data_Y6X # _chem_comp.id Y6X _chem_comp.name "(2R)-6-chloro-2-{[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino}-2,3-dihydro-1H-indene-4-carbonitrile" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H18 Cl N5 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-12 _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 395.842 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y6X _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 7G3T _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 Y6X C10 C1 C 0 1 Y N N N N N -12.146 5.367 43.919 4.207 0.669 0.194 C10 Y6X 1 Y6X C11 C2 C 0 1 N N N N N N -12.874 6.495 44.626 3.087 1.681 0.302 C11 Y6X 2 Y6X C16 C3 C 0 1 Y N N N N N -14.410 7.587 47.226 -0.517 1.429 -0.638 C16 Y6X 3 Y6X C18 C4 C 0 1 Y N N N N N -13.095 9.337 47.965 -2.672 1.951 -1.258 C18 Y6X 4 Y6X C19 C5 C 0 1 Y N N N N N -14.215 10.004 48.451 -3.138 0.883 -0.479 C19 Y6X 5 Y6X C20 C6 C 0 1 N N N N N N -14.148 14.627 48.767 -6.844 -2.141 -0.134 C20 Y6X 6 Y6X C22 C7 C 0 1 N N N N N N -14.784 14.171 50.768 -7.628 -0.290 0.487 C22 Y6X 7 Y6X C23 C8 C 0 1 N N N N N N -15.206 13.664 49.327 -6.301 -1.010 0.746 C23 Y6X 8 Y6X C24 C9 C 0 1 N N N N N N -16.631 13.743 48.685 -5.813 -1.279 2.166 C24 Y6X 9 Y6X C25 C10 C 0 1 N N N N N N -16.520 12.286 48.287 -4.429 -1.214 1.502 C25 Y6X 10 Y6X C27 C11 C 0 1 N N N N N N -14.099 11.337 49.031 -4.580 0.576 -0.400 C27 Y6X 11 Y6X C1 C12 C 0 1 N N N N N N -13.504 4.345 45.598 2.309 -0.275 -0.862 C1 Y6X 12 Y6X N2 N1 N 0 1 N N N N N N -10.686 7.700 41.793 6.365 2.805 1.904 N2 Y6X 13 Y6X C3 C13 C 0 1 N N N N N N -10.926 6.700 42.238 5.994 1.885 1.350 C3 Y6X 14 Y6X C4 C14 C 0 1 Y N N N N N -11.250 5.440 42.864 5.527 0.725 0.652 C4 Y6X 15 Y6X C5 C15 C 0 1 Y N N N N N -10.667 4.253 42.367 6.388 -0.350 0.430 C5 Y6X 16 Y6X CL6 CL1 CL 0 0 N N N N N N -10.334 1.619 42.320 6.996 -2.807 -0.522 CL6 Y6X 17 Y6X C7 C16 C 0 1 Y N N N N N -11.021 3.067 42.930 5.930 -1.466 -0.243 C7 Y6X 18 Y6X C8 C17 C 0 1 Y N N N N N -11.960 2.963 44.024 4.623 -1.516 -0.694 C8 Y6X 19 Y6X C9 C18 C 0 1 Y N N N N N -12.498 4.136 44.485 3.760 -0.454 -0.472 C9 Y6X 20 Y6X C12 C19 C 0 1 N N S N N N -13.319 5.814 45.946 1.796 0.886 0.013 C12 Y6X 21 Y6X N13 N2 N 0 1 N N N N N N -14.509 6.460 46.561 0.831 1.709 -0.720 N13 Y6X 22 Y6X C14 C20 C 0 1 Y N N N N N -15.431 9.331 48.331 -2.200 0.114 0.222 C14 Y6X 23 Y6X N15 N3 N 0 1 Y N N N N N -15.550 8.145 47.752 -0.919 0.412 0.113 N15 Y6X 24 Y6X N17 N4 N 0 1 Y N N N N N -13.153 8.177 47.356 -1.375 2.186 -1.310 N17 Y6X 25 Y6X O21 O1 O 0 1 N N N N N N -13.668 14.872 50.130 -7.717 -1.131 -0.683 O21 Y6X 26 Y6X N26 N5 N 0 1 N N N N N N -15.145 12.262 48.953 -5.022 -0.369 0.452 N26 Y6X 27 Y6X O28 O2 O 0 1 N N N N N N -13.080 11.695 49.606 -5.368 1.176 -1.105 O28 Y6X 28 Y6X H33 H1 H 0 1 N N N N N N -12.202 7.344 44.821 3.055 2.104 1.306 H33 Y6X 29 Y6X H34 H2 H 0 1 N N N N N N -13.740 6.839 44.042 3.219 2.471 -0.438 H34 Y6X 30 Y6X H38 H3 H 0 1 N N N N N N -12.127 9.799 48.096 -3.364 2.567 -1.813 H38 Y6X 31 Y6X H40 H4 H 0 1 N N N N N N -13.408 14.150 48.107 -6.118 -2.533 -0.847 H40 Y6X 32 Y6X H39 H5 H 0 1 N N N N N N -14.565 15.515 48.269 -7.365 -2.921 0.421 H39 Y6X 33 Y6X H42 H6 H 0 1 N N N N N N -14.486 13.374 51.465 -8.394 -0.493 1.235 H42 Y6X 34 Y6X H41 H7 H 0 1 N N N N N N -15.519 14.828 51.256 -7.519 0.771 0.264 H41 Y6X 35 Y6X H43 H8 H 0 1 N N N N N N -17.438 