data_YD4 # _chem_comp.id YD4 _chem_comp.name "4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl]amino}piperidin-3-yl]oxy}methyl)-1lambda~6~-thiane-1,1-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C26 H33 N5 O4 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-12-05 _chem_comp.pdbx_modified_date 2020-10-23 _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 511.636 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YD4 _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 6BSO _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 YD4 O3 O1 O 0 1 N N N 10.732 -37.636 -16.007 -0.723 2.056 3.677 O3 YD4 1 YD4 C22 C1 C 0 1 N N N 11.486 -36.691 -16.709 -1.369 1.544 2.779 C22 YD4 2 YD4 N3 N1 N 0 1 N N N 12.697 -37.035 -17.247 -0.877 0.460 2.153 N3 YD4 3 YD4 C23 C2 C 0 1 N N N 10.975 -35.297 -16.859 -2.619 2.100 2.427 C23 YD4 4 YD4 C24 C3 C 0 1 N N N 9.611 -34.945 -16.215 -3.136 3.312 3.159 C24 YD4 5 YD4 C25 C4 C 0 1 N N N 11.722 -34.348 -17.557 -3.355 1.546 1.430 C25 YD4 6 YD4 C26 C5 C 0 1 Y N N 12.969 -34.703 -18.123 -2.822 0.373 0.743 C26 YD4 7 YD4 C6 C6 C 0 1 Y N N 13.756 -33.792 -18.824 -3.523 -0.264 -0.304 C6 YD4 8 YD4 C4 C7 C 0 1 Y N N 13.350 -32.323 -19.104 -4.840 0.244 -0.755 C4 YD4 9 YD4 C3 C8 C 0 1 Y N N 12.159 -32.096 -19.782 -5.850 0.513 0.168 C3 YD4 10 YD4 N N2 N 0 1 Y N N 11.745 -30.831 -20.083 -7.021 0.965 -0.233 N YD4 11 YD4 C2 C9 C 0 1 Y N N 12.532 -29.764 -19.741 -7.285 1.180 -1.507 C2 YD4 12 YD4 C5 C10 C 0 1 Y N N 14.159 -31.246 -18.772 -5.088 0.468 -2.113 C5 YD4 13 YD4 C1 C11 C 0 1 Y N N 13.743 -29.969 -19.078 -6.336 0.938 -2.484 C1 YD4 14 YD4 C C12 C 0 1 N N N 14.611 -28.752 -18.702 -6.655 1.190 -3.935 C YD4 15 YD4 C21 C13 C 0 1 Y N N 13.447 -36.070 -17.956 -1.578 -0.147 1.134 C21 YD4 16 YD4 C9 C14 C 0 1 Y N N 14.651 -36.463 -18.487 -1.079 -1.273 0.466 C9 YD4 17 YD4 N8 N3 N 0 1 Y N N 15.426 -35.546 -19.190 -1.771 -1.831 -0.512 N8 YD4 18 YD4 C7 C15 C 0 1 Y N N 14.982 -34.220 -19.365 -2.949 -1.379 -0.901 C7 YD4 19 YD4 N1 N4 N 0 1 N N N 15.115 -37.835 -18.311 0.150 -1.805 0.835 N1 YD4 20 YD4 C10 C16 C 0 1 N N R 16.443 -38.196 -18.702 0.676 -2.983 0.139 C10 YD4 21 YD4 C14 C17 C 0 1 N N R 17.317 -38.201 -17.455 2.203 -3.003 0.251 C14 YD4 22 YD4 C13 C18 C 0 1 N N N 18.666 -38.884 -17.690 2.742 -4.267 -0.424 C13 YD4 23 YD4 N2 N5 N 0 1 N N N 18.632 -40.157 -18.401 2.170 -5.453 0.226 N2 YD4 24 YD4 C12 C19 C 0 1 N N N 17.290 -40.618 -18.684 0.708 -5.479 0.090 C12 YD4 25 YD4 C11 C20 C 0 1 N N N 16.439 -39.570 -19.406 0.108 -4.252 0.781 C11 YD4 26 YD4 O O2 O 0 1 N N N 17.527 -36.848 -17.064 2.744 -1.849 -0.394 O YD4 27 YD4 C15 C21 C 0 1 N N N 17.967 -36.681 -15.687 3.972 -1.388 0.173 C15 YD4 28 YD4 C16 C22 C 0 1 N N N 17.783 -35.197 -15.248 4.457 -0.156 -0.593 C16 YD4 29 YD4 C20 C23 C 0 1 N N N 18.383 -35.008 -13.854 5.828 0.258 -0.065 C20 YD4 30 YD4 C19 C24 C 0 1 N N N 18.442 -33.555 -13.412 6.441 1.321 -0.979 C19 YD4 31 YD4 S S1 S 0 1 N N N 16.786 -32.949 -13.628 5.402 2.810 -0.934 