 29 YD3 C20 C20 C 0 1 N N N -31.713 41.581 8.431 5.831 0.322 -0.038 C20 YD3 30 YD3 C19 C19 C 0 1 N N N -31.697 42.296 7.077 6.435 1.400 -0.941 C19 YD3 31 YD3 S S S 0 1 N N N -30.069 42.866 6.700 5.373 2.873 -0.894 S YD3 32 YD3 O1 O1 O 0 1 N N N -30.118 43.702 5.533 5.784 3.763 -1.923 O1 YD3 33 YD3 O2 O2 O 0 1 N N N -29.170 41.743 6.694 5.306 3.343 0.445 O2 YD3 34 YD3 C18 C18 C 0 1 N N N -29.735 43.867 8.114 3.762 2.166 -1.346 C18 YD3 35 YD3 C17 C17 C 0 1 N N N -29.934 43.040 9.372 3.444 1.006 -0.400 C17 YD3 36 YD3 H3 H3 H 0 1 N N N -26.747 43.036 12.861 -0.024 0.040 2.400 H3 YD3 37 YD3 H241 H241 H 0 0 N N N -23.598 45.519 9.250 -2.494 3.502 3.915 H241 YD3 38 YD3 H242 H242 H 0 0 N N N -22.837 44.738 10.677 -3.354 4.013 2.442 H242 YD3 39 YD3 H243 H243 H 0 0 N N N -23.582 43.728 9.392 -4.151 2.930 3.608 H243 YD3 40 YD3 H25 H25 H 0 1 N N N -25.656 46.445 9.668 -4.325 1.845 1.121 H25 YD3 41 YD3 H7 H7 H 0 1 N N N -30.167 47.373 11.161 -3.546 -1.863 -1.793 H7 YD3 42 YD3 HA HA H 0 1 N N N -26.138 48.498 10.995 -5.666 0.276 1.245 HA YD3 43 YD3 H5 H5 H 0 1 N N N -29.562 47.670 8.622 -4.389 0.339 -2.852 H5 YD3 44 YD3 H2 H2 H 0 1 N N N -27.077 51.012 7.835 -8.295 1.597 -1.681 H2 YD3 45 YD3 HC1 HC1 H 0 1 N N N -28.952 49.315 6.007 -6.464 2.337 -4.086 HC1 YD3 46 YD3 HC2 HC2 H 0 1 N N N -30.345 49.473 7.129 -6.173 0.635 -4.516 HC2 YD3 47 YD3 HC3 HC3 H 0 1 N N N -29.287 50.888 6.806 -7.798 1.161 -4.018 HC3 YD3 48 YD3 H8 H8 H 0 1 N N N -30.668 45.554 12.709 -1.364 -2.757 -1.110 H8 YD3 49 YD3 H1 H1 H 0 1 N N N -28.727 42.751 12.978 0.678 -1.421 1.534 H1 YD3 50 YD3 H10 H10 H 0 1 N N N -30.935 44.152 14.056 0.446 -2.956 -0.941 H10 YD3 51 YD3 H14 H14 H 0 1 N N N -30.371 41.281 13.174 2.535 -2.996 1.287 H14 YD3 52 YD3 H111 H111 H 0 0 N N N -29.444 41.916 15.504 0.422 -4.299 1.803 H111 YD3 53 YD3 H112 H112 H 0 0 N N N -29.692 43.598 16.086 -0.909 -4.305 0.619 H112 YD3 54 YD3 H131 H131 H 0 0 N N N -33.024 42.674 13.822 2.547 -4.238 -1.502 H131 YD3 55 YD3 H132 H132 H 0 0 N N N -32.794 40.967 13.311 3.902 -4.255 -0.348 H132 YD3 56 YD3 HB HB H 0 1 N N N -33.078 41.275 15.664 2.685 -6.282 -0.173 HB YD3 57 YD3 H121 H121 H 0 0 N N N -32.070 43.271 16.233 0.537 -5.478 -1.011 H121 YD3 58 YD3 H122 H122 H 0 0 N N N -31.258 41.914 17.085 0.416 -6.406 0.503 H122 YD3 59 YD3 H151 H151 H 0 0 N N N -30.678 40.982 10.952 3.830 -1.101 1.224 H151 YD3 60 YD3 H152 H152 H 0 0 N N N -32.444 41.307 10.996 4.761 -2.129 0.110 H152 YD3 61 YD3 H16 H16 H 0 1 N N N -32.046 43.353 9.600 4.563 -0.345 -1.638 H16 YD3 62 YD3 H201 H201 H 0 0 N N N -30.991 40.752 8.400 5.711 0.720 0.970 H201 YD3 63 YD3 H202 H202 H 0 0 N N N -32.723 41.182 8.607 6.498 -0.540 -0.008 H202 YD3 64 YD3 H171 H171 H 0 0 N N N -29.673 43.669 10.236 2.449 0.620 -0.622 H171 YD3 65 YD3 H172 H172 H 0 0 N N N -29.250 42.180 9.324 3.471 1.362 0.630 H172 YD3 66 YD3 H191 H191 H 0 0 N N N -32.026 41.597 6.294 7.432 1.658 -0.585 H191 YD3 67 YD3 H192 H192 H 0 0 N N N -32.382 43.156 7.113 6.496 1.027 -1.964 H192 YD3 68 YD3 H181 H181 H 0 0 N N N -28.697 44.228 8.072 