13.954 49.403 -6.012 -0.470 2.869 H43 Y6X 36 Y6X H44 H9 H 0 1 N N N N N N -16.705 14.438 47.836 -6.080 -2.263 2.553 H44 Y6X 37 Y6X H45 H10 H 0 1 N N N N N N -17.266 11.627 48.755 -3.683 -0.697 2.106 H45 Y6X 38 Y6X H46 H11 H 0 1 N N N N N N -16.505 12.109 47.201 -4.079 -2.179 1.135 H46 Y6X 39 Y6X H29 H12 H 0 1 N N N N N N -13.279 3.702 46.461 2.233 -0.014 -1.918 H29 Y6X 40 Y6X H30 H13 H 0 1 N N N N N N -14.528 4.146 45.249 1.743 -1.183 -0.654 H30 Y6X 41 Y6X H31 H14 H 0 1 N N N N N N -9.954 4.287 41.556 7.408 -0.310 0.783 H31 Y6X 42 Y6X H32 H15 H 0 1 N N N N N N -12.224 2.009 44.456 4.272 -2.391 -1.220 H32 Y6X 43 Y6X H35 H16 H 0 1 N N N N N N -12.481 5.889 46.655 1.360 0.506 0.937 H35 Y6X 44 Y6X H36 H17 H 0 1 N N N N N N -15.155 6.627 45.817 1.139 2.452 -1.263 H36 Y6X 45 Y6X H37 H18 H 0 1 N N N N N N -16.319 9.799 48.729 -2.520 -0.717 0.833 H37 Y6X 46 # 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 Y6X C1 C12 SING N N 1 Y6X C1 C9 SING N N 2 Y6X N2 C3 TRIP N N 3 Y6X C3 C4 SING N N 4 Y6X C4 C10 DOUB Y N 5 Y6X C4 C5 SING Y N 6 Y6X C5 C7 DOUB Y N 7 Y6X CL6 C7 SING N N 8 Y6X C7 C8 SING Y N 9 Y6X C8 C9 DOUB Y N 10 Y6X C9 C10 SING Y N 11 Y6X C10 C11 SING N N 12 Y6X C11 C12 SING N N 13 Y6X C12 N13 SING N N 14 Y6X N13 C16 SING N N 15 Y6X C14 C19 DOUB Y N 16 Y6X C14 N15 SING Y N 17 Y6X N15 C16 DOUB Y N 18 Y6X C16 N17 SING Y N 19 Y6X N17 C18 DOUB Y N 20 Y6X C18 C19 SING Y N 21 Y6X C19 C27 SING N N 22 Y6X C20 C23 SING N N 23 Y6X C20 O21 SING N N 24 Y6X O21 C22 SING N N 25 Y6X C22 C23 SING N N 26 Y6X C23 N26 SING N N 27 Y6X C23 C24 SING N N 28 Y6X C24 C25 SING N N 29 Y6X C25 N26 SING N N 30 Y6X N26 C27 SING N N 31 Y6X C27 O28 DOUB N N 32 Y6X C11 H33 SING N N 33 Y6X C11 H34 SING N N 34 Y6X C18 H38 SING N N 35 Y6X C20 H40 SING N N 36 Y6X C20 H39 SING N N 37 Y6X C22 H42 SING N N 38 Y6X C22 H41 SING N N 39 Y6X C24 H43 SING N N 40 Y6X C24 H44 SING N N 41 Y6X C25 H45 SING N N 42 Y6X C25 H46 SING N N 43 Y6X C1 H29 SING N N 44 Y6X C1 H30 SING N N 45 Y6X C5 H31 SING N N 46 Y6X C8 H32 SING N N 47 Y6X C12 H35 SING N N 48 Y6X N13 H36 SING N N 49 Y6X C14 H37 SING N N 50 # 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 Y6X SMILES ACDLabs 12.01 "O=C(N1CCC21COC2)c1cnc(NC2Cc3cc(Cl)cc(C#N)c3C2)nc1" Y6X InChI InChI 1.06 "InChI=1S/C20H18ClN5O2/c21-15-3-12-5-16(6-17(12)13(4-15)7-22)25-19-23-8-14(9-24-19)18(27)26-2-1-20(26)10-28-11-20/h3-4,8-9,16H,1-2,5-6,10-11H2,(H,23,24,25)/t16-/m1/s1" Y6X InChIKey InChI 1.06 IEGMVFCMBVSNLK-MRXNPFEDSA-N Y6X SMILES_CANONICAL CACTVS 3.385 "Clc1cc2C[C@@H](Cc2c(c1)C#N)Nc3ncc(cn3)C(=O)N4CCC45COC5" Y6X SMILES CACTVS 3.385 "Clc1cc2C[CH](Cc2c(c1)C#N)Nc3ncc(cn3)C(=O)N4CCC45COC5" Y6X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(cc(c2c1C[C@@H](C2)Nc3ncc(cn3)C(=O)N4CCC45COC5)C#N)Cl" Y6X SMILES "OpenEye OEToolkits" 2.0.7 "c1c(cc(c2c1CC(C2)Nc3ncc(cn3)C(=O)N4CCC45COC5)C#N)Cl" # 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 Y6X "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-6-chloro-2-{[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino}-2,3-dihydro-1H-indene-4-carbonitrile" Y6X "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-6-chloranyl-2-[[5-(6-oxa-1-azaspiro[3.3]heptan-1-ylcarbonyl)pyrimidin-2-yl]amino]-2,3-dihydro-1~{H}-indene-4-carbonitrile" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y6X "Create component" 2023-06-12 RCSB Y6X "Initial release" 2024-12-18 RCSB #