S YD4 32 YD4 O1 O3 O 0 1 N N N 16.786 -31.528 -13.457 5.819 3.687 -1.971 O1 YD4 33 YD4 O2 O4 O 0 1 N N N 15.953 -33.551 -12.637 5.351 3.289 0.403 O2 YD4 34 YD4 C18 C25 C 0 1 N N N 16.082 -33.384 -15.204 3.778 2.125 -1.371 C18 YD4 35 YD4 C17 C26 C 0 1 N N N 16.338 -34.877 -15.264 3.448 0.975 -0.415 C17 YD4 36 YD4 H1 H1 H 0 1 N N N 13.049 -37.965 -17.139 -0.017 0.100 2.422 H1 YD4 37 YD4 H2 H2 H 0 1 N N N 9.199 -35.836 -15.719 -2.414 3.612 3.918 H2 YD4 38 YD4 H3 H3 H 0 1 N N N 9.751 -34.144 -15.474 -3.281 4.129 2.452 H3 YD4 39 YD4 H4 H4 H 0 1 N N N 8.914 -34.604 -16.995 -4.086 3.071 3.635 H4 YD4 40 YD4 H5 H5 H 0 1 N N N 11.348 -33.341 -17.665 -4.312 1.963 1.152 H5 YD4 41 YD4 H6 H6 H 0 1 N N N 11.549 -32.937 -20.077 -5.672 0.348 1.220 H6 YD4 42 YD4 H7 H7 H 0 1 N N N 12.215 -28.761 -19.985 -8.258 1.551 -1.793 H7 YD4 43 YD4 H8 H8 H 0 1 N N N 15.106 -31.407 -18.278 -4.326 0.275 -2.855 H8 YD4 44 YD4 H9 H9 H 0 1 N N N 14.332 -28.398 -17.699 -6.391 2.215 -4.193 H9 YD4 45 YD4 H10 H10 H 0 1 N N N 15.672 -29.043 -18.706 -6.085 0.500 -4.557 H10 YD4 46 YD4 H11 H11 H 0 1 N N N 14.449 -27.946 -19.433 -7.721 1.035 -4.104 H11 YD4 47 YD4 H12 H12 H 0 1 N N N 15.591 -33.523 -19.922 -3.468 -1.876 -1.707 H12 YD4 48 YD4 H13 H13 H 0 1 N N N 14.492 -38.420 -18.831 0.660 -1.398 1.552 H13 YD4 49 YD4 H14 H14 H 0 1 N N N 16.840 -37.449 -19.405 0.388 -2.944 -0.911 H14 YD4 50 YD4 H15 H15 H 0 1 N N N 16.787 -38.743 -16.658 2.491 -3.001 1.303 H15 YD4 51 YD4 H16 H16 H 0 1 N N N 19.127 -39.062 -16.707 2.466 -4.261 -1.478 H16 YD4 52 YD4 H17 H17 H 0 1 N N N 19.295 -38.193 -18.271 3.828 -4.292 -0.333 H17 YD4 53 YD4 H18 H18 H 0 1 N N N 19.093 -40.846 -17.841 2.444 -5.501 1.196 H18 YD4 54 YD4 H20 H20 H 0 1 N N N 16.799 -40.874 -17.733 0.441 -5.468 -0.967 H20 YD4 55 YD4 H21 H21 H 0 1 N N N 17.353 -41.515 -19.317 0.316 -6.384 0.554 H21 YD4 56 YD4 H22 H22 H 0 1 N N N 15.402 -39.935 -19.456 0.363 -4.270 1.840 H22 YD4 57 YD4 H23 H23 H 0 1 N N N 16.832 -39.442 -20.425 -0.976 -4.263 0.666 H23 YD4 58 YD4 H24 H24 H 0 1 N N N 17.370 -37.332 -15.032 3.814 -1.127 1.219 H24 YD4 59 YD4 H25 H25 H 0 1 N N N 19.029 -36.956 -15.608 4.722 -2.176 0.105 H25 YD4 60 YD4 H26 H26 H 0 1 N N N 18.315 -34.549 -15.960 4.539 -0.400 -1.652 H26 YD4 61 YD4 H27 H27 H 0 1 N N N 17.770 -35.567 -13.132 5.720 0.663 0.941 H27 YD4 62 YD4 H28 H28 H 0 1 N N N 19.406 -35.413 -13.857 6.481 -0.614 -0.034 H28 YD4 63 YD4 H29 H29 H 0 1 N N N 18.747 -33.483 -12.358 7.445 1.566 -0.631 H29 YD4 64 YD4 H30 H30 H 0 1 N N N 19.147 -32.988 -14.037 6.492 0.940 -1.999 H30 YD4 65 YD4 H31 H31 H 0 1 N N N 16.589 -32.858 -16.027 3.018 2.901 -1.282 H31 YD4 66 YD4 H32 H32 H 0 1 N N N 15.005 -33.162 -15.235 3.802 1.753 -2.395 H32 YD4 67 YD4 H33 H33 H 0 1 N N N 15.897 -35.275 -16.190 2.446 0.604 -0.628 H33 YD4 68 YD4 H34 H34 H 0 1 N N N 15.860 -35.354 -14.396 3.488 1.337 0.613 H34 YD4 69 # # 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 YD4 N C3 DOUB Y N 1 YD4 N C2 SING Y N 2 YD4 C3 C4 SING Y N 3 YD4 C2 C1 