2.990 2.931 -1.258 H181 YD3 69 YD3 H182 H182 H 0 0 N N N -30.422 44.726 8.127 3.799 1.800 -2.372 H182 YD3 70 # 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 YD3 O3 C22 DOUB N N 1 YD3 C22 N3 SING N N 2 YD3 C22 C23 SING N N 3 YD3 N3 C21 SING N N 4 YD3 C23 C24 SING N N 5 YD3 C23 C25 DOUB N N 6 YD3 C25 C26 SING N N 7 YD3 C26 C6 DOUB Y N 8 YD3 C26 C21 SING Y N 9 YD3 C6 C4 SING N N 10 YD3 C6 C7 SING Y N 11 YD3 C4 C3 SING Y N 12 YD3 C4 C5 DOUB Y N 13 YD3 C3 N DOUB Y N 14 YD3 N C2 SING Y N 15 YD3 C2 C1 DOUB Y N 16 YD3 C5 C1 SING Y N 17 YD3 C1 C SING N N 18 YD3 C21 C9 DOUB Y N 19 YD3 C9 C8 SING Y N 20 YD3 C9 N1 SING N N 21 YD3 C8 C7 DOUB Y N 22 YD3 N1 C10 SING N N 23 YD3 C10 C14 SING N N 24 YD3 C10 C11 SING N N 25 YD3 C14 C13 SING N N 26 YD3 C14 O SING N N 27 YD3 C13 N2 SING N N 28 YD3 N2 C12 SING N N 29 YD3 C12 C11 SING N N 30 YD3 O C15 SING N N 31 YD3 C15 C16 SING N N 32 YD3 C16 C20 SING N N 33 YD3 C16 C17 SING N N 34 YD3 C20 C19 SING N N 35 YD3 C19 S SING N N 36 YD3 S O1 DOUB N N 37 YD3 S O2 DOUB N N 38 YD3 S C18 SING N N 39 YD3 C18 C17 SING N N 40 YD3 N3 H3 SING N N 41 YD3 C24 H241 SING N N 42 YD3 C24 H242 SING N N 43 YD3 C24 H243 SING N N 44 YD3 C25 H25 SING N N 45 YD3 C7 H7 SING N N 46 YD3 C3 HA SING N N 47 YD3 C5 H5 SING N N 48 YD3 C2 H2 SING N N 49 YD3 C HC1 SING N N 50 YD3 C HC2 SING N N 51 YD3 C HC3 SING N N 52 YD3 C8 H8 SING N N 53 YD3 N1 H1 SING N N 54 YD3 C10 H10 SING N N 55 YD3 C14 H14 SING N N 56 YD3 C11 H111 SING N N 57 YD3 C11 H112 SING N N 58 YD3 C13 H131 SING N N 59 YD3 C13 H132 SING N N 60 YD3 N2 HB SING N N 61 YD3 C12 H121 SING N N 62 YD3 C12 H122 SING N N 63 YD3 C15 H151 SING N N 64 YD3 C15 H152 SING N N 65 YD3 C16 H16 SING N N 66 YD3 C20 H201 SING N N 67 YD3 C20 H202 SING N N 68 YD3 C17 H171 SING N N 69 YD3 C17 H172 SING N N 70 YD3 C19 H191 SING N N 71 YD3 C19 H192 SING N N 72 YD3 C18 H181 SING N N 73 YD3 C18 H182 SING N N 74 # 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 YD3 InChI InChI 1.03 "InChI=1S/C27H34N4O4S/c1-17-11-20(14-29-13-17)21-3-4-24(26-22(21)12-18(2)27(32)31-26)30-23-5-8-28-15-25(23)35-16-19-6-9-36(33,34)10-7-19/h3-4,11-14,19,23,25,28,30H,5-10,15-16H2,1-2H3,(H,31,32)/t23-,25-/m1/s1" YD3 InChIKey InChI 1.03 KXXIBIBXJMYWNL-ILBGXUMGSA-N YD3 SMILES_CANONICAL CACTVS 3.385 "Cc1cncc(c1)c2ccc(N[C@@H]3CCNC[C@H]3OCC4CC[S](=O)(=O)CC4)c5NC(=O)C(=Cc25)C" YD3 SMILES CACTVS 3.385 "Cc1cncc(c1)c2ccc(N[CH]3CCNC[CH]3OCC4CC[S](=O)(=O)CC4)c5NC(=O)C(=Cc25)C" YD3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1cc(cnc1)c2ccc(c3c2C=C(C(=O)N3)C)N[C@@H]4CCNC[C@H]4OCC5CCS(=O)(=O)CC5" YD3 SMILES "OpenEye OEToolkits" 1.7.6 "Cc1cc(cnc1)c2ccc(c3c2C=C(C(=O)N3)C)NC4CCNCC4OCC5CCS(=O)(=O)CC5" # 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 YD3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "8-[[(3R,4R)-3-[[1,1-bis(oxidanylidene)thian-4-yl]methoxy]piperidin-4-yl]amino]-3-methyl-5-(5-methylpyridin-3-yl)-1H-quinolin-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 YD3 "Create component" 2015-07-11 EBI YD3 "Initial release" 2015-08-12 RCSB #