DOUB Y N 4 YD4 C11 C10 SING N N 5 YD4 C11 C12 SING N N 6 YD4 C7 N8 DOUB Y N 7 YD4 C7 C6 SING Y N 8 YD4 N8 C9 SING Y N 9 YD4 C4 C6 SING N N 10 YD4 C4 C5 DOUB Y N 11 YD4 C1 C5 SING Y N 12 YD4 C1 C SING N N 13 YD4 C6 C26 DOUB Y N 14 YD4 C10 N1 SING N N 15 YD4 C10 C14 SING N N 16 YD4 C12 N2 SING N N 17 YD4 C9 N1 SING N N 18 YD4 C9 C21 DOUB Y N 19 YD4 N2 C13 SING N N 20 YD4 C26 C21 SING Y N 21 YD4 C26 C25 SING N N 22 YD4 C21 N3 SING N N 23 YD4 C13 C14 SING N N 24 YD4 C25 C23 DOUB N N 25 YD4 C14 O SING N N 26 YD4 N3 C22 SING N N 27 YD4 O C15 SING N N 28 YD4 C23 C22 SING N N 29 YD4 C23 C24 SING N N 30 YD4 C22 O3 DOUB N N 31 YD4 C15 C16 SING N N 32 YD4 C17 C16 SING N N 33 YD4 C17 C18 SING N N 34 YD4 C16 C20 SING N N 35 YD4 C18 S SING N N 36 YD4 C20 C19 SING N N 37 YD4 S O1 DOUB N N 38 YD4 S C19 SING N N 39 YD4 S O2 DOUB N N 40 YD4 N3 H1 SING N N 41 YD4 C24 H2 SING N N 42 YD4 C24 H3 SING N N 43 YD4 C24 H4 SING N N 44 YD4 C25 H5 SING N N 45 YD4 C3 H6 SING N N 46 YD4 C2 H7 SING N N 47 YD4 C5 H8 SING N N 48 YD4 C H9 SING N N 49 YD4 C H10 SING N N 50 YD4 C H11 SING N N 51 YD4 C7 H12 SING N N 52 YD4 N1 H13 SING N N 53 YD4 C10 H14 SING N N 54 YD4 C14 H15 SING N N 55 YD4 C13 H16 SING N N 56 YD4 C13 H17 SING N N 57 YD4 N2 H18 SING N N 58 YD4 C12 H20 SING N N 59 YD4 C12 H21 SING N N 60 YD4 C11 H22 SING N N 61 YD4 C11 H23 SING N N 62 YD4 C15 H24 SING N N 63 YD4 C15 H25 SING N N 64 YD4 C16 H26 SING N N 65 YD4 C20 H27 SING N N 66 YD4 C20 H28 SING N N 67 YD4 C19 H29 SING N N 68 YD4 C19 H30 SING N N 69 YD4 C18 H31 SING N N 70 YD4 C18 H32 SING N N 71 YD4 C17 H33 SING N N 72 YD4 C17 H34 SING N N 73 # # 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 YD4 SMILES ACDLabs 12.01 "O=C1Nc3c(C=C1C)c(c2cc(cnc2)C)cnc3NC5C(OCC4CCS(=O)(=O)CC4)CNCC5" YD4 InChI InChI 1.03 "InChI=1S/C26H33N5O4S/c1-16-9-19(12-28-11-16)21-13-29-25(24-20(21)10-17(2)26(32)31-24)30-22-3-6-27-14-23(22)35-15-18-4-7-36(33,34)8-5-18/h9-13,18,22-23,27H,3-8,14-15H2,1-2H3,(H,29,30)(H,31,32)/t22-,23-/m1/s1" YD4 InChIKey InChI 1.03 ZIRMKCLZUOCUSC-DHIUTWEWSA-N YD4 SMILES_CANONICAL CACTVS 3.385 "Cc1cncc(c1)c2cnc(N[C@@H]3CCNC[C@H]3OCC4CC[S](=O)(=O)CC4)c5NC(=O)C(=Cc25)C" YD4 SMILES CACTVS 3.385 "Cc1cncc(c1)c2cnc(N[CH]3CCNC[CH]3OCC4CC[S](=O)(=O)CC4)c5NC(=O)C(=Cc25)C" YD4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1cc(cnc1)c2cnc(c3c2C=C(C(=O)N3)C)N[C@@H]4CCNC[C@H]4OCC5CCS(=O)(=O)CC5" YD4 SMILES "OpenEye OEToolkits" 2.0.6 "Cc1cc(cnc1)c2cnc(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 YD4 "SYSTEMATIC NAME" ACDLabs 12.01 "4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl]amino}piperidin-3-yl]oxy}methyl)-1lambda~6~-thiane-1,1-dione" YD4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "8-[[(3~{R},4~{R})-3-[[1,1-bis(oxidanylidene)thian-4-yl]methoxy]piperidin-4-yl]amino]-3-methyl-5-(5-methylpyridin-3-yl)-1~{H}-1,7-naphthyridin-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 YD4 "Create component" 2017-12-05 RCSB YD4 "Initial release" 2020-10-28 RCSB ##